@article{parada-rojas_childs_soto_salcedo_pecota_yencho_almeyda_kitavi_buell_conant_et al._2025, title={A reference-quality NLRome for the hexaploid sweetpotato and diploid wild relatives}, url={https://doi.org/10.1101/2025.01.13.632774}, DOI={10.1101/2025.01.13.632774}, abstractNote={Breeding for sweetpotato ( Ipomea batatas ) resistance requires accelerating our understanding genomic of sources of resistance. Nucleotide-binding domain leucine-rich repeat receptors (NLRs) proteins represent a key component of the plant immune system that mediate plant immune responses. We cataloged the NLR diversity in 32 hexaploid sweetpotato genotypes and three diploid wild relatives using resistance gene enrichment sequencing (RenSeq) to capture and sequence full NLRs. A custom designed NLR bait-library enriched NLR genes with an average 97% target capture rate. We employed a curated database of cloned and functionally characterized NLRs to assign sequenced sweetpotato NLRs to canonical phylogenetic clades. We identified between 800 to 1,200 complete NLRs, highlighting the expanded diversity of coiled-coil NLRs (CNLs) across all genotypes. NLRs among sweetpotato genotypes exhibited large conservation across genotypes. Phylogenetic distance between 6X (hexaploid) and 2X (diploid) genotypes revealed that a small repertoire of I. batatas CNLs diverged from the sweetpotato wild relatives. Finally, we obtained chromosome coordinates in hexaploid (Beauregard) and diploid ( Ipomoea trifida ) genomes and recorded clustering of NLRs on chromosomes arms. Our study provides a catalog of NLR genes that can be used to accelerate breeding and increase our understanding of evolutionary dynamics of sweetpotato NLRs.}, author={Parada-Rojas, C. H. and Childs, K. L. and Soto, M. Fernández and Salcedo, A. and Pecota, K. and Yencho, G. C. and Almeyda, C. and Kitavi, M. and Buell, C. R. and Conant, G. C. and et al.}, year={2025}, month={Jan} }
 @article{swanckaert_santos_chaves_ssali_mwanga_azevedo_mendes_de boeck_eyzaguirre_kitavi_et al._2025, title={Tester selection for combining ability estimation of storage root yield and sweetpotato virus disease in sweetpotato breeding}, volume={15}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-025-88609-w}, abstractNote={General combining ability (GCA) is the major selection criterion for new sweetpotato (Ipomoea batatas) parents in a reciprocal recurrent selection (RRS) scheme. Here we aimed to estimate GCA and specific combining ability (SCA) by using 16 potential testers involved in an 8 × 8 partial diallel and propose a procedure to identify testers in sweetpotato breeding. Data on storage root yield in tons per hectare (rytha), and sweetpotato virus disease (vir2) from 64 families (1,913 clones) were collected in five trials at two locations in Uganda. The estimates of the female GCA accounted for the largest additive genetic variation for storage root yield compared to the male GCA for both traits. Mid-parent heterosis ranged from - 6.2 to 7% for rytha, and - 1.1 to 1.3% for vir2 in the progeny families. A stepwise procedure to identify testers top-ranked 'NASPOT 7' as a dual tester for both traits. Besides this parent, 'Ejumula' and 'NASPOT 10 O' for rytha, and 'NASPOT 1', 'NK259L', 'SPK004', and 'NASPOT 11' for vir2 are particularly suitable as respective single-trait testers. Testers are important in many plant breeding programs to enhance efficiency of RRS, and thus other crop species might benefit from the strategy and methods applied herein.}, number={1}, journal={SCIENTIFIC REPORTS}, author={Swanckaert, Jolien and Santos, Iara Goncalves and Chaves, Saulo F. S. and Ssali, Reuben and Mwanga, Robert O. M. and Azevedo, Camila Ferreira and Mendes, Thiago O. and De Boeck, Bert and Eyzaguirre, Raul and Kitavi, Mercy and et al.}, year={2025}, month={Feb} }
 @article{fraher_watson_nguyen_moore_lewis_kudenov_yencho_gorny_2024, title={A Comparison of Three Automated Root-Knot Nematode Egg Counting Approaches Using Machine Learning, Image Analysis, and a Hybrid Model}, volume={108}, ISSN={0191-2917 1943-7692}, url={http://dx.doi.org/10.1094/PDIS-01-24-0217-SR}, DOI={10.1094/PDIS-01-24-0217-SR}, abstractNote={spp. (root-knot nematodes [RKNs]) are a major threat to a wide range of agricultural crops worldwide. Breeding crops for RKN resistance is an effective management strategy, yet assaying large numbers of breeding lines requires laborious bioassays that are time-consuming and require experienced researchers. In these bioassays, quantifying nematode eggs through manual counting is considered the current standard for quantifying establishing resistance in plant genotypes. Counting RKN eggs is highly laborious, and even experienced researchers are subject to fatigue or misclassification, leading to potential errors in phenotyping. Here, we present three automated egg counting models that rely on machine learning and image analysis to quantify RKN eggs extracted from tobacco and sweet potato plants. The first method relied on convolutional neural networks trained using annotated images to identify eggs (}, number={9}, journal={Plant Disease}, publisher={Scientific Societies}, author={Fraher, Simon P. and Watson, Mark and Nguyen, Hoang and Moore, Savannah and Lewis, Ramsey S. and Kudenov, Michael and Yencho, G. Craig and Gorny, Adrienne M.}, year={2024}, month={Sep}, pages={2625–2629} }
 @article{allan_thomas_pecota_yencho_johanningsmeier_2024, title={Acrylamide in Fried Sweetpotato: The Relationship with Free Asparagine and Effects of Asparaginase}, volume={11}, ISSN={["2692-1944"]}, url={https://doi.org/10.1021/acsfoodscitech.4c00631}, DOI={10.1021/acsfoodscitech.4c00631}, abstractNote={Fried sweetpotato products are prone to acrylamide formation, and identification of the limiting substrate was investigated for mitigation. Chips were prepared from 'Bayou Belle' sweetpotatoes grown at 3 locations (2 years); sugars, free asparagine, total nitrogen, and acrylamide formation were measured. Acrylamide formation was correlated with free asparagine contents of raw sweetpotatoes (r = 0.924) with 82–89% being degraded during frying. Total nitrogen was moderately correlated (r = 0.505). Sugars were not correlated with acrylamide levels, and less than 30% were degraded in frying. Blanching and a postblanching asparaginase treatment reduced acrylamide levels by 89–95 and 98–99%, respectively. In model solutions, acrylamide formation was associated with free asparagine concentrations (p < 0.001), but other free amino acids had an antagonistic effect when total free amino acids exceeded reducing sugars. Free asparagine was the limiting substrate for acrylamide formation in fried sweetpotato, and management of its levels will minimize acrylamide formation in fried sweetpotato products.}, journal={ACS FOOD SCIENCE & TECHNOLOGY}, author={Allan, Matthew C. and Thomas, Luke Shawn and Pecota, Kenneth V. and Yencho, G. Craig and Johanningsmeier, Suzanne D.}, year={2024}, month={Nov} }
 @article{allan_johanningsmeier_nakitto_guambe_abugu_v. pecota_yencho_2024, title={Baked sweetpotato textures and sweetness: An investigation into relationships between physicochemical and cooked attributes}, volume={21}, ISSN={["2590-1575"]}, DOI={10.1016/j.fochx.2023.101072}, abstractNote={Sweetpotato varieties vary greatly in perceived textures and sweetness. This study identified physicochemical factors that influence these attributes in cooked sweetpotatoes. Fifteen genotypes grown on three plots were baked and evaluated by a trained descriptive sensory analysis panel for sweetness and 13 texture attributes. Mechanical parameters were measured by texture profile analysis (TPA); and composition (starch, cell wall material, sugar contents), starch properties (thermal, granule type ratios, granule sizes), and amylase activities were characterized. TPA predicted fracturability and firmness well, whereas starch and sugar contents, B-type starch granule ratio, and amylase activities influenced prediction of mouthfeel textures. Sweetness perception was influenced by perceived particle size and sugar contents; and maltose generation during baking was highly correlated with raw sweetpotato starch content. These relationships between physicochemical sweetpotato properties and baked textures and sweetness could benefit breeders and processors in selecting biochemical traits that result in consumer preferred products.}, journal={FOOD CHEMISTRY-X}, author={Allan, Matthew C. and Johanningsmeier, Suzanne D. and Nakitto, Mariam and Guambe, Osvalda and Abugu, Modesta and V. Pecota, Kenneth and Yencho, G. Craig}, year={2024}, month={Mar} }
 @article{fraher_schwarz_heim_gesteira_mollinari_pereira_zeng_brown-guedira_gorny_yencho_2024, title={Discovery of a major QTL for resistance to the guava root-knot nematode (<i>Meloidogyne enterolobii</i>) in 'Tanzania', an African landrace sweetpotato (<i>Ipomoea batatas</i>)}, volume={137}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-024-04739-1}, number={10}, journal={THEORETICAL AND APPLIED GENETICS}, author={Fraher, Simon and Schwarz, Tanner and Heim, Chris and Gesteira, Gabriel De Siqueira and Mollinari, Marcelo and Pereira, Guilherme Da Silva and Zeng, Zhao-Bang and Brown-Guedira, Gina and Gorny, Adrienne and Yencho, G. Craig}, year={2024}, month={Oct} }
 @article{fraher_schwarz_heim_gesteira_mollinari_pereira_zeng_brown-guedira_gorny_yencho_2024, title={Discovery of a major QTL for resistance to the guava root-knot nematode (Meloidogyne enterolobii) in ‘Tanzania’, an African landrace sweetpotato (Ipomoea batatas)}, url={https://doi.org/10.21203/rs.3.rs-4595748/v1}, DOI={10.21203/rs.3.rs-4595748/v1}, abstractNote={<title>Abstract</title> Sweetpotato, <italic>Ipomoea batatas</italic> (L.) Lam. (2n = 6x = 90), is among the world’s most important food crops and is North Carolina’s most important vegetable crop. The recent introduction of <italic>Meloidogyne enterolobii</italic> poses a significant economic threat to North Carolina’s sweetpotato industry and breeding resistance into new varieties has become a high priority for the US sweetpotato industry. Previous studies have shown that ‘Tanzania’, a released African landrace, is resistant to <italic>M. enterolobii.</italic> We screened the biparental sweetpotato mapping population, ‘Tanzania’ x ‘Beauregard’, for resistance to <italic>M. enterolobii</italic> by inoculating 246 full-sibs with 10,000 eggs each under greenhouse conditions. ‘Tanzania’, the female parent, was highly resistant, while ‘Beauregard’ was highly susceptible. Our bioassays exhibited strong skewing toward resistance for three measures of resistance: reproductive factor, eggs per gram of root tissue, and root gall severity ratings. A 1:1 segregation for resistance suggested a major gene conferred <italic>M. enterolobii</italic> resistance. Using a random-effect multiple interval mapping model, we identified a single major QTL, herein designated as qIbMe-4.1, on linkage group 4 that explained 70% of variation in resistance to <italic>M. enterolobii.</italic> This study provides a new understanding of the genetic basis of <italic>M. enterolobii</italic> resistance in sweetpotato and represents a major step towards the identification of selectable markers for nematode resistance breeding.}, author={Fraher, Simon and Schwarz, Tanner and Heim, Chris and Gesteira, Gabriel De Siqueira and Mollinari, Marcelo and Pereira, Guilherme Da Silva and Zeng, Zhao-Bang and Brown-Guedira, Gina and Gorny, Adrienne and Yencho, Craig}, year={2024}, month={Jul} }
 @article{duque_hoffmann_pecota_yencho_2024, title={Early root architectural traits and their relationship with yield in <i>Ipomoea batatas</i> L}, volume={9}, ISSN={["1573-5036"]}, DOI={10.1007/s11104-024-06949-4}, journal={PLANT AND SOIL}, author={Duque, Luis O. and Hoffmann, Gabriella and Pecota, Kenneth V. and Yencho, G. Craig}, year={2024}, month={Sep} }
 @article{bowers_slonecki_olukolu_yencho_wadl_2024, title={Genome-Wide Association Study of Sweet Potato Storage Root Traits Using GWASpoly, a Gene Dosage-Sensitive Model}, volume={25}, ISSN={["1422-0067"]}, url={https://doi.org/10.3390/ijms252111727}, DOI={10.3390/ijms252111727}, abstractNote={Sweet potato (}, number={21}, journal={INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES}, author={Bowers, Robert R. and Slonecki, Tyler J. and Olukolu, Bode A. and Yencho, G. Craig and Wadl, Phillip A.}, year={2024}, month={Nov} }
 @article{agha_endelman_chitwood-brown_clough_coombs_de jong_douches_higgins_holm_novy_et al._2024, title={Genotype-by-environment interactions and local adaptation shape selection in the US National Chip Processing Trial}, volume={137}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-024-04610-3}, abstractNote={We find evidence of selection for local adaptation and extensive genotype-by-environment interaction in the potato National Chip Processing Trial (NCPT). We present a novel method for dissecting the interplay between selection, local adaptation and environmental response in plant breeding schemes. Balancing local adaptation and the desire for widely adapted cultivars is challenging for plant breeders and makes genotype-by-environment interactions (GxE) an important target of selection. Selecting for GxE requires plant breeders to evaluate plants across multiple environments. One way breeders have accomplished this is to test advanced materials across many locations. Public potato breeders test advanced breeding material in the National Chip Processing Trial (NCPT), a public-private partnership where breeders from ten institutions submit advanced chip lines to be evaluated in up to ten locations across the country. These clones are genotyped and phenotyped for important agronomic traits. We used these data to interrogate the NCPT for GxE. Further, because breeders submitting clones to the NCPT select in a relatively small geographic range for the first 3 years of selection, we examined these data for evidence of incidental selection for local adaptation, and the alleles underlying it, using an environmental genome-wide association study (envGWAS). We found genomic regions associated with continuous environmental variables and discrete breeding programs, as well as regions of the genome potentially underlying GxE for yield.}, number={5}, journal={THEORETICAL AND APPLIED GENETICS}, author={Agha, Husain I. and Endelman, Jeffrey B. and Chitwood-Brown, Jessica and Clough, Mark and Coombs, Joseph and De Jong, Walter S. and Douches, David S. and Higgins, Charles R. and Holm, David G. and Novy, Richard and et al.}, year={2024}, month={May} }
 @article{cham_adams_wadl_ojeda-zacarias_rutter_jackson_shoemaker_yencho_olukolu_2024, title={Metagenome-enabled models improve genomic predictive ability and identification of herbivory-limiting genes in sweetpotato}, volume={11}, ISSN={["2052-7276"]}, DOI={10.1093/hr/uhae135}, abstractNote={Abstract Plant–insect interactions are often influenced by host- or insect-associated metagenomic community members. The relative abundance of insects and the microbes that modulate their interactions were obtained from sweetpotato (Ipomoea batatas) leaf-associated metagenomes using quantitative reduced representation sequencing and strain/species-level profiling with the Qmatey software. Positive correlations were found between whitefly (Bemisia tabaci) and its endosymbionts (Candidatus Hamiltonella defensa, Candidatus Portiera aleyrodidarum, and Rickettsia spp.) and negative correlations with nitrogen-fixing bacteria that implicate nitric oxide in sweetpotato–whitefly interaction. Genome-wide associations using 252 975 dosage-based markers, and metagenomes as a covariate to reduce false positive rates, implicated ethylene and cell wall modification in sweetpotato–whitefly interaction. The predictive abilities (PA) for whitefly and Ocypus olens abundance were high in both populations (68%–69% and 33.3%–35.8%, respectively) and 69.9% for Frankliniella occidentalis. The metagBLUP (gBLUP) prediction model, which fits the background metagenome-based Cao dissimilarity matrix instead of the marker-based relationship matrix (G-matrix), revealed moderate PA (35.3%–49.1%) except for O. olens (3%–10.1%). A significant gain in PA after modeling the metagenome as a covariate (gGBLUP, ≤11%) confirms quantification accuracy and that the metagenome modulates phenotypic expression and might account for the missing heritability problem. Significant gains in PA were also revealed after fitting allele dosage (≤17.4%) and dominance effects (≤4.6%). Pseudo-diploidized genotype data underperformed for dominance models. Including segregation-distorted loci (SDL) increased PA by 6%–17.1%, suggesting that traits associated with fitness cost might benefit from the inclusion of SDL. Our findings confirm the holobiont theory of host–metagenome co-evolution and underscore its potential for breeding within the context of G × G × E interactions.}, number={7}, journal={HORTICULTURE RESEARCH}, author={Cham, Alhagie K. and Adams, Alison K. and Wadl, Phillip A. and Ojeda-Zacarias, Ma del Carmen and Rutter, William B. and Jackson, D. Michael and Shoemaker, D. Dewayne and Yencho, G. Craig and Olukolu, Bode A.}, year={2024}, month={Jul} }
 @article{adero_wokorach_stomeo_yao_machuka_njuguna_byarugaba_kreuze_yencho_otema_et al._2024, title={Next Generation Sequencing and Genetic Analyses Reveal Factors Driving Evolution of Sweetpotato Viruses in Uganda}, volume={13}, ISSN={["2076-0817"]}, DOI={10.3390/pathogens13100833}, abstractNote={Sweetpotato (Ipomoea batatas L.) is an essential food crop globally, especially for farmers facing resource limitations. Like other crops, sweetpotato cultivation faces significant production challenges due to viral infections. This study aimed to identify and characterize viruses affecting sweetpotato crops in Uganda, mostly those associated with sweetpotato virus disease (SPVD). Infected leaf samples were collected from farmers’ fields in multiple districts spanning three regions in Uganda. MiSeq, a next-generation sequencing platform, was used to generate reads from the viral nucleic acid. The results revealed nine viruses infecting sweetpotato crops in Uganda, with most plants infected by multiple viral species. Sweet potato pakakuy and sweet potato symptomless virus_1 are reported in Uganda for the first time. Phylogenetic analyses demonstrated that some viruses have evolved to form new phylogroups, likely due to high mutations and recombination, particularly in the coat protein, P1 protein, cylindrical inclusion, and helper component proteinase regions of the potyvirus. The sweet potato virus C carried more codons under positive diversifying selection than the closely related sweet potato feathery mottle virus, particularly in the P1 gene. This study provides valuable insights into the viral species infecting sweetpotato crops, infection severity, and the evolution of sweet potato viruses in Uganda.}, number={10}, journal={PATHOGENS}, author={Adero, Joanne and Wokorach, Godfrey and Stomeo, Francesca and Yao, Nasser and Machuka, Eunice and Njuguna, Joyce and Byarugaba, Denis K. and Kreuze, Jan and Yencho, G. Craig and Otema, Milton A. and et al.}, year={2024}, month={Oct} }
 @article{liu_hunt_yencho_pecota_mierop_williams_jones_2024, title={Predicting sweetpotato traits using machine learning: Impact of environmental and agronomic factors on shape and size}, volume={225}, ISSN={["1872-7107"]}, url={https://doi.org/10.1016/j.compag.2024.109215}, DOI={10.1016/j.compag.2024.109215}, abstractNote={Consumer preference in produce, defined by shape and size, heavily influences this market. Understanding the environmental and management factors that impact these features can improve a farmer's economic margins. Since sweetpotatoes are hand-harvested and tend to have varying shapes and sizes, this can result in unpredictable profit margins. Methods for predicting the aesthetic characteristics of sweetpotatoes using environmental and agronomic factors with machine learning have not been developed. Moreover, predicting crop shape and size using agricultural data analysis is challenging due to the need for integrating diverse and complex datasets, including genotypes, weather, field management, and spatial information, into predictive models. This study employed an iterative process involving data preparation, feature engineering, variable selection, and model selection to develop machine learning models that predict sweetpotato aesthetic traits from agronomic inputs. We collected and organized data from various sources with different formats, spatial, and temporal resolutions. After comparing the performance of different machine learning methods using cross validation, Bagging regression had the least predictive error in terms of RMSE and MAE for sweetpotato's length-to-width ratio (RMSE = 0.185, MAE = 0.147) and curvature (RMSE = 0.013, MAE = 0.010) predictions. Bagging regression outperformed a naive baseline by 29%–38% when predicting sweetpotato features Our study also determined that the Covington cultivar and GPS locations were the most important factors that influenced the shape and size of sweetpotatoes. Fertilizer prior to planting, rose as an important feature when predicting sweetpotato curvature. Precipitation had a greater impact on the prediction of length-to-width ratio when compared to predicting curvature. The methodology presented herein could be applied to other crops like cucumbers, eggplants, peppers, and potatoes, where the size and shape are important factors for determining their value.}, journal={COMPUTERS AND ELECTRONICS IN AGRICULTURE}, author={Liu, Hangjin and Hunt, Shelly and Yencho, G. Craig and Pecota, Kenneth V. and Mierop, Russell and Williams, Cranos M. and Jones, Daniela S.}, year={2024}, month={Oct} }
 @article{amankwaah_williamson_reynolds_ibrahem_pecota_zhang_olukolu_truong_carey_felde_et al._2023, title={Development of NIRS calibration curves for sugars in baked sweetpotato}, volume={7}, ISSN={["1097-0010"]}, DOI={10.1002/jsfa.12800}, abstractNote={Abstract Background Variability in sugar content between raw and cooked sweetpotato storage roots impact nutritional and dietary importance with implications for consumer preference. High‐throughput phenotyping is required to breed varieties that satisfy consumer preferences. Results Near‐infrared reflectance spectroscopy (NIRS) calibration curves were developed for analysing sugars in baked storage roots using 147 genotypes from a population segregating for sugar content and other traits. The NIRS prediction curves had high coefficients of determination in calibration ( R 2 c ) of 0.96 (glucose), 0.93 (fructose), 0.96 (sucrose), and 0.96 (maltose). The corresponding coefficients of determination for cross‐validation ( R 2 cv ) were 0.92 (glucose), 0.89 (fructose), 0.96 (sucrose) and 0.93 (maltose) and were similar to the R 2 c for all sugars measured. The ratios of the standard deviation of the reference set to the standard error of cross‐validation were greater than three for all sugars. These results confirm the applicability of the NIRS curves in efficiently determining sugar content in baked sweetpotato storage roots. External validation was performed on an additional 70 genotypes. Coefficients of determination ( r 2 ) were 0.88 (glucose), 0.88 (fructose), 0.86 (sucrose) and 0.49 (maltose). The results were comparable to those found for the calibration and cross‐validation in fructose, glucose, and sucrose, but were moderate for maltose due to the low variability of maltose content in the population. Conclusions NIRS can be used for screening sugar content in baked sweetpotato storage roots in breeding programs and can be used to assist with the development of improved sweetpotato varieties that better meet consumer preferences. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.}, journal={JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE}, author={Amankwaah, Victor A. and Williamson, Sharon and Reynolds, Rong and Ibrahem, Ragy and Pecota, Kenneth V. and Zhang, Xiaofei and Olukolu, Bode A. and Truong, Van-Den and Carey, Edward and Felde, Thomas Zum and et al.}, year={2023}, month={Jul} }
 @article{slonecki_rutter_olukolu_yencho_jackson_wadl_2023, title={Genetic diversity, population structure, and selection of breeder germplasm subsets from the USDA sweetpotato (Ipomoea batatas) collection}, volume={13}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2022.1022555}, abstractNote={Sweetpotato (Ipomoea batatas) is the sixth most important food crop and plays a critical role in maintaining food security worldwide. Support for sweetpotato improvement research in breeding and genetics programs, and maintenance of sweetpotato germplasm collections is essential for preserving food security for future generations. Germplasm collections seek to preserve phenotypic and genotypic diversity through accession characterization. However, due to its genetic complexity, high heterogeneity, polyploid genome, phenotypic plasticity, and high flower production variability, sweetpotato genetic characterization is challenging. Here, we characterize the genetic diversity and population structure of 604 accessions from the sweetpotato germplasm collection maintained by the United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Plant Genetic Resources Conservation Unit (PGRCU) in Griffin, Georgia, United States. Using the genotyping-by-sequencing platform (GBSpoly) and bioinformatic pipelines (ngsComposer and GBSapp), a total of 102,870 polymorphic SNPs with hexaploid dosage calls were identified from the 604 accessions. Discriminant analysis of principal components (DAPC) and Bayesian clustering identified six unique genetic groupings across seven broad geographic regions. Genetic diversity analyses using the hexaploid data set revealed ample genetic diversity among the analyzed collection in concordance with previous analyses. Following population structure and diversity analyses, breeder germplasm subsets of 24, 48, 96, and 384 accessions were established using K-means clustering with manual selection to maintain phenotypic and genotypic diversity. The genetic characterization of the PGRCU sweetpotato germplasm collection and breeder germplasm subsets developed in this study provide the foundation for future association studies and serve as precursors toward phenotyping studies aimed at linking genotype with phenotype.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Slonecki, Tyler J. and Rutter, William B. and Olukolu, Bode A. and Yencho, G. Craig and Jackson, D. Michael and Wadl, Phillip A.}, year={2023}, month={Feb} }
 @article{mugisa_karungi_musana_odama_anyanga_edema_gibson_ssali_campos_oloka_et al._2023, title={Heterotic gains, transgressive segregation and fitness cost of sweetpotato weevil resistance expression in a partial diallel cross of sweetpotato}, volume={219}, ISSN={0014-2336 1573-5060}, url={http://dx.doi.org/10.1007/s10681-023-03225-x}, DOI={10.1007/s10681-023-03225-x}, abstractNote={Abstract Heterosis-exploiting breeding schemes are currently under consideration as a means of accelerating genetic gains in sweetpotato ( Ipomoea batatas ) breeding. This study was aimed at establishing heterotic gains, fitness costs and transgressive segregation associated with sweetpotato weevil (SPW) resistance in a partial diallel cross of sweetpotato. A total of 1896 clones were tested at two sites, for two seasons each in Uganda. Data on weevil severity (WED), weevil incidence (WI), storage root yield (SRY) and dry matter content (DM) were obtained. Best linear unbiased predictors (BLUPs) for each clone across environments were used to estimate heterotic gains and for regression analyses to establish relationships between key traits. In general, low mid-parent heterotic gains were detected with the highest favorable levels recorded for SRY (14.7%) and WED (− 7.9%). About 25% of the crosses exhibited desirable and significant mid-parent heterosis for weevil resistance. Over 16% of the clones displayed superior transgressive segregation, with the highest percentages recorded for SRY (21%) and WED (18%). A yield penalty of 10% was observed to be associated with SPW resistance whereas no decline in DM was detected in relation to the same. Chances of improving sweetpotato through exploiting heterosis in controlled crosses using parents of mostly similar background are somewhat minimal, as revealed by the low heterotic gains. The yield penalty detected due to SPW resistance suggests that a trade-off may be necessary between maximizing yields and developing weevil-resistant cultivars if the current needs for this crop are to be met in weevil-prone areas.}, number={10}, journal={Euphytica}, publisher={Springer Science and Business Media LLC}, author={Mugisa, Immaculate and Karungi, Jeninah and Musana, Paul and Odama, Roy and Anyanga, Milton O. and Edema, Richard and Gibson, Paul and Ssali, Reuben T. and Campos, Hugo and Oloka, Bonny M. and et al.}, year={2023}, month={Sep} }
 @article{osaru_karungi_odama_chelangat_musana_otema_oloka_gibson_edema_ssali_et al._2023, title={Identification of the key morphological sweetpotato weevil resistance predictors in Ugandan sweetpotato genotypes using correlation and path‐coefficient analysis}, volume={63}, ISSN={0011-183X 1435-0653}, url={http://dx.doi.org/10.1002/csc2.20915}, DOI={10.1002/csc2.20915}, abstractNote={Abstract Sweetpotato weevils (SPWs) can cause up to 100% yield losses in sweetpotato ( Ipomoea batatas ). Nevertheless, there has been limited success in breeding for SPW resistance globally. This is attributed partly to difficulty in screening for resistance because resistance to the SPW is complex and is mediated by several resistance indicators. Measuring all these resistance indicators is costly and time consuming. To enhance efficiency in selection for SPW resistance, there is need to profile and identify key resistance indicators. Potentially, this will better enable breeders to timely and precisely select for SPW resistance. The objective of this study was to identify the most efficient morphological resistance indicators against SPW. Thirty sweetpotato genotypes that varied in resistance to SPW comprising local collections, released varieties, and breeding lines were evaluated at three locations for two seasons in Uganda using an alpha lattice design. Data were collected on storage root yield, SPW root and stem damage, and weevil resistance indicators such as vine vigor (VV), ground cover (GC), vine weight (VW), storage root neck length (NL), latex content, cortex thickness (CT), and dry matter content (DM). Genotype means for all measured traits varied significantly except for CT. Negative relationships were observed between SPW root damage and GC, VW, CT, VV, NL, and DM. However, path coefficient analysis showed storage root NL (direct effect of −0.43, p < 0.001) as the most important morphological resistance indicator. Therefore, NL could be the most reliable predictor of resistance to SPW among breeding clones, especially at early breeding stages.}, number={3}, journal={Crop Science}, publisher={Wiley}, author={Osaru, Florence and Karungi, Jeninah and Odama, Roy and Chelangat, Doreen Murenju and Musana, Paul and Otema, Milton Anyanga and Oloka, Bonny and Gibson, Paul and Edema, Richard and Ssali, Reuben Tendo and et al.}, year={2023}, month={Mar}, pages={1126–1138} }
 @article{amankwaah_williamson_olukolu_truong_carey_ssali_yencho_2023, title={Interrelations of & alpha;- and & beta;-amylase activity with starch, sugars, and culinary and nutritional quality attributes in sweetpotato storage roots}, volume={7}, ISSN={["1097-0010"]}, url={https://doi.org/10.1002/jsfa.12832}, DOI={10.1002/jsfa.12832}, abstractNote={BACKGROUND Little information is available on α- and β-amylase activity and their associations with starch, sugars and other culinary qualities in sweetpotato. The objective of this study was to assess sweetpotato storage root α- and β-amylase activity in relation to starch, sugars, β-carotene content and storage root flesh color. RESULTS α- and β-amylase activity (α-AA and β-AA) were assayed from a Tanzania (T) x Beauregard (B) genetic mapping population in their uncured (raw), cured and stored (~ 11 weeks) forms during 2016 and 2017. The Ceralpha and Betamyl methods, with modifications to suit a high-throughput microplate assay format, were used to quantify α-AA and β-AA, respectively. Storage root dry matter, starch, glucose, fructose, sucrose, and β-carotene content were predicted using near infrared reflectance spectroscopy (NIRS). There was little relationship (r2 = 0.02–0.08, p-value ≤0.05 in 2016 and r2 = 0.05–0.11, p-value ≤0.05 in 2017) between α-AA and β-AA. We observed negative linear associations between α-AA and dry matter content and generally no correlations between β-AA and dry matter content. β-AA and sugars were weakly positively correlated. β-AA and β-carotene content were positively correlated (r = 0.3–0.4 in 2016 and 0.3–0.5 in 2017). CONCLUSIONS Generally, the correlation coefficient for amylase enzyme activity and sugar components of storage roots at harvest increased after curing and during post-harvest storage. This study is a major step forward in sweetpotato breeding by providing a better understanding of how α- and β-amylase activity are inter-associated with several culinary quality attributes. This article is protected by copyright. All rights reserved.}, journal={JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE}, author={Amankwaah, Victor A. A. and Williamson, Sharon and Olukolu, Bode A. A. and Truong, Van-Den and Carey, Edward and Ssali, Reuben and Yencho, George Craig}, year={2023}, month={Jul} }
 @article{adams_kristy_gorman_balint-kurti_yencho_olukolu_2023, title={Qmatey: an automated pipeline for fast exact matching-based alignment and strain-level taxonomic binning and profiling of metagenomes}, volume={24}, ISSN={["1477-4054"]}, url={https://doi.org/10.1093/bib/bbad351}, DOI={10.1093/bib/bbad351}, abstractNote={Metagenomics is a powerful tool for understanding organismal interactions; however, classification, profiling and detection of interactions at the strain level remain challenging. We present an automated pipeline, quantitative metagenomic alignment and taxonomic exact matching (Qmatey), that performs a fast exact matching-based alignment and integration of taxonomic binning and profiling. It interrogates large databases without using metagenome-assembled genomes, curated pan-genes or k-mer spectra that limit resolution. Qmatey minimizes misclassification and maintains strain level resolution by using only diagnostic reads as shown in the analysis of amplicon, quantitative reduced representation and shotgun sequencing datasets. Using Qmatey to analyze shotgun data from a synthetic community with 35% of the 26 strains at low abundance (0.01-0.06%), we revealed a remarkable 85-96% strain recall and 92-100% species recall while maintaining 100% precision. Benchmarking revealed that the highly ranked Kraken2 and KrakenUniq tools identified 2-4 more taxa (92-100% recall) than Qmatey but produced 315-1752 false positive taxa and high penalty on precision (1-8%). The speed, accuracy and precision of the Qmatey pipeline positions it as a valuable tool for broad-spectrum profiling and for uncovering biologically relevant interactions.}, number={6}, journal={BRIEFINGS IN BIOINFORMATICS}, author={Adams, Alison K. and Kristy, Brandon D. and Gorman, Myranda and Balint-Kurti, Peter and Yencho, G. Craig and Olukolu, Bode A.}, year={2023}, month={Sep} }
 @article{duque_sanchez_pecota_yencho_2022, title={A Win-Win Situation: Performance and Adaptability of Petite Sweetpotato Production in a Temperate Region}, volume={8}, ISSN={["2311-7524"]}, url={https://doi.org/10.3390/horticulturae8020172}, DOI={10.3390/horticulturae8020172}, abstractNote={New-found interest in sweetpotato production in the Mid-Atlantic and Northeastern U.S. has been steadily increasing in the last several years. Sweetpotatoes are usually grown for fresh market use and novel marketing strategies and new consumer niches are providing farmers options of growing new sweetpotato varieties with exciting colors and flavor profiles that are adapted to the Mid-Atlantic and Northeastern U.S. Petite sweetpotatoes have gained market attention because they are easier to handle and faster to cook compared to U.S. No. 1 storage roots. The goal of this research was to determine the performance and adaptableness of eight commercial sweetpotato varieties and two unreleased accessions for U.S. No.1 and Petite sweetpotato production under black plastic mulch tailored for the mild temperate growing conditions of the Mid-Atlantic and Northeastern U.S. Two in-row spacings (15 cm and 30 cm) and two harvest dates (90 and 120 days after planting, DAP) were evaluated during the 2018 and 2019 growing seasons. Our results showed that the ideal harvest time is at least 120 DAP compared to an early harvest at 90 DAP as there was a 2-fold difference in marketable yield at both 15 and 30 cm in-row spacing with marketable yield between 20 and 54 t ha−1. ‘Averre’ and ‘Beauregard’ produced the highest U.S. No. 1 and Petite yields under both in-row spacing treatments harvested at 120 DAP for both years evaluated, though the general effect of in-row spacing and DAP interaction (separate years) on yield performance was cultivar specific. We also found that growing degree days is a better predictor for harvest than days after planting, with an accumulation of at least ~700 GDD (base temperature 15.5 °C) or ~1300 GDD (base temperature 10 °C) for both U.S. No. 1 and Petite roots. Additional studies are required to identify the stability of cultivars tested and treatments imposed with environmental interactions in this region. In addition, there is an urgency for updated sweetpotato management practices exclusively designed for sweetpotato varieties for the Mid-Atlantic and Northeastern U.S.}, number={2}, journal={HORTICULTURAE}, author={Duque, Luis O. and Sanchez, Elsa and Pecota, Kenneth and Yencho, Craig}, year={2022}, month={Feb} }
 @article{morales_ogbonna_ellerbrock_bauchet_tantikanjana_tecle_powell_lyon_menda_simoes_et al._2022, title={Breedbase: a digital ecosystem for modern plant breeding}, volume={12}, DOI={10.1093/g3journal/jkac078}, abstractNote={Abstract Modern breeding methods integrate next-generation sequencing and phenomics to identify plants with the best characteristics and greatest genetic merit for use as parents in subsequent breeding cycles to ultimately create improved cultivars able to sustain high adoption rates by farmers. This data-driven approach hinges on strong foundations in data management, quality control, and analytics. Of crucial importance is a central database able to (1) track breeding materials, (2) store experimental evaluations, (3) record phenotypic measurements using consistent ontologies, (4) store genotypic information, and (5) implement algorithms for analysis, prediction, and selection decisions. Because of the complexity of the breeding process, breeding databases also tend to be complex, difficult, and expensive to implement and maintain. Here, we present a breeding database system, Breedbase (https://breedbase.org/, last accessed 4/18/2022). Originally initiated as Cassavabase (https://cassavabase.org/, last accessed 4/18/2022) with the NextGen Cassava project (https://www.nextgencassava.org/, last accessed 4/18/2022), and later developed into a crop-agnostic system, it is presently used by dozens of different crops and projects. The system is web based and is available as open source software. It is available on GitHub (https://github.com/solgenomics/, last accessed 4/18/2022) and packaged in a Docker image for deployment (https://hub.docker.com/u/breedbase, last accessed 4/18/2022). The Breedbase system enables breeding programs to better manage and leverage their data for decision making within a fully integrated digital ecosystem.}, number={7}, journal={G3-GENES GENOMES GENETICS}, author={Morales, Nicolas and Ogbonna, Alex C. and Ellerbrock, Bryan J. and Bauchet, Guillaume J. and Tantikanjana, Titima and Tecle, Isaak Y. and Powell, Adrian F. and Lyon, David and Menda, Naama and Simoes, Christiano C. and et al.}, year={2022}, month={Jul}, pages={jkac078} }
 @article{mugisa_karungi_musana_odama_alajo_chelangat_anyanga_oloka_gonçalves dos santos_talwana_et al._2022, title={Combining ability and heritability analysis of sweetpotato weevil resistance, root yield, and dry matter content in sweetpotato}, volume={13}, ISSN={1664-462X}, url={http://dx.doi.org/10.3389/fpls.2022.956936}, DOI={10.3389/fpls.2022.956936}, abstractNote={Efficient breeding and selection of superior genotypes requires a comprehensive understanding of the genetics of traits. This study was aimed at establishing the general combining ability (GCA), specific combining ability (SCA), and heritability of sweetpotato weevil ( Cylas spp.) resistance, storage root yield, and dry matter content in a sweetpotato multi-parental breeding population. A population of 1,896 F 1 clones obtained from an 8 × 8 North Carolina II design cross was evaluated with its parents in the field at two sweetpotato weevil hotspots in Uganda, using an augmented row-column design. Clone roots were further evaluated in three rounds of a no-choice feeding laboratory bioassay. Significant GCA effects for parents and SCA effects for families were observed for most traits and all variance components were highly significant ( p ≤ 0.001). Narrow-sense heritability estimates for weevil severity, storage root yield, and dry matter content were 0.35, 0.36, and 0.45, respectively. Parental genotypes with superior GCA for weevil resistance included “Mugande,” NASPOT 5, “Dimbuka-bukulula,” and “Wagabolige.” On the other hand, families that displayed the highest levels of resistance to weevils included “Wagabolige” × NASPOT 10 O, NASPOT 5 × “Dimbuka-bukulula,” “Mugande” × “Dimbuka-bukulula,” and NASPOT 11 × NASPOT 7. The moderate levels of narrow-sense heritability observed for the traits, coupled with the significant GCA and SCA effects, suggest that there is potential for their improvement through conventional breeding via hybridization and progeny selection and advancement. Although selection for weevil resistance may, to some extent, be challenging for breeders, efforts could be boosted through applying genomics-assisted breeding. Superior parents and families identified through this study could be deployed in further research involving the genetic improvement of these traits.}, journal={Frontiers in Plant Science}, publisher={Frontiers Media SA}, author={Mugisa, Immaculate and Karungi, Jeninah and Musana, Paul and Odama, Roy and Alajo, Agnes and Chelangat, Doreen M. and Anyanga, Milton O. and Oloka, Bonny M. and Gonçalves dos Santos, Iara and Talwana, Herbert and et al.}, year={2022}, month={Sep} }
 @misc{maren_duan_da_yencho_ranney_liu_2022, title={Genotype-independent plant transformation}, volume={9}, ISSN={["2052-7276"]}, DOI={10.1093/hr/uhac047}, abstractNote={Abstract Plant transformation and regeneration remain highly species- and genotype-dependent. Conventional hormone-based plant regeneration via somatic embryogenesis or organogenesis is tedious, time-consuming, and requires specialized skills and experience. Over the last 40 years, significant advances have been made to elucidate the molecular mechanisms underlying embryogenesis and organogenesis. These pioneering studies have led to a better understanding of the key steps and factors involved in plant regeneration, resulting in the identification of crucial growth and developmental regulatory genes that can dramatically improve regeneration efficiency, shorten transformation time, and make transformation of recalcitrant genotypes possible. Co-opting these regulatory genes offers great potential to develop innovative genotype-independent genetic transformation methods for various plant species, including specialty crops. Further developing these approaches has the potential to result in plant transformation without the use of hormones, antibiotics, selectable marker genes, or tissue culture. As an enabling technology, the use of these regulatory genes has great potential to enable the application of advanced breeding technologies such as genetic engineering and gene editing for crop improvement in transformation-recalcitrant crops and cultivars. This review will discuss the recent advances in the use of regulatory genes in plant transformation and regeneration, and their potential to facilitate genotype-independent plant transformation and regeneration.}, journal={HORTICULTURE RESEARCH}, author={Maren, Nathan A. and Duan, Hui and Da, Kedong and Yencho, G. Craig and Ranney, Thomas G. and Liu, Wusheng}, year={2022}, month={Jan} }
 @article{hoopes_meng_hamilton_achakkagari_guesdes_bolger_coombs_esselink_kaiser_kodde_et al._2022, title={Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity}, volume={15}, ISSN={["1752-9867"]}, DOI={10.1016/j.molp.2022.01.003}, abstractNote={Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity, including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome, which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations are predicted to have a high negative impact on protein function, complicating breeder's efforts to reduce genetic load. The StCDF1 locus controls maturity, and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.}, number={3}, journal={MOLECULAR PLANT}, author={Hoopes, Genevieve and Meng, Xiaoxi and Hamilton, John P. and Achakkagari, Sai Reddy and Guesdes, Fernanda de Alves Freitas and Bolger, Marie E. and Coombs, Joseph J. and Esselink, Danny and Kaiser, Natalie R. and Kodde, Linda and et al.}, year={2022}, month={Mar}, pages={520–536} }
 @article{mwanga_swanckaert_da silva pereira_andrade_makunde_grüneberg_kreuze_david_de boeck_carey_et al._2021, title={Breeding Progress for Vitamin A, Iron and Zinc Biofortification, Drought Tolerance, and Sweetpotato Virus Disease Resistance in Sweetpotato}, volume={5}, ISSN={2571-581X}, url={http://dx.doi.org/10.3389/fsufs.2021.616674}, DOI={10.3389/fsufs.2021.616674}, abstractNote={Sweetpotato is a resilient food crop with great potential to contribute to reduced hunger in the world. Sweetpotato shows significant potential to contribute to reducing the Global Hunger Index, which reflects deficiencies in calories and micronutrients based on the components of hunger, undernourishment, under-five mortality rate, stunting and wasting. Its genetic diversity has been harnessed through breeding to increase vitamin A, iron, and zinc content, virus resistance and climate resilience for the world's food needs. Africa and India are the most food-insecure regions. The main objectives of this research were to: provide information and a knowledge base on sweetpotato breeding in Africa for biofortification of vitamin A, iron, and zinc, drought tolerance and virus resistance; recommend procedures for generating new breeding populations and varieties; and develop new tools, technologies and methods for sweetpotato improvement. The research was implemented between 2009 and 2020 in 14 collaborating African countries using introduced and local genotypes. The redesigned accelerated breeding scheme resulted in increased genetic gains for vitamin A, iron, zinc contents and virus resistance, and the release by sub-Saharan African countries of 158 varieties; 98 of them orange-fleshed; 55 varieties bred by an accelerated breeding scheme; 27 drought-tolerant and two with enhanced iron and zinc content. Our experience has demonstrated that through the use of more optimized, standardized and collaborative breeding procedures by breeding programs across Africa, it is possible to speed official sweetpotato variety release and contribute to reducing the severe micronutrient deficiencies on the continent.}, journal={Frontiers in Sustainable Food Systems}, publisher={Frontiers Media SA}, author={Mwanga, Robert O. M. and Swanckaert, Jolien and da Silva Pereira, Guilherme and Andrade, Maria I. and Makunde, Godwill and Grüneberg, Wolfgang J. and Kreuze, Jan and David, Maria and De Boeck, Bert and Carey, Edward and et al.}, year={2021}, month={Mar} }
 @article{haque_lobaton_nelson_yencho_pecota_mierop_kudenov_boyette_williams_2021, title={Computer vision approach to characterize size and shape phenotypes of horticultural crops using high-throughput imagery}, volume={182}, ISSN={0168-1699}, url={http://dx.doi.org/10.1016/j.compag.2021.106011}, DOI={10.1016/j.compag.2021.106011}, abstractNote={For many horticultural crops, variation in quality (e.g., shape and size) contributes significantly to the crop’s market value. Metrics characterizing less subjective harvest quantities (e.g., yield and total biomass) are routinely monitored. In contrast, metrics quantifying more subjective crop quality characteristics such as ideal size and shape remain difficult to characterize objectively at the production-scale due to the lack of modular technologies for high-throughput sensing and computation. Several horticultural crops are sent to packing facilities after having been harvested, where they are sorted into boxes and containers using high-throughput scanners. These scanners capture images of each fruit or vegetable being sorted and packed, but the images are typically used solely for sorting purposes and promptly discarded. With further analysis, these images could offer unparalleled insight on how crop quality metrics vary at the industrial production-scale and provide further insight into how these characteristics translate to overall market value. At present, methods for extracting and quantifying quality characteristics of crops using images generated by existing industrial infrastructure have not been developed. Furthermore, prior studies that investigated horticultural crop quality metrics, specifically of size and shape, used a limited number of samples, did not incorporate deformed or non-marketable samples, and did not use images captured from high-throughput systems. In this work, using sweetpotato (SP) as a use case, we introduce a computer vision algorithm for quantifying shape and size characteristics in a high-throughput manner. This approach generates 3D model of SPs from two 2D images captured by an industrial sorter 90 degrees apart and extracts 3D shape features in a few hundred milliseconds. We applied the 3D reconstruction and feature extraction method to thousands of image samples to demonstrate how variations in shape features across SP cultivars can be quantified. We created a SP shape dataset containing SP images, extracted shape features, and qualitative shape types (U.S. No. 1 or Cull). We used this dataset to develop a neural network-based shape classifier that was able to predict Cull vs. U.S. No. 1 SPs with 84.59% accuracy. In addition, using univariate Chi-squared tests and random forest, we identified the most important features for determining qualitative shape type (U.S. No. 1 or Cull) of the SPs. Our study serves as a key step towards enabling big data analytics for industrial SP agriculture. The methodological framework is readily transferable to other horticultural crops, particularly those that are sorted using commercial imaging equipment.}, journal={Computers and Electronics in Agriculture}, publisher={Elsevier BV}, author={Haque, Samiul and Lobaton, Edgar and Nelson, Natalie and Yencho, G. Craig and Pecota, Kenneth V. and Mierop, Russell and Kudenov, Michael W. and Boyette, Mike and Williams, Cranos M.}, year={2021}, month={Mar}, pages={106011} }
 @article{oloka_da silva pereira_amankwaah_mollinari_pecota_yada_olukolu_zeng_yencho_2021, title={Discovery of a major QTL for root-knot nematode (Meloidogyne incognita) resistance in cultivated sweetpotato (Ipomoea batatas)}, volume={134}, ISSN={0040-5752 1432-2242}, url={http://dx.doi.org/10.1007/s00122-021-03797-z}, DOI={10.1007/s00122-021-03797-z}, abstractNote={Utilizing a high-density integrated genetic linkage map of hexaploid sweetpotato, we discovered a major dominant QTL for root-knot nematode (RKN) resistance and modeled its effects. This discovery is useful for development of a modern sweetpotato breeding program that utilizes marker-assisted selection and genomic selection approaches for faster genetic gain of RKN resistance. The root-knot nematode [Meloidogyne incognita (Kofoid & White) Chitwood] (RKN) causes significant storage root quality reduction and yields losses in cultivated sweetpotato [Ipomoea batatas (L.) Lam.]. In this study, resistance to RKN was examined in a mapping population consisting of 244 progenies derived from a cross (TB) between 'Tanzania,' a predominant African landrace cultivar with resistance to RKN, and 'Beauregard,' an RKN susceptible major cultivar in the USA. We performed quantitative trait loci (QTL) analysis using a random-effect QTL mapping model on the TB genetic map. An RKN bioassay incorporating potted cuttings of each genotype was conducted in the greenhouse and replicated five times over a period of 10 weeks. For each replication, each genotype was inoculated with ca. 20,000 RKN eggs, and root-knot galls were counted ~62 days after inoculation. Resistance to RKN in the progeny was highly skewed toward the resistant parent, exhibiting medium to high levels of resistance. We identified one major QTL on linkage group 7, dominant in nature, which explained 58.3% of the phenotypic variation in RKN counts. This work represents a significant step forward in our understanding of the genetic architecture of RKN resistance and sets the stage for future utilization of genomics-assisted breeding in sweetpotato breeding programs.}, number={7}, journal={Theoretical and Applied Genetics}, publisher={Springer Science and Business Media LLC}, author={Oloka, Bonny Michael and da Silva Pereira, Guilherme and Amankwaah, Victor A. and Mollinari, Marcelo and Pecota, Kenneth V. and Yada, Benard and Olukolu, Bode A. and Zeng, Zhao-Bang and Yencho, G. Craig}, year={2021}, month={Apr}, pages={1945–1955} }
 @article{kudenov_scarboro_altaqui_boyette_yencho_williams_2021, title={Internal defect scanning of sweetpotatoes using interactance spectroscopy}, volume={16}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0246872}, abstractNote={While standard visible-light imaging offers a fast and inexpensive means of quality analysis of horticultural products, it is generally limited to measuring superficial (surface) defects. Using light at longer (near-infrared) or shorter (X-ray) wavelengths enables the detection of superficial tissue bruising and density defects, respectively; however, it does not enable the optical absorption and scattering properties of sub-dermal tissue to be quantified. This paper applies visible and near-infrared interactance spectroscopy to detect internal necrosis in sweetpotatoes and develops a Zemax scattering simulation that models the measured optical signatures for both healthy and necrotic tissue. This study demonstrates that interactance spectroscopy can detect the unique near-infrared optical signatures of necrotic tissues in sweetpotatoes down to a depth of approximately 5±0.5 mm. We anticipate that light scattering measurement methods will represent a significant improvement over the current destructive analysis methods used to assay for internal defects in sweetpotatoes.}, number={2}, journal={PLOS ONE}, author={Kudenov, Michael W. and Scarboro, Clifton G. and Altaqui, Ali and Boyette, Mike and Yencho, G. Craig and Williams, Cranos M.}, year={2021}, month={Feb} }
 @article{park_massa_douches_coombs_akdemir_yencho_whitworth_novy_2021, title={Linkage and QTL mapping for tuber shape and specific gravity in a tetraploid mapping population of potato representing the russet market class}, volume={21}, ISSN={["1471-2229"]}, DOI={10.1186/s12870-021-03265-2}, abstractNote={Tuber shape and specific gravity (dry matter) are important agronomic traits in potato processing and impact production costs, quality, and consistency of the final processed food products such as French fries and potato chips. In this study, linkage and QTL mapping were performed for these two traits to allow for the implementation of marker-assisted selection to facilitate breeding efforts in the russet market class. Two parents, Rio Grande Russet (female) and Premier Russet (male) and their 205 F1 progenies were initially phenotyped for tuber shape and specific gravity in field trials conducted in Idaho and North Carolina in 2010 and 2011, with specific gravity also being measured in Minnesota in 2011. Progenies and parents were previously genotyped using the Illumina SolCAP Infinium 8303 Potato SNP array, with ClusterCall and MAPpoly (R-packages) subsequently used for autotetraploid SNP calling and linkage mapping in this study. The 12 complete linkage groups and phenotypic data were then imported into QTLpoly, an R-package designed for polyploid QTL analyses.Significant QTL for tuber shape were detected on chromosomes 4, 7, and 10, with heritability estimates ranging from 0.09 to 0.36. Significant tuber shape QTL on chromosomes 4 and 7 were specific to Idaho and North Carolina environments, respectively, whereas the QTL on chromosome 10 was significant regardless of growing environment. Single marker analyses identified alleles in the parents associated with QTL on chromosomes 4, 7, and 10 that contributed to significant differences in tuber shape among progenies. Significant QTL were also identified for specific gravity on chromosomes 1 and 5 with heritability ranging from 0.12 to 0.21 and were reflected across environments.Fully automated linkage mapping and QTL analysis were conducted to identify significant QTL for tuber shape and dry matter in a tetraploid mapping population representing the russet market class. The findings are important for the development of molecular markers useful to potato breeders for marker-assisted selection for the long tuber shape and acceptable dry matter required by the potato industry within this important market class.}, number={1}, journal={BMC PLANT BIOLOGY}, author={Park, Jaebum and Massa, Alicia N. and Douches, David and Coombs, Joseph and Akdemir, Deniz and Yencho, G. Craig and Whitworth, Jonathan L. and Novy, Richard G.}, year={2021}, month={Nov} }
 @article{da silva pereira_mollinari_qu_thill_zeng_haynes_yencho_2021, title={Quantitative Trait Locus Mapping for Common Scab Resistance in a Tetraploid Potato Full-Sib Population}, volume={105}, ISSN={0191-2917 1943-7692}, url={http://dx.doi.org/10.1094/PDIS-10-20-2270-RE}, DOI={10.1094/PDIS-10-20-2270-RE}, abstractNote={Despite the negative impact of common scab (Streptomyces spp.) on the potato industry, little is known about the genetic architecture of resistance to this bacterial disease in the crop. We evaluated a mapping population (∼150 full sibs) derived from a cross between two tetraploid potatoes ('Atlantic' × B1829-5) in three environments (MN11, PA11, ME12) under natural common scab pressure. Three measures to common scab reaction, namely percentage of scabby tubers and disease area and lesion indices, were found to be highly correlated (>0.76). Because of the large environmental effect, heritability values were zero for all three traits in MN11, but moderate to high in PA11 and ME12 (∼0.44 to 0.79). We identified a single quantitative trait locus (QTL) for lesion index in PA11, ME12, and joint analyses on linkage group 3, explaining ∼22 to 30% of the total variation. The identification of QTL haplotypes and candidate genes contributing to disease resistance can support genomics-assisted breeding approaches in the crop.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.}, number={10}, journal={Plant Disease}, publisher={Scientific Societies}, author={da Silva Pereira, Guilherme and Mollinari, Marcelo and Qu, Xinshun and Thill, Christian and Zeng, Zhao-Bang and Haynes, Kathleen and Yencho, G. Craig}, year={2021}, month={Oct}, pages={3048–3054} }
 @article{schwarz_li_yencho_pecota_heim_davis_2021, title={Screening Sweetpotato Genotypes for Resistance to a North Carolina Isolate of Meloidogyne enterolobii}, volume={105}, ISSN={0191-2917 1943-7692}, url={http://dx.doi.org/10.1094/PDIS-02-20-0389-RE}, DOI={10.1094/PDIS-02-20-0389-RE}, abstractNote={Potential resistance to the guava root-knot nematode, Meloidogyne enterolobii, in 91 selected sweetpotato (Ipomoea batatas [L.] Lam.) genotypes was evaluated in six greenhouse experiments. Ten thousand eggs of M. enterolobii were inoculated on each sweetpotato genotype grown in a 3:1 sand to soil mixture. Sixty days after inoculation, the percentage of total roots with nematode-induced galls was determined, and nematode eggs were extracted from roots. Significant differences (P < 0.001) between sweetpotato genotypes were found in all six tests for gall rating, total eggs, and eggs per gram of root. Resistant sweetpotato genotypes were calculated as final eggs per root system divided by the initial inoculum, where Pf/Pi < 1 (reproduction factor; final egg count divided by initial inoculum of 10,000 eggs), and statistical mean separations were confirmed by Fisher’s least significant difference t test. Our results indicated that 19 out of 91 tested sweetpotato genotypes were resistant to M. enterolobii. Some of the susceptible genotypes included ‘Covington,’ ‘Beauregard,’ ‘NCDM04-001’, and ‘Hernandez.’ Some of the resistant sweetpotato genotypes included ‘Tanzania,’ ‘Murasaki-29,’ ‘Bwanjule,’ ‘Dimbuka-Bukulula,’ ‘Jewel,’ and ‘Centennial.’ Most of the 19 resistant sweetpotato genotypes supported almost no M. enterolobii reproduction, with <20 eggs/g root of M. enterolobii. A number of segregants from a ‘Tanzania’ × ‘Beauregard’ cross demonstrated strong resistance to M. enterolobii observed in the ‘Tanzania’ parent. In collaboration with North Carolina State University sweetpotato breeding program, several genotypes evaluated in these tests are being used to incorporate the observed resistance to M. enterolobii into commercial sweetpotato cultivars.}, number={4}, journal={PLANT DISEASE}, publisher={Scientific Societies}, author={Schwarz, Tanner R. and Li, Chunying and Yencho, G. Craig and Pecota, Kenneth V and Heim, Chris R. and Davis, Eric L.}, year={2021}, month={Apr}, pages={1101–1107} }
 @article{parada-rojas_pecota_almeyda_yencho_quesada-ocampo_2021, title={Sweetpotato Root Development Influences Susceptibility to Black Rot Caused by the Fungal Pathogen <i>Ceratocystis fimbriata}, volume={111}, ISSN={0031-949X 1943-7684}, url={http://dx.doi.org/10.1094/PHYTO-12-20-0541-R}, DOI={10.1094/PHYTO-12-20-0541-R}, abstractNote={Black rot of sweetpotato, caused by Ceratocystis fimbriata, is an important reemerging disease threatening sweetpotato production in the United States. This study assessed disease susceptibility of the storage root surface, storage root cambium, and slips (vine cuttings) of 48 sweetpotato cultivars, advanced breeding lines, and wild relative accessions. We also characterized the effect of storage root development on susceptibility to C. fimbriata. None of the cultivars examined at the storage root level were resistant, with most cultivars exhibiting similar levels of susceptibility. In storage roots, Jewel and Covington were the least susceptible and significantly different from White Bonita, the most susceptible cultivar. In the slip, significant differences in disease incidence were observed for above- and below-ground plant structures among cultivars, advanced breeding lines, and wild relative accessions. Burgundy and Ipomoea littoralis displayed less below-ground disease incidence compared with NASPOT 8, Sunnyside, and LSU-417, the most susceptible cultivars. Correlation of black rot susceptibility between storage roots and slips was not significant, suggesting that slip assays are not useful to predict resistance in storage roots. Immature, early-developing storage roots were comparatively more susceptible than older, fully developed storage roots. The high significant correlation between the storage root cross-section area and the cross-sectional lesion ratio suggests the presence of an unfavorable environment for C. fimbriata as the storage root develops. Incorporating applications of effective fungicides at transplanting and during early-storage root development when sweetpotato tissues are most susceptible to black rot infection may improve disease management efforts.}, number={9}, journal={Phytopathology®}, publisher={Scientific Societies}, author={Parada-Rojas, C. H. and Pecota, Kenneth and Almeyda, C. and Yencho, G. Craig and Quesada-Ocampo, L. M.}, year={2021}, month={Sep}, pages={1660–1669} }
 @article{da silva pereira_mollinari_schumann_clough_zeng_yencho_2021, title={The recombination landscape and multiple QTL mapping in a Solanum tuberosum cv. ‘Atlantic’-derived F1 population}, volume={126}, ISSN={0018-067X 1365-2540}, url={http://dx.doi.org/10.1038/s41437-021-00416-x}, DOI={10.1038/s41437-021-00416-x}, abstractNote={Abstract There are many challenges involved with the genetic analyses of autopolyploid species, such as the tetraploid potato, Solanum tuberosum (2 n = 4 x = 48). The development of new analytical methods has made it valuable to re-analyze an F 1 population ( n = 156) derived from a cross involving ‘Atlantic’, a widely grown chipping variety in the USA. A fully integrated genetic map with 4285 single nucleotide polymorphisms, spanning 1630 cM, was constructed with MAPpoly software. We observed that bivalent configurations were the most abundant ones (51.0~72.4% depending on parent and linkage group), though multivalent configurations were also observed (2.2~39.2%). Seven traits were evaluated over four years (2006–8 and 2014) and quantitative trait loci (QTL) mapping was carried out using QTLpoly software. Based on a multiple-QTL model approach, we detected 21 QTL for 15 out of 27 trait-year combination phenotypes. A hotspot on linkage group 5 was identified with co-located QTL for maturity, plant yield, specific gravity, and internal heat necrosis resistance evaluated over different years. Additional QTL for specific gravity and dry matter were detected with maturity-corrected phenotypes. Among the genes around QTL peaks, we found those on chromosome 5 that have been previously implicated in maturity ( StCDF1 ) and tuber formation ( POTH1 ). These analyses have the potential to provide insights into the biology and breeding of tetraploid potato and other autopolyploid species.}, number={5}, journal={Heredity}, publisher={Springer Science and Business Media LLC}, author={da Silva Pereira, Guilherme and Mollinari, Marcelo and Schumann, Mitchell J. and Clough, Mark E. and Zeng, Zhao-Bang and Yencho, G. Craig}, year={2021}, month={Mar}, pages={817–830} }
 @article{kuster_yencho_olukolu_2021, title={ngsComposer: an automated pipeline for empirically based NGS data quality filtering}, volume={22}, ISSN={["1477-4054"]}, DOI={10.1093/bib/bbab092}, abstractNote={Abstract Next-generation sequencing (NGS) enables massively parallel acquisition of large-scale omics data; however, objective data quality filtering parameters are lacking. Although a useful metric, evidence reveals that platform-generated Phred values overestimate per-base quality scores. We have developed novel and empirically based algorithms that streamline NGS data quality filtering. The pipeline leverages known sequence motifs to enable empirical estimation of error rates, detection of erroneous base calls and removal of contaminating adapter sequence. The performance of motif-based error detection and quality filtering were further validated with read compression rates as an unbiased metric. Elevated error rates at read ends, where known motifs lie, tracked with propagation of erroneous base calls. Barcode swapping, an inherent problem with pooled libraries, was also effectively mitigated. The ngsComposer pipeline is suitable for various NGS protocols and platforms due to the universal concepts on which the algorithms are based.}, number={5}, journal={BRIEFINGS IN BIOINFORMATICS}, author={Kuster, Ryan D. and Yencho, G. Craig and Olukolu, Bode A.}, year={2021}, month={Sep} }
 @article{zhou_olukolu_gemenet_wu_gruneberg_cao_fei_zeng_george_khan_et al._2020, title={Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations}, volume={52}, ISSN={1061-4036 1546-1718}, url={http://dx.doi.org/10.1038/s41588-020-00717-7}, DOI={10.1038/s41588-020-00717-7}, abstractNote={Despite advances in sequencing technologies, assembly of complex plant genomes remains elusive due to polyploidy and high repeat content. Here we report PolyGembler for grouping and ordering contigs into pseudomolecules by genetic linkage analysis. Our approach also provides an accurate method with which to detect and fix assembly errors. Using simulated data, we demonstrate that our approach is of high accuracy and outperforms three existing state-of-the-art genetic mapping tools. Particularly, our approach is more robust to the presence of missing genotype data and genotyping errors. We used our method to construct pseudomolecules for allotetraploid lawn grass utilizing PacBio long reads in combination with restriction site-associated DNA sequencing, and for diploid Ipomoea trifida and autotetraploid potato utilizing contigs assembled from Illumina reads in combination with genotype data generated by single-nucleotide polymorphism arrays and genotyping by sequencing, respectively. We resolved 13 assembly errors for a published I. trifida genome assembly and anchored eight unplaced scaffolds in the published potato genome.}, number={11}, journal={Nature Genetics}, publisher={Springer Science and Business Media LLC}, author={Zhou, Chenxi and Olukolu, Bode and Gemenet, Dorcus C. and Wu, Shan and Gruneberg, Wolfgang and Cao, Minh Duc and Fei, Zhangjun and Zeng, Zhao-Bang and George, Andrew W. and Khan, Awais and et al.}, year={2020}, month={Oct}, pages={1256–1264} }
 @article{jacobs_adhikari_pattison_yencho_fernandez_louws_2020, title={Assessing Rate-Reducing Foliar Resistance to Anthracnose Crown Rot and Fruit Rot in Strawberry}, volume={104}, ISSN={0191-2917 1943-7692}, url={http://dx.doi.org/10.1094/PDIS-04-19-0687-RE}, DOI={10.1094/PDIS-04-19-0687-RE}, abstractNote={Anthracnose fruit rot and anthracnose crown rot (ACR) caused by two species complexes of the fungus referred to as Colletotrichum acutatum and Colletotrichum gloeosporioides, respectively, are major pathogens of strawberry in North Carolina. Anthracnose epidemics are common when susceptible cultivars and asymptomatic planting stocks carrying quiescent Colletotrichum infection or hemibiotrophic infection (HBI) are planted. The main objective of this study was to assess resistance to HBI and ACR in strawberry. Strawberry cultivars and breeding lines were spray inoculated with isolates of C. acutatum or C. gloeosporioides. Four epidemiological parameters providing estimates of rate-reducing resistance to HBI and ACR in strawberry cultivars and lines were evaluated in repeated experiments in controlled environments in a greenhouse. HBI severity, measured as the percentage of total leaf area covered by acervuli, was estimated visually and by image analysis. ACR severity was rated weekly for wilt symptoms, and relative area under disease progress curve scores were calculated for comparing strawberry cultivars and lines. Significant differences (P ≤ 0.005) in HBI severity were found among strawberry genotypes; however, the correlations were not remarkable between Colletotrichum species (r = 0.4251). Although significant variation in resistance was observed for ACR, this was also weakly correlated (r = 0.2430) with resistance to C. gloeosporioides HBI. Overall, rate-reducing resistance to HBI and ACR in strawberry identified in this study could be utilized in breeding programs to develop durable resistance to anthracnose in North Carolina.}, number={2}, journal={Plant Disease}, publisher={Scientific Societies}, author={Jacobs, Raymond L. and Adhikari, Tika B. and Pattison, Jeremy and Yencho, G. Craig and Fernandez, Gina E. and Louws, Frank J.}, year={2020}, month={Feb}, pages={398–407} }
 @article{nhanala_yencho_2020, title={Assessment of the potential of wild
            <i>Ipomoea
            spp. for the improvement of drought tolerance in cultivated sweetpotato
            <i>Ipomoea batatas
            (L.) Lam}, volume={61}, ISSN={0011-183X 1435-0653}, url={http://dx.doi.org/10.1002/csc2.20363}, DOI={10.1002/csc2.20363}, abstractNote={Abstract Sweetpotato [ Ipomoea batatas (L.) Lam] is cultivated worldwide, and it is a staple food in many developing countries. In some regions (e.g., Africa) drought is a major production constraint that results in significant yield loss. Climate change is predicted to result in even greater losses due to long periods of drought and elevated temperatures. The goal of this study was to assess the potential of wild Ipomoea spp. as a source of drought tolerance in cultivated sweetpotato. We evaluated the drought tolerance of I. batatas , I. cynanchifolia , I. leucantha , I. trifida and I. triloba in a randomized complete block design, with five levels of simulated drought: control (daily irrigation), and no irrigation for 7, 9, 21 and 50 days. We observed that post drought re‐irrigation of the wild species subjected to 21 days of stress resulted in plant recovery and an increase of the stomatal conductance of up to 99% in I. leucantha . However, under extreme stress (50 d) the wild plants did not respond to re‐irrigation, resulting in up to 89% ( I. leucantha ) plant mortality. The wild species did not produce storage roots, while the I. batatas cultivars produced storage roots. Under 50 days of stress I. batatas had a survival rate between 44% (cv. Tanzania) and 89% (cv. Beauregard). We concluded that the wild genotypes screened may not be a valuable source of germplasm for drought tolerance and that significant levels of drought tolerance may exist in cultivated sweetpotato.}, number={1}, journal={Crop Science}, publisher={Wiley}, author={Nhanala, Stella E. C. and Yencho, G. Craig}, year={2020}, month={Nov}, pages={234–249} }
 @article{gemenet_kitavi_david_ndege_ssali_swanckaert_makunde_yencho_gruneberg_carey_et al._2020, title={Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs}, volume={15}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0232173}, DOI={10.1371/journal.pone.0232173}, abstractNote={Quality assurance and control (QA/QC) is an essential element of a breeding program's optimization efforts towards increased genetic gains. Due to auto-hexaploid genome complexity, a low-cost marker platform for routine QA/QC in sweetpotato breeding programs is still unavailable. We used 662 parents of the International Potato Center (CIP)'s global breeding program spanning Peru, Uganda, Mozambique and Ghana, to develop a low-density highly informative single nucleotide polymorphism (SNP) marker set to be deployed for routine QA/QC. Segregation of the selected 30 SNPs (two SNPs per base chromosome) in a recombined breeding population was evaluated using 282 progeny from some of the parents above. The progeny were replicated from in-vitro, screenhouse and field, and the selected SNP-set was confirmed to identify relatively similar mislabeling error rates as a high density SNP-set of 10,159 markers. Six additional trait-specific markers were added to the selected SNP set from previous quantitative trait loci mapping studies. The 36-SNP set will be deployed for QA/QC in breeding pipelines and in fingerprinting of advanced clones or released varieties to monitor genetic gains in famers' fields. The study also enabled evaluation of CIP's global breeding population structure and the effect of some of the most devastating stresses like sweetpotato virus disease on genetic variation management. These results will inform future deployment of genomic selection in sweetpotato.}, number={4}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Gemenet, Dorcus C. and Kitavi, Mercy N. and David, Maria and Ndege, Dorcah and Ssali, Reuben T. and Swanckaert, Jolien and Makunde, Godwill and Yencho, G. Craig and Gruneberg, Wolfgang and Carey, Edward and et al.}, editor={Kumar, AjayEditor}, year={2020}, month={Apr}, pages={e0232173} }
 @article{da silva pereira_gemenet_mollinari_olukolu_wood_diaz_mosquera_gruneberg_khan_buell_et al._2020, title={Multiple QTL Mapping in Autopolyploids: A Random-Effect Model Approach with Application in a Hexaploid Sweetpotato Full-Sib Population}, volume={215}, ISSN={1943-2631}, url={http://dx.doi.org/10.1534/genetics.120.303080}, DOI={10.1534/genetics.120.303080}, abstractNote={In developing countries, the sweetpotato, Ipomoea batatas (L.) Lam. [Formula: see text], is an important autopolyploid species, both socially and economically. However, quantitative trait loci (QTL) mapping has remained limited due to its genetic complexity. Current fixed-effect models can fit only a single QTL and are generally hard to interpret. Here, we report the use of a random-effect model approach to map multiple QTL based on score statistics in a sweetpotato biparental population ('Beauregard' × 'Tanzania') with 315 full-sibs. Phenotypic data were collected for eight yield component traits in six environments in Peru, and jointly adjusted means were obtained using mixed-effect models. An integrated linkage map consisting of 30,684 markers distributed along 15 linkage groups (LGs) was used to obtain the genotype conditional probabilities of putative QTL at every centiMorgan position. Multiple interval mapping was performed using our R package QTLpoly and detected a total of 13 QTL, ranging from none to four QTL per trait, which explained up to 55% of the total variance. Some regions, such as those on LGs 3 and 15, were consistently detected among root number and yield traits, and provided a basis for candidate gene search. In addition, some QTL were found to affect commercial and noncommercial root traits distinctly. Further best linear unbiased predictions were decomposed into additive allele effects and were used to compute multiple QTL-based breeding values for selection. Together with quantitative genotyping and its appropriate usage in linkage analyses, this QTL mapping methodology will facilitate the use of genomic tools in sweetpotato breeding as well as in other autopolyploids.}, number={3}, journal={Genetics}, publisher={Oxford University Press (OUP)}, author={da Silva Pereira, Guilherme and Gemenet, Dorcus C and Mollinari, Marcelo and Olukolu, Bode A and Wood, Joshua C and Diaz, Federico and Mosquera, Veronica and Gruneberg, Wolfgang J and Khan, Awais and Buell, C Robin and et al.}, year={2020}, month={Jul}, pages={579–595} }
 @article{eserman_sosef_simao-bianchini_utteridge_barbosa_buril_chatrou_clay_delgado_desquilbet_et al._2020, title={Proposal to change the conserved type of Ipomoea, nom. cons. (Convolvulaceae)}, volume={69}, ISSN={["1996-8175"]}, url={http://dx.doi.org/10.1002/tax.12400}, DOI={10.1002/tax.12400}, abstractNote={(2786) Ipomoea L., Sp. Pl.: 159. 1 Mai 1753 [Convolvul.], nom. cons. Typus: I. triloba L., typ. cons. prop. Ipomoea L. is the largest (650–900 species, depending on the concept adopted) and most iconic genus in Convolvulaceae, a family of c. 1880 species (data from Staples, Convolvulaceae Unlimited, 2012 at: http//convolvulaceae.myspecies.info), including the important crop sweetpotato, Ipomoea batatas (L.) Lam. (Tabl. Encycl. 1: 465. 1793), and several ornamental species commonly known as "bindweeds" or "morning glories" (Wilkin in Kew Bull. 54: 853–876. 1999; Mabberley, Mabberley's Plant-book. 2008). The genus has a long history of taxonomic and nomenclatural problems, mainly for the lack of a clear morphological circumscription and overlap with other genera. In his Species plantarum (1753), Linnaeus distinguished two genera, Convolvulus L. and Ipomoea, whose species suffered numerous re-arrangements, between Ipomoea and Convolvulus, but especially into numerous more recently described genera, which amount today to a total of 60 (Staples in World Checklist of Vascular Plants, v.2.0. 2020, http://wcvp.science.kew.org/ retrieved 2 Apr 2020). Linnaeus included 17 species in Ipomoea. However, of these, only the first, I. quamoclit L., truly matched his earlier generic description published in 1737 (Gen. Pl.: 47; "Petalum infundibuliforme; Tubus sere cylindraceus, longissimus"). Linnaeus actually replaced the name Quamoclit of Tournefort (Inst. Rei Herb., ed. 3, 2: t. 39. 1719) with his own Ipomoea (see Manitz in Taxon 25: 193–194. 1976). Hence, I. quamoclit would be the logical type of Ipomoea. However, in the past, some argued for a separation between the genus Quamoclit Mill. and Ipomoea (Roberty in Candollea 14: 11–65. 1952) that would result in an unfortunate recombination of hundreds of Ipomoea names, and which led Manitz (l.c.) to propose to conserve the name Ipomoea with another, conserved, type, I. pes-tigridis L., which was accepted (see Taxon 30: 145. 1981, 31: 310. 1982). More recently, molecular phylogenetic analyses have greatly assisted in obtaining a better understanding of the classification and phylogeny of the family as a whole and a much more stable taxonomy is now emerging. These studies have also shown that within the tribe Ipomoeeae Hall. f. s.l., Ipomoea is paraphyletic with 10 genera nested within it: Argyreia Lour., Astripomoea A. Meeuse, Blinkworthia Choisy, Lepistemon Blume, Lepistemonopsis Dammer, Mina Cerv., Paralepistemon Lejoly & Lisowski, Rivea Choisy, Stictocardia Hall. f., and Turbina Raf. (Wilkin, l.c.; Manos & al. in Syst. Bot. 26: 585–602. 2001; Miller & al. in Syst. Biol. 51: 740–753. 2002; Stefanović & al. in Amer. J. Bot. 89: 1510–1522. 2002, in Syst. Bot. 28: 701–806. 2003; Eserman & al. in Amer. J. Bot. 101: 92–103. 2014; Simões & al. in Bot. J. Linn. Soc. 179: 374–387. 2015). This furthered the debate about the actual identity of Ipomoea. Wilkin (l.c.) proposed the inclusion of all genera of Ipomoeeae into an Ipomoea s.l. This was recently taken up by Munõz-Rodríguez & al. (in Nature, Pl. 5: 1136–1154. 2019), soaring the genus to c. 900 species, without proposing any infrageneric classification and allowing huge morphological variation. As molecular phylogenetic results have also demonstrated, tribe Ipomoeeae can be subdivided into two main clades (Stefanović & al., l.c. 2003; Wood & al. in Phytokeys 143: 1–823. 2020) with the informal names "Astripomoeinae" and "Argyreiinae". While the first concentrates a large diversity of the Neotropical Ipomoea, the latter is more widely distributed throughout Africa, Asia, Australia, and many of the Pacific islands, and is mostly absent from the Neotropics. Unfortunately, "Argyreiinae" includes the presently conserved type of Ipomoea, I. pes-tigridis L. Hence, implementing a new classification with the distinction of several clades at genus level would result in around 600 name changes for the Ipomoea within the "Astripomoeinae" clade, affecting mostly the American species of the genus, many of which have ornamental value. Moreover, the most economically important species, I. batatas (L.) Lam., also does not belong to the clade including the type; therefore, a potential segregation of Ipomoea s.l. into smaller genera would result in the renaming of sweetpotato. With an annual production of over 90 million metric tons (data from Shahbandeh, Global sweet potato production volume 2010–2018. 2020, https://www.statista.com/statistics/812343/global-sweet-potato-production) and hundreds if not thousands of registered cultivars (in Asia and the Pacific region alone, there exists an estimated 12,000 landraces, while in 1994 the International Potato Center (CIP) in Peru held a total of 6500 sweetpotato accessions; Takagi & al. in Flach & Rumawas, PROSEA 9, Plants Yielding Non-seed Carbohydrates: 102–107. 1999), a name change in sweetpotato would certainly result in a very costly and extreme effort by the commercial enterprises involved. As shown above (Wilkin, l.c.; Munõz-Rodriguez & al., l.c.), some authors regard the presence of the type of Ipomoea in the "Argyreiinae" clade as an obstacle towards a most useful renewal of the re-circumscription of the genera in tribe Ipomoeeae because of the sheer amount of necessary name changes and have preferred to advocate the inclusion of all the taxonomic diversity into a mega-genus Ipomoea. We think nomenclature should not block the development of a more stable and logical classification and here propose to replace the conserved type of the genus with a species included in the "Astripomoeinae" clade. This would permit those who wish to create a new classification to do so with far fewer nomenclatorial consequences. Thus, the generic name Ipomoea would be retained for the clade with the highest taxonomic diversity (c. 600 species), while preventing a name change in the economically important I. batatas. There are numerous examples of changes in nomenclature that are rejected by the scientific community when they cause significant destabilization. For example, the recent taxonomic changes in "monkeyflowers" (Mimulus, Phrymaceae; Barker & al. in Phytoneuron 39: 1–60. 2012, Lowry & al. in Taxon 68: 617–623. 2019, Nesom & al. in Taxon 68: 624–627. 2019) were rejected by the evolutionary biology community and have brought to the forefront discussions about when nomenclatural changes are appropriate. Most scientists recognize the importance of naming groups based on evolutionary lineages, but to what extent this is applied must be done with the utmost consideration. As it concerns Ipomoea, it is a priority to allow the possibility to subdivide the genus into smaller genera, while maintaining maximal nomenclatural stability. Manitz (l.c.), in proposing to conserve Ipomoea with a conserved type, identified the early confusion in the circumscription of Ipomoea and Convolvulus and acknowledged the need to stabilize nomenclature. His argument followed previous authors, especially House (in Ann. New York Acad. Sci. 18: 181–263. 1908) in considering that, although I. quamoclit would be the "historically correct" species to be selected, its morphological particularities (red tubular corolla) might have blocked those who wanted to regard Quamoclit as a distinct genus because of the very high number of new names that would then be needed to accommodate the remainder of the Ipomoea species. What Manitz did not know, was that the type House had already proposed, Ipomoea pes-tigridis L., and which he selected for conservation, would later lead to almost the same situation. In view of the recent molecular and systematic works that suggest the phylogenetic position of I. pes-tigridis as distantly related to the largest part of the genus Ipomoea, we would propose alternatively I. triloba L. as the conserved type for the genus. The broad-scale molecular phylogenetic study of Wood & al. (l.c.) demonstrated with ample sampling that I. triloba is one of the most closely related species to I. batatas. A range of important ornamental species are also fairly closely related to I. batatas and I. triloba, when considering a broader clade (e.g., I. nil (L.) Roth, I. tricolor Cav., and I. purpurea (L.) Roth). Therefore, our proposed type will allow future studies to re-assess the generic delimitation within tribe Ipomoeeae, without the fear of destabilizing the nomenclature of the group, in particular the species with greatest economic importance. LAE, https://orcid.org/0000-0002-0208-6632 MSMS, https://orcid.org/0000-0002-6997-5813 RS-B, https://orcid.org/0000-0001-9738-9494 TMAU, https://orcid.org/0000-0003-2823-0337 JCJB, https://orcid.org/0000-0002-8753-4915 MTB, https://orcid.org/0000-0001-9615-2057 LWC, https://orcid.org/0000-0003-0131-0302 KC, https://orcid.org/0000-0002-3956-0887 GD, https://orcid.org/0000-0002-6693-1540 TED, https://orcid.org/0000-0002-2119-4524 PPAF, https://orcid.org/0000-0003-1134-7918 JRGA, https://orcid.org/0000-0002-7066-0608 ALH, https://orcid.org/0000-0003-2172-6356 GH-R, https://orcid.org/0000-0002-8209-0366 RLJ, https://orcid.org/0000-0002-0426-6186 RKK, https://orcid.org/0000-0002-8538-8694 SL, https://orcid.org/0000-0003-0028-2450 JAAML, https://orcid.org/0000-0003-4741-1723 IDM, https://orcid.org/0000-0002-7567-470X REM, https://orcid.org/0000-0002-5802-2267 SM, https://orcid.org/0000-0002-7712-7785 ALCM, https://orcid.org/0000-0003-0862-0135 IM-M, https://orcid.org/0000-0003-0203-5795 SN, https://orcid.org/0000-0002-1829-7290 MP, https://orcid.org/0000-0002-2936-8920 FSP, https://orcid.org/0000-0002-8380-843X PPi, https://orcid.org/0000-0003-1746-1439 PPo, https://orcid.org/0000-0002-7998-2064 JR, https://orcid.org/0000-0003-1980-5557 FDSS, https://orcid.org/0000-0002-0053-1333 VBS, https://orcid.org/0000-0002-7028-1114 SSS, https://orcid.org/0000-0002-6318-3137 JRS, https://orcid.org/0000-0003-3349-2964 PT, https://orcid.org/0000-0001-8051-5722 LVV, https://orcid.org/0000-0003-1724-2068 MLW, https://orcid.org/0000-0001-9406-8951 AV, https://orcid.org/0000-0002-2844-723X JY, https://orcid.org/0000-0002-0371-8814 CY, https://orcid.org/0000-0001-6583-0628 BH, https://orcid.org/0000-0002-9792-8512 ARGS, https://orcid.org/0000-0001-7267-8353 We are thankful for useful comments from Dr. Mihai Costea (Wilfrid Laurier University, Canada) and Dr. Saša Stefanović (University of Toronto Mississauga, Canada).}, number={6}, journal={TAXON}, author={Eserman, Lauren A. and Sosef, Marc S. M. and Simao-Bianchini, Rosangela and Utteridge, Timothy M. A. and Barbosa, Juliana C. J. and Buril, Maria Teresa and Chatrou, Lars W. and Clay, Keith and Delgado, Geadelande and Desquilbet, Thibaut E. and et al.}, year={2020}, month={Dec}, pages={1369–1371} }
 @article{silva pereira_mollinari_qu_thill_zeng_haynes_yencho_2020, title={Quantitative trait locus mapping for common scab resistance in a tetraploid potato full-sib population}, url={https://doi.org/10.1101/2020.10.24.353557}, DOI={10.1101/2020.10.24.353557}, abstractNote={Abstract Despite the negative impact of common scab ( Streptomyces spp.) to the potato industry, little is known about the genetic architecture of resistance to this bacterial disease in the crop. We evaluated a mapping population (~150 full-sibs) derived from a cross between two tetraploid potatoes (‘Atlantic’ × B1829-5) in three environments (MN11, PA11, ME12) under natural common scab pressure. Three measures to common scab reaction were assessed, namely percentage of scabby tubers, and disease area and lesion indices, which were highly correlated (>0.76). Due to large environmental effect, heritability values were zero for all three traits in MN11, but moderate to high in PA11 and ME12 (0.44~0.79). We identified a single quantitative trait locus (QTL) for lesion index in PA11, ME12 and joint analyses on linkage group 3, explaining 22~30% of the total variation. The identification of QTL haplotypes and candidate genes contributing to disease resistance can support genomics-assisted breeding approaches.}, journal={bioRxiv}, author={Silva Pereira, Guilherme and Mollinari, Marcelo and Qu, Xinshun and Thill, Christian and Zeng, Zhao-Bang and Haynes, Kathleen and Yencho, G. Craig}, year={2020}, month={Oct} }
 @article{gemenet_lindqvist-kreuze_de boeck_da silva pereira_mollinari_zeng_craig yencho_campos_2020, title={Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops}, volume={133}, ISSN={0040-5752 1432-2242}, url={http://dx.doi.org/10.1007/s00122-020-03673-2}, DOI={10.1007/s00122-020-03673-2}, abstractNote={Key message Polypoid crop breeders can balance resources between density and sequencing depth, dosage information and fewer highly informative SNPs recommended, non-additive models and QTL advantages on prediction dependent on trait architecture. Abstract The autopolyploid nature of potato and sweetpotato ensures a wide range of meiotic configurations and linkage phases leading to complex gene-action and pose problems in genotype data quality and genomic selection analyses. We used a 315-progeny biparental F 1 population of hexaploid sweetpotato and a diversity panel of 380 tetraploid potato, genotyped using different platforms to answer the following questions: (i) do polyploid crop breeders need to invest more for additional sequencing depth? (ii) how many markers are required to make selection decisions? (iii) does considering non-additive genetic effects improve predictive ability (PA)? (iv) does considering dosage or quantitative trait loci (QTL) offer significant improvement to PA? Our results show that only a small number of highly informative single nucleotide polymorphisms (SNPs; ≤ 1000) are adequate for prediction in the type of populations we analyzed. We also show that considering dosage information and models considering only additive effects had the best PA for most traits, while the comparative advantage of considering non-additive genetic effects and including known QTL in the predictive model depended on trait architecture. We conclude that genomic selection can help accelerate the rate of genetic gains in potato and sweetpotato. However, application of genomic selection should be considered as part of optimizing the entire breeding program. Additionally, since the predictions in the current study are based on single populations, further studies on the effects of haplotype structure and inheritance on PA should be studied in actual multi-generation breeding populations.}, number={12}, journal={Theoretical and Applied Genetics}, publisher={Springer Science and Business Media LLC}, author={Gemenet, Dorcus C. and Lindqvist-Kreuze, Hannele and De Boeck, Bert and da Silva Pereira, Guilherme and Mollinari, Marcelo and Zeng, Zhao-Bang and Craig Yencho, G. and Campos, Hugo}, year={2020}, month={Sep}, pages={3345–3363} }
 @article{silva pereira_mollinari_schumann_clough_zeng_yencho_2020, title={The recombination landscape and multiple QTL mapping in aSolanum tuberosumcv. ‘Atlantic’-derived F1population}, url={https://doi.org/10.1101/2020.08.24.265397}, DOI={10.1101/2020.08.24.265397}, abstractNote={Abstract There are many challenges involved with the genetic analyses of autopolyploid species, such as the tetraploid potato, Solanum tuberosum (2 n = 4 x = 48). The development of new analytical methods has made it valuable to re-analyze an F1 population ( n = 156) derived from a cross involving ‘Atlantic’, a widely grown chipping variety in the USA. A fully integrated genetic map with 4,285 single nucleotide polymorphisms, spanning 1,630 cM, was constructed with MAPpoly software. We observed that bivalent configurations were the most abundant ones (51.0∼72.4% depending on parent and linkage group), though multivalent configurations were also observed (2.2∼39.2%). Seven traits were evaluated over four years (2006-8 and 2014) and quantitative trait loci (QTL) mapping was carried out using QTLpoly software. Based on a multiple-QTL model approach, we detected 21 QTL for 15 out of 27 trait-year combination phenotypes. A hotspot on linkage group 5 was identified as QTL for maturity, plant yield, specific gravity and internal heat necrosis resistance over different years were co-located. Additional QTL for specific gravity and dry matter were detected with maturity-corrected phenotypes. Among the genes around QTL peaks, we found those on chromosome 5 that have been previously implicated in maturity ( StCDF1 ) and tuber formation ( POTH1 ). These analyses have the potential to provide insights into the biology and breeding of tetraploid potato and other autopolyploid species.}, author={Silva Pereira, Guilherme and Mollinari, Marcelo and Schumann, Mitchell J. and Clough, Mark E. and Zeng, Zhao-Bang and Yencho, G. Craig}, year={2020}, month={Aug} }
 @article{zuleta-correa_chinn_alfaro-córdoba_truong_yencho_bruno-bárcena_2020, place={George Craig Yencho}, title={Use of unconventional mixed Acetone-Butanol-Ethanol solvents for anthocyanin extraction from Purple-Fleshed sweetpotatoes}, volume={314}, ISSN={0308-8146}, url={http://dx.doi.org/10.1016/j.foodchem.2019.125959}, DOI={10.1016/j.foodchem.2019.125959}, abstractNote={Anthocyanins from purple-fleshed sweetpotatoes constitute highly valued natural colorants and functional ingredients. In the past, anthocyanin extraction conditions and efficiencies using a single acidified solvent have been assessed. However, the potential of solvent mixes that can be generated by fermentation of biomass-derived sugars have not been explored. In this study, the effects of single and mixed solvent, time, temperature, sweetpotato genotype and preparation, on anthocyanin and phenolic extraction were evaluated. Results indicated that unconventional diluted solvent mixes containing acetone, butanol, and ethanol were superior or equally efficient for extracting anthocyanins when compared to commonly used concentrated extractants. In addition, analysis of anthocyanidins concentrations including cyanidin (cy), peonidin (pe), and pelargonidin (pl), indicated that different ratios of pn/cy were obtained depending on the solvent used. These results could be useful when selecting processing conditions that better suit particular end-use applications and more environmentally friendly process development for purple sweetpotatoes.}, journal={Food Chemistry}, publisher={Elsevier BV}, author={Zuleta-Correa, Ana and Chinn, Mari Sum and Alfaro-Córdoba, Marcela and Truong, Van-Den and Yencho, George Craig and Bruno-Bárcena, José Manuel}, year={2020}, month={Jun}, pages={125959} }
 @article{musabyemungu_wasswa_alajo_chelagat_otema_musana_rukundo_gibson_edema_pecota_et al._2019, title={Adaptability of a U.S. purple-fleshed sweetpotato breeding population in Uganda}, volume={13}, ISSN={1835-2693 1835-2707}, url={http://dx.doi.org/10.21475/ajcs.19.13.01.p1023}, DOI={10.21475/ajcs.19.13.01.p1023}, abstractNote={Purple-fleshed sweetpotato varieties are important for their nutraceutical value due primarily to their high anthocyanin content.These varieties also often have high dry matter content preferred by consumers and processors in sub-Saharan Africa.However, improved purple-fleshed sweetpotatoes are not available in Uganda.This study was conducted to evaluate the adaptability of purple-fleshed sweetpotato genotypes for storage root yield, dry matter and anthocyanin content in Uganda.A bi-parental population of 159 clones from the cross NCP06-020 × NC09-188 introduced to Uganda from North Carolina State University was evaluated with three local checks in two sites and two seasons in Uganda.The trials were planted in two locations using alpha lattice design with two replicates and five sweetpotato vine cuttings per genotype.Storage roots and vines were harvested after five months and the agronomic characteristics were recorded.Dry matter and anthocyanin content of storage roots were analysed after harvesting.The mean storage root yield of clones across the two locations was 37.8 t/ha and 24.2 t/ha in the first season (2015A) and second season (2015B); respectively, with an overall mean of 31.0 t/ha.Storage root dry matter content ranged from 21.5 to 33.7% across locations and seasons with an overall mean of 29.1%.Storage root anthocyanin content across the two locations ranged from 0 to 12.6 mg/100g FW with the overall mean of 3.9 mg/100g FW.A total of ten genotypes showed significantly stable performance (P ≤ 0.001) across two locations and two seasons.Highly significant difference between genotypes for dry matter content, anthocyanin content and total storage root yields revealed significant genetic variability among the tested genotypes, which can be exploited for future crop improvement.}, number={01}, journal={Australian Journal of Crop Science}, publisher={Southern Cross Publishing}, author={Musabyemungu, Anastasie and Wasswa, Peter and Alajo, Agnes and Chelagat, Doreen M. and Otema, Milton A. and Musana, Paul and Rukundo, Placide and Gibson, Paul and Edema, Richard and Pecota, Kenneth V. and et al.}, year={2019}, month={Jan}, pages={17–25} }
 @article{gemenet_kitavi_david_ndege_ssali_swanckaert_makunde_yencho_gruneberg_carey_et al._2019, title={Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs}, volume={10}, url={https://doi.org/10.1101/826792}, DOI={10.1101/826792}, abstractNote={Abstract Quality assurance and control (QA/QC) is an essential element of a breeding program’s optimization efforts towards increased genetic gains. Due to auto-hexaploid genome complexity, a low-cost marker platform for routine QA/QC in sweetpotato breeding programs is still unavailable. We used 662 parents of the International Potato Center (CIP)’s global breeding program spanning Peru, Uganda, Mozambique and Ghana, to develop a low-density highly informative single nucleotide polymorphism (SNP) marker set to be deployed for routine QA/QC. Segregation of the selected 30 SNPs (two SNPs per base chromosome) in a recombined breeding population was evaluated using 282 progeny from some of the parents above. The progeny were replicated from in-vitro , screenhouse and field, and the selected SNP-set was confirmed to identify relatively similar mislabeling error rates as a high density SNP-set of 10,159 markers. Six additional trait-specific markers were added to the selected SNP set from previous quantitative trait loci mapping. The 36-SNP set will be deployed for QA/QC in breeding pipelines and in fingerprinting of advanced clones or released varieties to monitor genetic gains in famers fields. The study also enabled evaluation of CIP’s global breeding population structure and the effect of some of the most devastating biotic stresses like sweetpotato virus disease on genetic variation management. These results will inform future deployment of genomic selection in sweetpotato. Key Message A 36-SNP diagnostic marker set has been developed for quality assurance and control to support global sweetpotato breeding optimization efforts. Breeding population structure is shaped by sweetpotato virus disease prevalence.}, publisher={Cold Spring Harbor Laboratory}, author={Gemenet, Dorcus C and Kitavi, Mercy N and David, Maria and Ndege, Dorcah and Ssali, Reuben T and Swanckaert, Jolien and Makunde, Godwill and Yencho, G Craig and Gruneberg, Wolfgang and Carey, Edward and et al.}, year={2019}, month={Oct} }
 @article{schmitz carley_coombs_clough_de jong_douches_haynes_higgins_holm_miller_navarro_et al._2019, title={Genetic Covariance of Environments in the Potato National Chip Processing Trial}, volume={59}, ISSN={0011-183X}, url={http://dx.doi.org/10.2135/cropsci2018.05.0314}, DOI={10.2135/cropsci2018.05.0314}, abstractNote={The National Chip Processing Trial is a collaborative effort between public breeding programs and the potato ( Solanum tuberosum L.) industry to identify new clones with broad adaptation. The objective of this study was to investigate the genetic covariance of trial locations, based on 337 clones evaluated in 10 states from 2011 to 2016. Three models were considered: (I) assuming a uniform genetic correlation between locations within a year, (II) using a factor‐analytic (FA) model of the total genetic covariance of environments (location–year combinations), and (III) using a FA model of the additive genetic covariance based on 5278 single‐nucleotide polymorphism (SNP) markers. With Model I, the genetic correlation between locations was 0.50 for vine maturity, 0.54 for tuber yield, and 0.72 for specific gravity. The Akaike information criterion decreased as model complexity increased, from Models I to II to III, for maturity and yield but not specific gravity. Of the 10 states in the dataset, Florida stood out for having environments with substantial (up to 88%) genetic variance unexplained by the latent factors. Linear discriminants (LD) of the factor loadings were used to visualize the genetic correlation between locations. For vine maturity, LD1 separated Florida from the other locations, and LD2 separated the remaining southern locations from the northern ones. For yield, LD1 separated Texas from the other locations. This study has created a foundation for the design of more efficient trialing and selection programs for the US potato community.}, number={1}, journal={Crop Science}, publisher={Crop Science Society of America}, author={Schmitz Carley, Cari A. and Coombs, Joseph J. and Clough, Mark E. and De Jong, Walter S. and Douches, David S. and Haynes, Kathleen G. and Higgins, Charles R. and Holm, David G. and Miller, J. Creighton and Navarro, Felix M. and et al.}, year={2019}, pages={107} }
 @article{jacobs_adhikari_pattison_yencho_fernandez_louws_2019, title={Inheritance of Resistance to Colletotrichum gloeosporioides and C. acutatum in Strawberry}, volume={109}, ISSN={0031-949X 1943-7684}, url={http://dx.doi.org/10.1094/PHYTO-08-18-0283-R}, DOI={10.1094/PHYTO-08-18-0283-R}, abstractNote={Information on the inheritance of resistance to Colletotrichum gloeosporioides and C. acutatum hemibiotrophic infections (HBI) in strawberry leaf tissue and the genetic control of anthracnose crown rot (ACR) in crown tissue are relatively unknown. Six parental genotypes were crossed in a half-diallel mating design to generate 15 full-sib families. HBI and ACR experiments were conducted concurrently. Both seedlings and parental clones were inoculated with 1 × 106 conidia/ml of C. gloeosporioides or C. acutatum. Percent sporulating leaf area, wilt symptoms, and relative area under the disease progress curve were calculated to characterize resistance among genotypes and full-sib families. Low dominance/additive variance ratios for C. acutatum HBI (0.13) and C. gloeosporioides ACR (0.20) were observed, indicating additive genetic control of resistance to these traits. Heritability estimates were low for C. acutatum HBI (0.25) and C. gloeosporioides HBI (0.16) but moderate for C. gloeosporioides ACR (0.61). A high genetic correlation (rA = 0.98) between resistance to C. acutatum HBI and C. gloeosporioides HBI was observed, suggesting that resistance to these two Colletotrichum spp. may be controlled by common genes in strawberry leaf tissue. In contrast, negative genetic correlations between ACR and both HBI traits (rA = -0.85 and -0.61) suggest that resistance in crown tissue is inherited independently of resistance in leaf tissue in the populations tested. Overall, these findings provide valuable insight into the genetic basis of resistance, and the evaluation and deployment of resistance to HBIs and ACR in strawberry breeding programs.}, number={3}, journal={Phytopathology}, publisher={Scientific Societies}, author={Jacobs, Raymond L. and Adhikari, Tika B. and Pattison, Jeremy and Yencho, G. Craig and Fernandez, Gina E. and Louws, Frank J.}, year={2019}, month={Mar}, pages={428–435} }
 @article{gemenet_da silva pereira_de boeck_wood_mollinari_olukolu_diaz_mosquera_ssali_david_et al._2019, title={Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively associated β-carotene and starch content in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.]}, volume={133}, ISSN={0040-5752 1432-2242}, url={http://dx.doi.org/10.1007/s00122-019-03437-7}, DOI={10.1007/s00122-019-03437-7}, abstractNote={β-Carotene content in sweetpotato is associated with the Orange and phytoene synthase genes; due to physical linkage of phytoene synthase with sucrose synthase, β-carotene and starch content are negatively correlated. In populations depending on sweetpotato for food security, starch is an important source of calories, while β-carotene is an important source of provitamin A. The negative association between the two traits contributes to the low nutritional quality of sweetpotato consumed, especially in sub-Saharan Africa. Using a biparental mapping population of 315 F}, number={1}, journal={Theoretical and Applied Genetics}, publisher={Springer Science and Business Media LLC}, author={Gemenet, Dorcus C. and da Silva Pereira, Guilherme and De Boeck, Bert and Wood, Joshua C. and Mollinari, Marcelo and Olukolu, Bode A. and Diaz, Federico and Mosquera, Veronica and Ssali, Reuben T. and David, Maria and et al.}, year={2019}, month={Oct}, pages={23–36} }
 @article{mollinari_olukolu_pereira_khan_gemenet_yencho_zeng_2019, title={Unraveling the Hexaploid Sweetpotato Inheritance Using Ultra-Dense Multilocus Mapping}, volume={10}, ISSN={2160-1836}, url={http://dx.doi.org/10.1534/g3.119.400620}, DOI={10.1534/g3.119.400620}, abstractNote={The hexaploid sweetpotato (}, number={1}, journal={G3&#58; Genes|Genomes|Genetics}, publisher={Genetics Society of America}, author={Mollinari, Marcelo and Olukolu, Bode A. and Pereira, Guilherme da S. and Khan, Awais and Gemenet, Dorcus and Yencho, G. Craig and Zeng, Zhao-Bang}, year={2019}, month={Nov}, pages={281–292} }
 @article{mollinari_olukolu_s. pereira guilherme_khan_gemenet_yencho_zeng_2019, title={Unraveling the hexaploid sweetpotato inheritance using ultra-dense multilocus mapping}, volume={7}, url={https://doi.org/10.1101/689638}, DOI={10.1101/689638}, abstractNote={Abstract The hexaploid sweetpotato ( Ipomoea batatas (L.) Lam., 2n = 6x = 90) is an important staple food crop worldwide and has a vital role in alleviating famine in developing countries. Due to its high ploidy level, genetic studies in sweetpotato lag behind major diploid crops significantly. We built an ultra-dense multilocus integrated genetic map and characterized the inheritance system in a sweetpotato full-sib family using our newly implemented software, MAPpoly. The resulting genetic map revealed 96.5% collinearity between I. batatas and its diploid relative I. trifida. We computed the genotypic probabilities across the whole genome for all individuals in the mapping population and inferred their complete hexaploid haplotypes. We provide evidence that most of the meiotic configurations (73.3%) were resolved in bivalents, although a small portion of multivalent signatures (15.7%), among other inconclusive configurations (11.0%) were also observed. Except for low levels of preferential pairing in linkage group 2, we observed a hexasomic inheritance mechanism in all linkage groups. We propose that the hexasomic-bivalent inheritance promotes stability to the allelic transmission in sweetpotato.}, publisher={Cold Spring Harbor Laboratory}, author={Mollinari, Marcelo and Olukolu, Bode A. and S. Pereira Guilherme and Khan, Awais and Gemenet, Dorcus and Yencho, Craig and Zeng, Zhao-Bang}, year={2019}, month={Jul} }
 @article{wadl_olukolu_branham_jarret_yencho_jackson_2018, title={Genetic Diversity and Population Structure of the USDA Sweetpotato (Ipomoea batatas) Germplasm Collections Using GBSpoly}, volume={9}, ISSN={1664-462X}, url={http://dx.doi.org/10.3389/fpls.2018.01166}, DOI={10.3389/fpls.2018.01166}, abstractNote={Sweetpotato (Ipomoea batatas) plays a critical role in food security and is the most important root crop worldwide following potatoes and cassava. In the United States (US), it is valued at over $700 million USD. There are two sweetpotato germplasm collections (Plant Genetic Resources Conservation Unit and US Vegetable Laboratory) maintained by the USDA, ARS for sweetpotato crop improvement. To date, no genome-wide assessment of genetic diversity within these collections has been reported in the published literature. In our study, population structure and genetic diversity of 417 USDA sweetpotato accessions originating from 8 broad geographical regions (Africa, Australia, Caribbean, Central America, Far East, North America, Pacific Islands, and South America) were determined using single nucleotide polymorphisms (SNPs) identified with a genotyping-by-sequencing (GBS) protocol, GBSpoly, optimized for highly heterozygous and polyploid species. Population structure using Bayesian clustering analyses (STRUCTURE) with 32,784 segregating SNPs grouped the accessions into four genetic groups and indicated a high degree of mixed ancestry. A neighbor-joining cladogram and principal components analysis based on a pairwise genetic distance matrix of the accessions supported the population structure analysis. Pairwise FST values between broad geographical regions based on the origin of accessions ranged from 0.017 (Far East - Pacific Islands) to 0.110 (Australia - South America) and supported the clustering of accessions based on genetic distance. The markers developed for use with this collection of accessions provide an important genomic resource for the sweetpotato community, and contribute to our understanding of the genetic diversity present within the US sweetpotato collection and the species.}, journal={Frontiers in Plant Science}, publisher={Frontiers Media SA}, author={Wadl, Phillip A. and Olukolu, Bode A. and Branham, Sandra E. and Jarret, Robert L. and Yencho, G. Craig and Jackson, D. Michael}, year={2018}, month={Aug} }
 @article{endelman_carley_bethke_coombs_clough_da silva_de jong_douches_frederick_haynes_et al._2018, title={Genetic Variance Partitioning and Genome-Wide Prediction with Allele Dosage Information in Autotetraploid Potato}, volume={209}, ISSN={0016-6731 1943-2631}, url={http://dx.doi.org/10.1534/genetics.118.300685}, DOI={10.1534/genetics.118.300685}, abstractNote={Abstract As one of the world’s most important food crops, the potato (Solanum tuberosum L.) has spurred innovation in autotetraploid genetics, including in the use of SNP arrays to determine allele dosage at thousands of markers. By combining genotype and pedigree information with phenotype data for economically important traits, the objectives of this study were to (1) partition the genetic variance into additive vs. nonadditive components, and (2) determine the accuracy of genome-wide prediction. Between 2012 and 2017, a training population of 571 clones was evaluated for total yield, specific gravity, and chip fry color. Genomic covariance matrices for additive (G), digenic dominant (D), and additive × additive epistatic (G#G) effects were calculated using 3895 markers, and the numerator relationship matrix (A) was calculated from a 13-generation pedigree. Based on model fit and prediction accuracy, mixed model analysis with G was superior to A for yield and fry color but not specific gravity. The amount of additive genetic variance captured by markers was 20% of the total genetic variance for specific gravity, compared to 45% for yield and fry color. Within the training population, including nonadditive effects improved accuracy and/or bias for all three traits when predicting total genotypic value. When six F1 populations were used for validation, prediction accuracy ranged from 0.06 to 0.63 and was consistently lower (0.13 on average) without allele dosage information. We conclude that genome-wide prediction is feasible in potato and that it will improve selection for breeding value given the substantial amount of nonadditive genetic variance in elite germplasm.}, number={1}, journal={Genetics}, publisher={Genetics Society of America}, author={Endelman, Jeffrey B. and Carley, Cari A. Schmitz and Bethke, Paul C. and Coombs, Joseph J. and Clough, Mark E. and da Silva, Washington L. and De Jong, Walter S. and Douches, David S. and Frederick, Curtis M. and Haynes, Kathleen G. and et al.}, year={2018}, month={Mar}, pages={77–87} }
 @article{wu_lau_cao_hamilton_sun_zhou_eserman_gemenet_olukolu_wang_et al._2018, title={Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement}, volume={9}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/s41467-018-06983-8}, DOI={10.1038/s41467-018-06983-8}, abstractNote={Sweetpotato [Ipomoea batatas (L.) Lam.] is a globally important staple food crop, especially for sub-Saharan Africa. Agronomic improvement of sweetpotato has lagged behind other major food crops due to a lack of genomic and genetic resources and inherent challenges in breeding a heterozygous, clonally propagated polyploid. Here, we report the genome sequences of its two diploid relatives, I. trifida and I. triloba, and show that these high-quality genome assemblies are robust references for hexaploid sweetpotato. Comparative and phylogenetic analyses reveal insights into the ancient whole-genome triplication history of Ipomoea and evolutionary relationships within the Batatas complex. Using resequencing data from 16 genotypes widely used in African breeding programs, genes and alleles associated with carotenoid biosynthesis in storage roots are identified, which may enable efficient breeding of varieties with high provitamin A content. These resources will facilitate genome-enabled breeding in this important food security crop.}, number={1}, journal={Nature Communications}, publisher={Springer Nature}, author={Wu, Shan and Lau, Kin H. and Cao, Qinghe and Hamilton, John P. and Sun, Honghe and Zhou, Chenxi and Eserman, Lauren and Gemenet, Dorcus C. and Olukolu, Bode A. and Wang, Haiyan and et al.}, year={2018}, month={Nov} }
 @article{zhou_duarte_silvestre_rossel_mwanga_khan_george_fei_yencho_ellis_et al._2018, title={Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes}, volume={2}, DOI={10.12688/gatesopenres.12856.1}, abstractNote={<ns5:p><ns5:bold>Background:</ns5:bold>The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA.</ns5:p><ns5:p><ns5:bold>Methods:</ns5:bold>We constructed a complete circular cp genome assembly for the hexaploid sweetpotato using extremely low coverage (<1×) Oxford Nanopore whole-genome sequencing (WGS) data coupled with Illumina sequencing data for polishing.</ns5:p><ns5:p><ns5:bold>Results:</ns5:bold>The sweetpotato cp genome of 161,274 bp contains 152 genes, of which there are 96 protein coding genes, 8 rRNA genes and 48 tRNA genes. Using the cp genome assembly as a reference, we constructed complete cp genome assemblies for a further 17 sweetpotato cultivars from East Africa and an<ns5:italic>I. triloba</ns5:italic>line using Illumina WGS data. Analysis of the sweetpotato cp genomes demonstrated the presence of two distinct subpopulations in East Africa. Phylogenetic analysis of the cp genomes of the species from the Convolvulaceae<ns5:italic>Ipomoea</ns5:italic>section<ns5:italic>Batatas</ns5:italic>revealed that the most closely related diploid wild species of the hexaploid sweetpotato is<ns5:italic>I. trifida</ns5:italic>.</ns5:p><ns5:p><ns5:bold>Conclusions:</ns5:bold>Nanopore long reads are helpful in construction of cp genome assemblies, especially in solving the two long inverted repeats. We are generally able to extract cp sequences from WGS data of sufficiently high coverage for assembly of cp genomes. The cp genomes can be used to investigate the population structure and the phylogenetic relationship for the sweetpotato.</ns5:p>}, journal={Gates Open Research}, publisher={F1000 Research, Ltd.}, author={Zhou, Chenxi and Duarte, Tania and Silvestre, Rocio and Rossel, Genoveva and Mwanga, Robert O. M. and Khan, Awais and George, Andrew W. and Fei, Zhangjun and Yencho, G. Craig and Ellis, David and et al.}, year={2018}, month={Sep}, pages={41} }
 @article{massa_manrique-carpintero_coombs_haynes_bethke_brandt_gupta_yencho_novy_douches_et al._2018, title={Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato}, volume={19}, ISSN={1471-2156}, url={http://dx.doi.org/10.1186/s12863-018-0672-1}, DOI={10.1186/s12863-018-0672-1}, abstractNote={Genome-wide single nucleotide polymorphism (SNP) markers coupled with allele dosage information has emerged as a powerful tool for studying complex traits in cultivated autotetraploid potato (Solanum tuberosum L., 2n = 4× = 48). To date, this approach has been effectively applied to the identification of quantitative trait loci (QTLs) underlying highly heritable traits such as disease resistance, but largely unexplored for traits with complex patterns of inheritance. In this study, an F1 tetraploid russet mapping population (162 individuals) was evaluated for multiple quantitative traits over two years and two locations to identify QTLs associated with tuber sugar concentration, processing quality, vine maturity, and other high-value agronomic traits. We report the linkage maps for the 12 potato chromosomes and the QTL location with corresponding genetic models and candidate SNPs explaining the highest phenotypic variation for tuber quality and maturity related traits. Significant QTLs for tuber glucose concentration and tuber fry color were detected on chromosomes 4, 5, 6, 10, and 11. Collectively, these QTLs explained between 24 and 46% of the total phenotypic variation for tuber glucose and fry color, respectively. The QTL on chromosome 10 was associated with apoplastic invertases, with 'Premier Russet' contributing the favorable allele for fry processing quality. On chromosome 5, minor-effect QTLs for tuber glucose concentration and fry color co-localized with various major-effect QTLs, including vine maturity, growth habit, tuber shape, early blight (Altenaria tenuis), and Verticillium wilt (Verticillium spp.). Linkage analysis and QTL mapping in a russet mapping population (A05141) using SNP dosage information successfully identified favorable alleles and candidate SNPs for resistance to the accumulation of tuber reducing sugars. These novel markers have a high potential for the improvement of tuber processing quality. Moreover, the discovery of different genetic models for traits with overlapping QTLs at the maturity locus clearly suggests an independent genetic control.}, number={1}, journal={BMC Genetics}, publisher={Springer Science and Business Media LLC}, author={Massa, Alicia N. and Manrique-Carpintero, Norma C. and Coombs, Joseph and Haynes, Kathleen G. and Bethke, Paul C. and Brandt, Tina L. and Gupta, Sanjay K. and Yencho, G. Craig and Novy, Richard G. and Douches, David S. and et al.}, year={2018}, month={Sep} }
 @inbook{truong_avula_pecota_yencho_2018, edition={2nd}, title={Sweetpotato Production, Processing, and Nutritional Quality}, url={http://dx.doi.org/10.1002/9781119098935.ch35}, DOI={10.1002/9781119098935.ch35}, abstractNote={This chapter provides a contemporary review of production, quality, and processing aspects of sweetpotatoes. It tabulates the world and regional sweetpotato production for 1994-2014. The chapter shows the nutritional values of sweetpotato roots and leaves and selected processed products. The nutrient composition of sweetpotato roots varies widely, depending on the cultivar, growing conditions, maturity, and storage. In developing countries, storage of sweetpotatoes has been done for hundreds of years and is still practiced using various pit, or underground storage structures. The success of these structures depends on how close they come to maintaining the ideal temperature, moisture, and oxygen levels as described in the chapter. Sweetpotato roots and other plant parts are used as human food, animal feed, and processing industry. For industrial processing, starch, sugars, and natural colorants are the major intermediate products that can be used in both food and nonfood processing industry.}, booktitle={Handbook of Vegetables and Vegetable Processing}, publisher={John Wiley & Sons, Ltd}, author={Truong, V. D. and Avula, R. Y. and Pecota, K. V. and Yencho, G. C.}, editor={Siddiq, M. and Uebersax, M.A.Editors}, year={2018}, month={Feb}, pages={811–838} }
 @article{sato_truong_johanningsmeier_reynolds_pecota_yencho_2017, title={Chemical Constituents of Sweetpotato Genotypes in Relation to Textural Characteristics of Processed French Fries}, volume={83}, ISSN={0022-1147}, url={http://dx.doi.org/10.1111/1750-3841.13978}, DOI={10.1111/1750-3841.13978}, abstractNote={Sweetpotato French fries (SPFF) are growing in popularity, however limited information is available on SPFF textural properties in relation to chemical composition. This study investigated the relationship between chemical components of different sweetpotato varieties and textural characteristics of SPFF. Sixteen sweetpotato genotypes were evaluated for (1) chemical constituents; (2) instrumental and sensory textural properties of SPFF; and (3) the relationship between chemical components, instrumental measurements, and sensory attributes. Dry matter (DM), alcohol-insoluble solids (AIS), starch, sugar, and oil content, and also α- and β-amylase activities were quantified in raw sweetpotatoes and SPFF. Peak force and overall hardness describing instrumental textural properties of SPFF were measured using a texture analyzer. Descriptive sensory analysis was conducted and 10 attributes were evaluated by a trained panel. Results showed that DM, AIS, and starch content in raw sweetpotatoes were significantly correlated (P < 0.05) with instrumental peak force and overall hardness (r = 0.41 to 0.68), and with sensory surface roughness, hardness, fracturability, and crispness (r = 0.63 to 0.90). Total sugar content in raw sweetpotatoes was positively correlated with sensory smoothness and moistness (r = 0.77), and negatively correlated with instrumental peak force and overall hardness (r = -0.62 to -0.69). Instrumental measurements were positively correlated with sensory attributes of hardness, fracturability, and crispness (r = 0.68 to 0.96) and negatively correlated with oiliness, smoothness, moistness, and cohesiveness (r = -0.61 to -0.91). Therefore, DM, AIS, starch, and total sugar contents and instrumental measurements could be used as indicators to evaluate sweetpotato genotypes for SPFF processing.In recent years, sweetpotato French fries (SPFF) have grown in popularity, but limited information is available on SPFF textural properties in relation to the differences in chemical constituents among sweetpotato varieties. This study demonstrated that sensory texture attributes of SPFF varied widely and were significantly correlated with chemical components such as dry matter, starch, and total sugar contents of raw sweetpotatoes and instrumental texture measurements of SPFF. The knowledge generated from this study will benefit the food industry and breeding programs with the selection of sweetpotato varieties for improved SPFF quality.}, number={1}, journal={Journal of Food Science}, publisher={Wiley}, author={Sato, Ai and Truong, Van-Den and Johanningsmeier, Suzanne D. and Reynolds, Rong and Pecota, Kenneth V. and Yencho, G. Craig}, year={2017}, month={Nov}, pages={60–73} }
 @article{yada_brown-guedira_alajo_ssemakula_owusu-mensah_carey_mwanga_yencho_2017, title={Genetic analysis and association of simple sequence repeat markers with storage root yield, dry matter, starch and β-carotene content in sweetpotato}, volume={67}, ISSN={1344-7610 1347-3735}, url={http://dx.doi.org/10.1270/jsbbs.16089}, DOI={10.1270/jsbbs.16089}, abstractNote={Molecular markers are needed for enhancing the development of elite sweetpotato (Ipomoea batatas (L.) Lam) cultivars with a wide range of commercially important traits in sub-Saharan Africa. This study was conducted to estimate the heritability and determine trait correlations of storage root yield, dry matter, starch and β-carotene content in a cross between 'New Kawogo' × 'Beauregard'. The study was also conducted to identify simple sequence repeat (SSR) markers associated with these traits. A total of 287 progeny and the parents were evaluated for two seasons at three sites in Uganda and genotyped with 250 SSR markers. Broad sense heritability (H2) for storage root yield, dry matter, starch and β-carotene content were 0.24, 0.68, 0.70 and 0.90, respectively. Storage root β-carotene content was negatively correlated with dry matter (r = −0.59, P < 0.001) and starch (r = −0.93, P < 0.001) content, while storage root yield was positively correlated with dry matter (r = 0.57, P = 0.029) and starch (r = 0.41, P = 0.008) content. Through logistic regression, a total of 12, 4, 6 and 8 SSR markers were associated with storage root yield, dry matter, starch and β-carotene content, respectively. The SSR markers used in this study may be useful for quantitative trait loci analysis and selection for these traits in future.}, number={2}, journal={Breeding Science}, publisher={Japanese Society of Breeding}, author={Yada, Benard and Brown-Guedira, Gina and Alajo, Agnes and Ssemakula, Gorrettie N. and Owusu-Mensah, Eric and Carey, Edward E. and Mwanga, Robert O.M. and Yencho, G. Craig}, year={2017}, pages={140–150} }
 @article{yada_alajo_ssemakula_brown-guedira_otema_stevenson_mwanga_yencho_2017, title={Identification of simple sequence repeat markers for sweetpotato weevil resistance}, volume={213}, ISSN={["1573-5060"]}, DOI={10.1007/s10681-017-1917-1}, abstractNote={Abstract The development of sweetpotato [ Ipomoea batatas (L.) Lam] germplasm with resistance to sweetpotato weevil (SPW) requires an understanding of the biochemical and genetic mechanisms of resistance to optimize crop resistance. The African sweetpotato landrace, ‘New Kawogo’, was reported to be moderately resistant to two species of SPW, Cylas puncticollis and Cylas brunneus . Resistance has been associated with the presence of hydroxycinnamic acids esters (HCAs), but the underlying genetic basis remains unknown. To determine the genetic basis of this resistance, a bi-parental sweetpotato population from a cross between the moderately resistant, white-fleshed ‘New Kawogo’ and the highly susceptible, orange-fleshed North American variety ‘Beauregard’ was evaluated for SPW resistance and genotyped with simple sequence repeat (SSR) markers to identify weevil resistance loci. SPW resistance was measured on the basis of field storage root SPW damage severity and total HCA ester concentrations. Moderate broad sense heritability (H 2 = 0.49) was observed for weevil resistance in the population. Mean genotype SPW severity scores ranged from 1.0 to 9.0 and 25 progeny exhibited transgressive segregation for SPW resistance. Mean genotype total HCA ester concentrations were significantly different (P < 0.0001). A weak but significant correlation (r = 0.103, P = 0.015) was observed between total HCA ester concentration and SPW severity. A total of five and seven SSR markers were associated with field SPW severity and total HCA ester concentration, respectively. Markers IBS11, IbE5 and IbJ544b showed significant association with both field and HCA-based resistance, representing potential markers for the development of SPW resistant sweetpotato cultivars.}, number={6}, journal={Euphytica}, publisher={Springer Nature}, author={Yada, B. and Alajo, A. and Ssemakula, G. N. and Brown-Guedira, G. and Otema, M. A. and Stevenson, P. C. and Mwanga, R. O. M. and Yencho, G. C.}, year={2017}, pages={129} }
 @article{schumann_zeng_clough_yencho_2017, title={Linkage map construction and QTL analysis for internal heat necrosis in autotetraploid potato}, volume={130}, ISSN={0040-5752 1432-2242}, url={http://dx.doi.org/10.1007/s00122-017-2941-1}, DOI={10.1007/s00122-017-2941-1}, abstractNote={A tetraploid potato population was mapped for internal heat necrosis (IHN) using the Infinium  ®  8303 potato SNP array, and QTL for IHN were identified on chromosomes 1, 5, 9 and 12 that explained 28.21% of the variation for incidence and 25.3% of the variation for severity. This research represents a significant step forward in our understanding of IHN, and sets the stage for future research focused on testing the utility of these markers in additional breeding populations. Internal heat necrosis (IHN) is a significant non-pathogenic disorder of potato tubers and previous studies have identified AFLP markers linked to IHN susceptibility in the tetraploid, B2721 potato mapping population. B2721 consists of an IHN susceptible×resistant cross: Atlantic×B1829-5. We developed a next-generation SNP-based linkage map of this cross using the Infinium ®  8303 SNP array and conducted additional QTL analyses of IHN susceptibility in the B2721 population. Using SNP dosage sensitive markers, linkage maps for both parents were simultaneously analyzed. The linkage map contained 3427 SNPs and totaled 1397.68 cM. QTL were detected for IHN on chromosomes 1, 5, 9, and 12 using LOD permutation thresholds and colocation of high LOD scores across multiple years. Genetic effects were modeled for each putative QTL. Markers associated with a QTL were regressed in models of effects for IHN incidence and severity for all years. In the full model, the SNP markers were shown to have significant effects for IHN (p < 0.0001), and explained 28.21% of the variation for incidence and 25.3% of the variation for severity. We were able to utilize SNP dosage information to identify and model the effects of putative QTL, and identify SNP loci associated with IHN resistance that need to be confirmed. This research represents a significant step forward in our understanding of IHN, and sets the stage for future research focused on testing the utility of these markers in additional breeding populations.}, number={10}, journal={Theoretical and Applied Genetics}, publisher={Springer Nature}, author={Schumann, Mitchell J. and Zeng, Zhao-Bang and Clough, Mark E. and Yencho, G. Craig}, year={2017}, month={Jun}, pages={2045–2056} }
 @article{endelman_carley_douches_coombs_bizimungu_de jong_haynes_holm_miller_novy_et al._2017, title={Pedigree Reconstruction with Genome-Wide Markers in Potato}, volume={94}, ISSN={["1874-9380"]}, DOI={10.1007/s12230-016-9556-y}, number={2}, journal={AMERICAN JOURNAL OF POTATO RESEARCH}, publisher={Springer Nature}, author={Endelman, Jeffrey B. and Carley, Cari A. Schmitz and Douches, David S. and Coombs, Joseph J. and Bizimungu, Benoit and De Jong, Walter S. and Haynes, Kathleen G. and Holm, David G. and Miller, J. Creighton, Jr. and Novy, Richard G. and et al.}, year={2017}, month={Apr}, pages={184–190} }
 @article{anyanga_yada_yencho_ssemakula_alajo_farman_mwanga_stevenson_2017, title={Segregation of Hydroxycinnamic Acid Esters Mediating Sweetpotato Weevil Resistance in Storage Roots of Sweetpotato}, volume={8}, DOI={10.3389/fpls.2017.01011}, abstractNote={Resistance to sweetpotato weevils (Cylas spp.) has been identified in several sweetpotato (Ipomoea batatas) landraces from East Africa and shown to be conferred by hydroxycinnamic acids that occur on the surface of storage roots. The segregation of resistance in this crop is unknown and could be monitored using these chemical traits as markers for resistance in F1 offspring from breeding programs. For the first time in a segregating population, we quantified the plant chemicals that confer resistance and evaluated levels of insect colonization of the same progeny in field and laboratory studies. We used a bi-parental mapping population of 287 progenies from a cross between I. batatas 'New Kawogo,' a weevil resistant Ugandan landrace and I. batatas 'Beauregard' a North American orange-fleshed and weevil susceptible cultivar. The progenies were evaluated for resistance to sweetpotato weevil, Cylas puncticollis at three field locations that varied climatically and across two seasons to determine how environment and location influenced resistance. To augment our field open-choice resistance screening, each clone was also evaluated in a no choice experiment with weevils reared in the laboratory. Chemical analysis was used to determine whether differences in resistance to weevils were associated with plant compounds previously identified as conferring resistance. We established linkage between field and laboratory resistance to Cylas spp. and sweetpotato root chemistry. The data also showed that resistance in sweetpotato was mediated by root chemicals in most but not all cases. Multi-location trials especially from Serere data provided evidence that the hydroxycinnamic acid esters are produced constitutively within the plants in different clonal genotypes and that the ecological interaction of these chemicals in sweetpotato with weevils confers resistance. Our data suggest that these chemical traits are controlled quantitatively and that ultimately a knowledge of the genetics of resistance will facilitate management of these traits, enhance our understanding of the mechanistic basis of resistance and speed the development of new sweetpotato varieties with resistance to sweetpotato weevil.}, journal={Frontiers in Plant Science}, publisher={Frontiers Media SA}, author={Anyanga, M. O. and Yada, B. and Yencho, G. C. and Ssemakula, G. N. and Alajo, A. and Farman, D. I. and Mwanga, R. O. M. and Stevenson, P. C.}, year={2017}, pages={1011} }
 @article{yada_alajo_ssemakula_mwanga_brown-guedira_yencho_2017, title={Selection of simple sequence repeat markers associated with inheritance of sweetpotato virus disease resistance in sweetpotato}, volume={57}, DOI={10.2135/cropsci2016.08.0695}, abstractNote={Sweetpotato virus disease (SPVD), a complex of Sweet potato chlorotic stunt virus (SPCSV; Crinivirus ) and Sweet potato feathery mottle virus (SPFMV; Potyvirus ) causes high yield losses in sub‐Saharan Africa (SSA). The development of resistant cultivars to SPVD has been limited by the complex sweetpotato [ Ipomoea batatas (L.) Lam. var. batatas ] genetics and high levels of mutations in the causal viruses. The objectives of this study were to understand the inheritance of SPVD resistance and identify simple‐sequence repeat (SSR) markers associated with its resistance in a biparental sweetpotato mapping population. A total of 287 progeny and parents of the ‘New Kawogo’ × ‘Beauregard’ population were genotyped with 250 SSR markers and phenotyped for SPVD resistance at three sites and two seasons in Uganda. The broad‐sense heritability for SPVD resistance was 0.51. Two progeny showed positive transgressive segregation for overall genotype mean SPVD severity across sites and seasons. A total of seven SSR markers were significantly associated with SPVD resistance in this population. These markers and other SSRs need to be used to fine map the quantitative trait loci (QTL) of SPVD resistance for future implementation of marker‐assisted selection (MAS) for SPVD resistance in sweetpotato.}, number={3}, journal={Crop Science}, publisher={Crop Science Society of America}, author={Yada, B. and Alajo, A. and Ssemakula, G. N. and Mwanga, R. O. M. and Brown-Guedira, G. and Yencho, G. C.}, year={2017}, pages={1421–1430} }
 @article{mwanga_andrade_carey_low_yencho_grüneberg_2017, title={Sweetpotato (Ipomoea batatas L.)}, DOI={10.1007/978-3-319-59819-2_6}, journal={Genetic Improvement of Tropical Crops}, publisher={Springer International Publishing}, author={Mwanga, Robert O. M. and Andrade, Maria I. and Carey, Edward E. and Low, Jan W. and Yencho, G. Craig and Grüneberg, Wolfgang J.}, year={2017}, pages={181–218} }
 @article{mwanga_kyalo_ssemakula_niringiye_yada_otema_namakula_alajo_kigozi_makumbi_et al._2016, title={'NASPOT 12 O' and 'NASPOT 13 O' Sweetpotato}, volume={51}, ISSN={["2327-9834"]}, DOI={10.21273/hortsci.51.3.291}, abstractNote={Two sweetpotato [Ipomoea batatas L. (Lam.)] cultivars, NASPOT 12 O (Namulonge sweetpotato 12 orange-fleshed) and NASPOT 13 O (Namulonge sweetpotato 13 orange-fleshed) were approved for release by the Ugandan Plant Variety Release Committee (UPVRC) in Nov. 2013 (Ssemakula et al., 2013). This brings to 22, the number of sweetpotato cultivars officially released between 1999 and 2013 by the National Sweetpotato Program in Uganda (Mwanga et al., 2011; Ssemakula et al., 2013). The two cultivars herein described and released in 2013, have high average storage root yields, 43.1 t·ha (‘NASPOT 12 O’) and 27.8 t·ha (‘NASPOT 13 O’) on station, and 14.9 t·ha (‘NASPOT 12 O’) and 9.7 t·ha (‘NASPOT 13 O’) on farm compared with the national on-farm average for Uganda of 4.5 t·ha (FAOSTAT 2010; Low et al., 2009). The cultivars have acceptable root shape, high dry matter content (DMC) (>30%) with good-to-excellent consumer qualities. The cultivars also have moderate levels of field resistance to sweetpotato virus disease (SPVD) and alternaria bataticola blight. The two cultivars were bred targeting development of vitamin A–rich (biofortified) orange-fleshed sweetpotato (OFSP). OFSP have been shown to be both effective for increasing maternal and child vitamin A intake and status (Hotz et al., 2012; Ruel and Alderman, 2013). The potential of the two OFSP cultivars to contribute to food and nutrition security in Uganda and the developing world is high (Low et al., 2007; Ruel, 2001), especially where high dry matter and starchy sweetpotatoes are preferred. The cultivars can be used directly if adapted in similar agroecologies in sub-Saharan Africa and globally and/or used as parents in breeding programs to develop locally adapted cultivars that meet high dry matter consumer preferences.}, number={3}, journal={HORTSCIENCE}, author={Mwanga, Robert O. M. and Kyalo, Gerald and Ssemakula, Gorrettie N. and Niringiye, Charles and Yada, Benard and Otema, Milton A. and Namakula, Joweria and Alajo, Agnes and Kigozi, Benjamin and Makumbi, Rose N. M. and et al.}, year={2016}, month={Mar}, pages={291–295} }
 @article{adedipe_johanningsmeier_truong_yencho_2016, title={Development and Validation of a Near-Infrared Spectroscopy Method for the Prediction of Acrylamide Content in French-Fried Potato}, volume={64}, ISSN={["1520-5118"]}, DOI={10.1021/acs.jafc.5b04733}, abstractNote={This study investigated the ability of near-infrared spectroscopy (NIRS) to predict acrylamide content in French-fried potato. Potato flour spiked with acrylamide (50–8000 μg/kg) was used to determine if acrylamide could be accurately predicted in a potato matrix. French fries produced with various pretreatments and cook times (n = 84) and obtained from quick-service restaurants (n = 64) were used for model development and validation. Acrylamide was quantified using gas chromatography–mass spectrometry, and reflectance spectra (400–2500 nm) of each freeze-dried sample were captured on a Foss XDS Rapid Content Analyzer-NIR spectrometer. Partial least-squares (PLS) discriminant analysis and PLS regression modeling demonstrated that NIRS could accurately detect acrylamide content as low as 50 μg/kg in the model potato matrix. Prediction errors of 135 μg/kg (R2 = 0.98) and 255 μg/kg (R2 = 0.93) were achieved with the best PLS models for acrylamide prediction in Russet Norkotah French-fried potato and multiple samples of unknown varieties, respectively. The findings indicate that NIRS can be used as a screening tool in potato breeding and potato processing research to reduce acrylamide in the food supply.}, number={8}, journal={JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY}, author={Adedipe, Oluwatosin E. and Johanningsmeier, Suzanne D. and Truong, Van-Den and Yencho, G. Craig}, year={2016}, month={Mar}, pages={1850–1860} }
 @article{schultheis_george_pecota_thompson_yencho_2016, title={Potential yields of industrial sweetpotatoes using cut seed pieces planted at various dates}, volume={1118}, ISSN={0567-7572 2406-6168}, url={http://dx.doi.org/10.17660/ActaHortic.2016.1118.12}, DOI={10.17660/actahortic.2016.1118.12}, number={1118}, journal={Acta Horticulturae}, publisher={International Society for Horticultural Science (ISHS)}, author={Schultheis, J.R. and George, N.A. and Pecota, K.V. and Thompson, W.B. and Yencho, G.C.}, year={2016}, month={May}, pages={79–88} }
 @inbook{grüneberg_ma_mwanga_carey_huamani_diaz_eyzaguirre_guaf_jusuf_karuniawan_et al._2015, title={Advances in sweetpotato breeding from 1992 to 2012.}, ISBN={9781780644202}, url={http://dx.doi.org/10.1079/9781780644202.0003}, DOI={10.1079/9781780644202.0003}, abstractNote={Sweetpotato, with a global annual planting area of approximately 9 million ha, is the second most important tropical root crop. It is widely adapted, being grown in more than 110 countries. Early maturing varieties grow in 3-4 months. It is hardy and has multiple uses. Both roots and foliage are edible and provide energy and nutrients in diets. Distinct quality types have different uses, with orange-fleshed sweetpotato being valued for its extremely high provitamin A content, and other types used in varied fresh and processed forms. Sweetpotato is easily bred, as true seed is easily obtained and generation cycles are short. There are five objectives of this review. The first objective is to briefly describe recent production and utilization trends by region; the second is to review knowledge about the origin and genetic nature of sweetpotato; the third is to review selected breeding objectives. The fourth objective is to review advances in understanding of breeding methods, including: (i) generation of seed through polycross nurseries and controlled cross breeding; (ii) a description of a new accelerated breeding approach; (iii) recent efforts to systematically exploit heterosis; and (iv) new approaches of genomic selection. The fifth objective is to provide information about variety releases during the past 20 years in West, East and Southern Africa, South Asia, East and South-east Asia, China and the Pacific.}, booktitle={Potato and sweetpotato in Africa: transforming the value chains for food and nutrition security}, publisher={CABI}, author={Grüneberg, W. J. and Ma, D. and Mwanga, R. O. M. and Carey, E. E. and Huamani, K. and Diaz, F. and Eyzaguirre, R. and Guaf, E. and Jusuf, M. and Karuniawan, A. and et al.}, year={2015}, month={Nov}, pages={3–68} }
 @article{todd_truong_pecota_yencho_2015, title={Combining ability of sweetpotato germplasm for yield, dry matter content, and anthocyanin production}, volume={140}, DOI={10.21273/JASHS.140.3.272}, abstractNote={Interest in the potential of sweetpotato ( Ipomoea batatas ) for the production of industrial products is increasing. As part of an effort to evaluate the potential of sweetpotatoes for starch and anthocyanin production in the southeastern United States, a 5 × 5 North Carolina mating design II (NCII mating design) was developed to estimate the relative importance of general and specific combining abilities for dry matter (DM) content, total monomeric anthocyanin (TMA) concentration, fresh yield, and total DM and anthocyanin yields. All five traits had significant general combining abilities (GCA). Yield and DM yield had significant specific combining abilities. Significant differences among parents were observed for all traits. Yield, DM content, DM yield, and TMA yield were significantly impacted by spatial gradients within the field, but TMA concentration was not. Many trait-pairs of interest had either genotypic and/or phenotypic correlations. Phenotypic and family mean correlations among yield, DM content, and DM yield; as well as among yield, TMA, and TMA yield suggested that improving one trait will not negatively impact other traits of importance.}, number={3}, journal={Journal of the American Society for Horticultural Science}, author={Todd, S. M. and Truong, V. D. and Pecota, K. V. and Yencho, G. C.}, year={2015}, pages={272–279} }
 @article{ceballos_kawuki_gracen_yencho_hershey_2015, title={Conventional breeding, marker-assisted selection, genomic selection and inbreeding in clonally propagated crops: a case study for cassava}, volume={128}, DOI={10.1007/s00122-015-2555-4}, abstractNote={Consolidates relevant molecular and phenotypic information on cassava to demonstrate relevance of heterosis, and alternatives to exploit it by integrating different tools. Ideas are useful to other asexually reproduced crops. Asexually propagated crops offer the advantage that all genetic effects can be exploited in farmers' production fields. However, non-additive effects complicate selection because, while influencing the performance of the materials under evaluation, they cannot be transmitted efficiently to the following cycle of selection. Cassava can be used as a model crop for asexually propagated crops because of its diploid nature and the absence of (known) incompatibility effects. New technologies such as genomic selection (GS), use of inbred progenitors based on doubled haploids and induction of flowering can be employed for accelerating genetic gains in cassava. Available information suggests that heterosis, non-additive genetic effects and within-family variation are relatively large for complex traits such as fresh root yield, moderate for dry matter or starch content in the roots, and low for defensive traits (pest and disease resistance) and plant architecture. The present article considers the potential impact of different technologies for maximizing gains for key traits in cassava, and highlights the advantages of integrating them. Exploiting heterosis would be optimized through the implementation of reciprocal recurrent selection. The advantages of using inbred progenitors would allow shifting the current cassava phenotypic recurrent selection method into line improvement, which in turn would allow designing outstanding hybrids rather than finding them by trial and error.}, number={9}, journal={Theoretical and Applied Genetics}, author={Ceballos, H. and Kawuki, R. S. and Gracen, V. E. and Yencho, G. C. and Hershey, C. H.}, year={2015}, pages={1647–1667} }
 @article{khoury_heider_castaã±eda-ãlvarez_achicanoy_sosa_miller_scotland_wood_rossel_eserman_et al._2015, title={Distributions, ex situ conservation priorities, and genetic resource potential of crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas]}, volume={6}, ISSN={1664-462X}, url={http://dx.doi.org/10.3389/fpls.2015.00251}, DOI={10.3389/fpls.2015.00251}, abstractNote={Crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas] have the potential to contribute to breeding objectives for this important root crop. Uncertainty in regard to species boundaries and their phylogenetic relationships, the limited availability of germplasm with which to perform crosses, and the difficulty of introgression of genes from wild species has constrained their utilization. Here we compile geographic occurrence data on relevant sweetpotato wild relatives and produce potential distribution models for the species. We then assess the comprehensiveness of ex situ germplasm collections, contextualize these results with research and breeding priorities, and use ecogeographic information to identify species with the potential to contribute desirable agronomic traits. The fourteen species that are considered the closest wild relatives of sweetpotato generally occur from the central United States to Argentina, with richness concentrated in Mesoamerica and in the extreme southeastern United States. Currently designated species differ among themselves and in comparison to the crop in their adaptations to temperature, precipitation, and edaphic characteristics and most species also show considerable intraspecific variation. With 79% of species identified as high priority for further collecting, we find that these crop genetic resources are highly under-represented in ex situ conservation systems and thus their availability to breeders and researchers is inadequate. We prioritize taxa and specific geographic locations for further collecting in order to improve the completeness of germplasm collections. In concert with enhanced conservation of sweetpotato wild relatives, further taxonomic research, characterization and evaluation of germplasm, and improving the techniques to overcome barriers to introgression with wild species are needed in order to mobilize these genetic resources for crop breeding.}, journal={Frontiers in Plant Science}, publisher={Frontiers Media SA}, author={Khoury, Colin K. and Heider, Bettina and Castañeda-Álvarez, Nora P. and Achicanoy, Harold A. and Sosa, Chrystian C. and Miller, Richard E. and Scotland, Robert W. and Wood, John R. I. and Rossel, Genoveva and Eserman, Lauren A. and et al.}, year={2015}, month={Apr} }
 @article{haynes_yencho_clough_henninger_qu_christ_peck_porter_hutchinson_gergela_et al._2015, title={Peter Wilcox: a New Purple-Skin, Yellow-Flesh Fresh Market Potato Cultivar with Moderate Resistance to Powdery Scab}, volume={92}, ISSN={1099-209X 1874-9380}, url={http://dx.doi.org/10.1007/s12230-015-9470-8}, DOI={10.1007/s12230-015-9470-8}, number={5}, journal={American Journal of Potato Research}, publisher={Springer Science and Business Media LLC}, author={Haynes, K. G. and Yencho, G. C. and Clough, M. E. and Henninger, M. R. and Qu, X. S. and Christ, B. J. and Peck, M. W. and Porter, G. A. and Hutchinson, C. M. and Gergela, D. M. and et al.}, year={2015}, month={Sep}, pages={573–581} }
 @article{kivuva_githiri_yencho_sibiya_2015, title={Screening sweetpotato genotypes for tolerance to drought stress}, volume={171}, ISSN={["1872-6852"]}, DOI={10.1016/j.fcr.2014.10.018}, abstractNote={Soil moisture stress due to drought results in low storage root yield of sweetpotato. Eighty-four sweetpotato clones were evaluated at Kenya Agricultural Research Institute (KARI), Kiboko and Thika between May 2011 and September 2012 for drought tolerance. A split plot design with drought stress and no drought stress conditions as whole plots, and clones as subplots, arranged in a 14 × 6 alpha lattice design with two replicates repeated in two seasons was used. Approximately 30 cm long vine cuttings of each clone were planted 10 cm deep on 25 cm high beds, in single rows of 6 hills spaced at 30 × 90 cm. The field study was also validated in screenhouse box experiments at KARI-Muguga. Data on growth and yield characteristics were recorded and analysed using SAS 9.2 edition. Across sites, data indicated that genotype, environment, and their interaction significantly differed for fresh storage root weight (FSR) (kg plant−1), total fresh biomass weight (FB) (kg plant−1), marketable fresh storage root weight (MFSR) (kg plant−1), harvest index (HI) and chlorophyll content (CC) (8.47%) at (P ≤ 0.05). Comparing data from both environments, drought stress caused a reduction of FSR (59.3%), FB (72.1%), MFSR (75.5%), NSR (25.6%), but seemed to increase percent root dry matter (%RDM) (−0.29%), and HI (−26.6%). Clones 194555.7, Unawazambane06-01, 189150.1, Tanzania, Chingova, W119, 441725, and Xiadla-xa-kau, had ≥75 days to permanent wilting point (DPWP), drought stress index (DSI) <1 and high FSR yield under drought stress and no drought stress conditions. These clones may be used in a drought tolerance breeding programme. Clones that had low DSI values, also had low FSR yield difference under drought and no drought environment, indicating they were drought tolerant, but had less DPWP. However, high yielding clones under no drought, also had relatively high yield difference between drought and no drought environments, and high DSI values, which implied less drought tolerance. Thus, DPWP demonstrates high discriminative power to identify clones with both drought tolerance and improved yielding ability, especially in root crops such as sweetpotato, which occasionally produce pencil roots instead of edible storage roots even under adequate moisture conditions.}, journal={FIELD CROPS RESEARCH}, publisher={Elsevier BV}, author={Kivuva, Benjamin M. and Githiri, Stephen M. and Yencho, George C. and Sibiya, Julia}, year={2015}, month={Feb}, pages={11–22} }
 @article{yada_brown-guedira_alajo_ssemakula_mwanga_yencho_2015, title={Simple Sequence Repeat Marker Analysis of Genetic Diversity among Progeny of a Biparental Mapping Population of Sweetpotato}, volume={50}, ISSN={0018-5345 2327-9834}, url={http://dx.doi.org/10.21273/hortsci.50.8.1143}, DOI={10.21273/hortsci.50.8.1143}, abstractNote={Genetic diversity is critical in sweetpotato improvement as it is the source of genes for desired genetic gains. Knowledge of the level of genetic diversity in a segregating family contributes to our understanding of the genetic diversity present in crosses and helps breeders to make selections for population improvement and cultivar release. Simple sequence repeat (SSR) markers have become widely used markers for diversity and linkage analysis in plants. In this study, we screened 405 sweetpotato SSR markers for polymorphism on the parents and progeny of a biparental cross of New Kawogo × Beauregard cultivars. Thereafter, we used the informative markers to analyze the diversity in this population. A total of 250 markers were polymorphic on the parents and selected progeny; of these, 133 were informative and used for diversity analysis. The polymorphic information content (PIC) values of the 133 markers ranged from 0.1 to 0.9 with an average of 0.7, an indication of high level of informativeness. The pairwise genetic distances among the progeny and parents ranged from 0.2 to 0.9, and they were grouped into five main clusters. The 133 SSR primers were informative and are recommended for use in sweetpotato diversity and linkage analysis.}, number={8}, journal={HortScience}, publisher={American Society for Horticultural Science}, author={Yada, Benard and Brown-Guedira, Gina and Alajo, Agnes and Ssemakula, Gorrettie N. and Mwanga, Robert O.M. and Yencho, G. Craig}, year={2015}, month={Aug}, pages={1143–1147} }
 @article{george_pecota_yencho_2015, title={The carbohydrate yield of sweetpotato (Ipomoea batatas) grown from slips and root pieces in North Carolina}, volume={50}, number={11}, journal={HortScience}, author={George, N. A. and Pecota, K. V. and Yencho, G. C.}, year={2015}, pages={1610–1617} }
 @article{musembi_githiri_yencho_sibiya_2014, title={Combining ability and heterosis for yield and drought tolerance traits under managed drought stress in sweetpotato}, volume={201}, ISSN={0014-2336 1573-5060}, url={http://dx.doi.org/10.1007/s10681-014-1230-1}, DOI={10.1007/s10681-014-1230-1}, number={3}, journal={Euphytica}, publisher={Springer Nature}, author={Musembi, Kivuva Benjamin and Githiri, Stephen Mwangi and Yencho, George Craig and Sibiya, Julia}, year={2014}, month={Aug}, pages={423–440} }
 @article{haynes_gergela_qu_peck_yencho_clough_henninger_halseth_porter_ocaya_et al._2014, title={Elkton: A New Potato Variety with Resistance to Internal Heat Necrosis and Hollow Heart and Suitable for Chipping Directly from the Field in the Southern United States}, volume={91}, ISSN={["1874-9380"]}, DOI={10.1007/s12230-013-9347-7}, number={3}, journal={AMERICAN JOURNAL OF POTATO RESEARCH}, author={Haynes, K. G. and Gergela, D. M. and Qu, X. S. and Peck, M. W. and Yencho, G. C. and Clough, M. E. and Henninger, M. R. and Halseth, D. E. and Porter, G. A. and Ocaya, P. C. and et al.}, year={2014}, month={Jun}, pages={269–276} }
 @article{kivuva_githiri_githiri_yencho_yencho_sibiya_sibiya_2014, title={Genotype X Environment Interaction for Storage Root Yield in Sweetpotato Under Managed Drought Stress Conditions}, volume={6}, DOI={10.5539/jas.v6n10p41}, abstractNote={Most crops, including sweetpotato vary widely in yield performance across different agro-ecological environments. This study was set up to determine the genotype x environment interaction (GEI) for storage root yield performance of 24 sweetpotato genotypes in eight environments; two locations - Kiboko and Thika, two moisture stress conditions - drought stress and no drought stress, and two years - 2011 and 2012 in Kenya. Plots of three rows each of 10 plants per genotype, at density of 0.9 m × 0.30 m were panted during dry season under split plot design replicated twice. Managed irrigation was applied to control moisture stress during the growth period. Fresh storage root yield (FSR) data was collected, and drought susceptibility indices (DSI) determined. Additive Main Effects and Multiplicative Interactions (AMMI) genotype main effect by genotype-environment (GGE) interaction biplots and regression analyses were done using Genstat 14th edition to determine GEI effects. The environment, genotype main effects, and the GEI were all significant (P < 0.001). The DSI showed significant variation of genotypes in different environments. The highest yielding genotypes across the environments were G7, G14, G15, and G10 while most stable genotypes were G5, G22 and G2 and the least stable was G24. Thus, genotypes G5, G22 and G2 may be used across environments, while genotypes G7 and G14 could be used, 1) in specific locations to boost production under unpredictable rainfall conditions, 2) incorporated into drought screening breeding programmes to develop a new generation of drought tolerant sweetpotato varieties to meet changing climatic conditions.}, number={10}, journal={Journal of Agricultural Science}, publisher={Canadian Center of Science and Education}, author={Kivuva, Benjamin M. and Githiri, Stephen M. and Githiri, Stephen M. and Yencho, George C. and Yencho, George C. and Sibiya, Julia and Sibiya, Julia}, year={2014}, month={Sep} }
 @article{grace_yousef_gustafson_truong_yencho_lila_2014, title={Phytochemical changes in phenolics, anthocyanins, ascorbic acid, and carotenoids associated with sweetpotato storage and impacts on bioactive properties}, volume={145}, ISSN={["1873-7072"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84884340315&partnerID=MN8TOARS}, DOI={10.1016/j.foodchem.2013.08.107}, abstractNote={Sweetpotato phytochemical content was evaluated in four genotypes (NCPUR06-020, Covington, Yellow Covington, and NC07-847) at harvest and after curing/storage for 4 or 8 months. Curing and storage for up to 8 months did not significantly affect total phenolic content in Covington, Yellow Covington, and NC07-847, however for NCPUR06-020, a purple-fleshed selection, total phenolic content declined mainly due to anthocyanin degradation during storage. Covington had the highest carotenoid content at harvest time (281.9 μg/g DM), followed by NC07-847 (26.2 μg/g DM), and after 8 months, total carotenoids had increased by 25% and 50%, respectively. Antioxidant activity gradually declined during storage, and freshly harvested sweetpotatoes also demonstrated higher anti-inflammatory capacity as gauged by inhibition of lipopolysaccharide-induced reactive oxygen species (ROS) in SH-SY5Y cells. Gradual changes in sweetpotato phytochemical content and antioxidant and anti-inflammatory capacity were noted during normal long-term storage, but the specific effects were genotype-dependent.}, journal={FOOD CHEMISTRY}, publisher={Elsevier BV}, author={Grace, Mary H. and Yousef, Gad G. and Gustafson, Sally J. and Truong, Van-Den and Yencho, G. Craig and Lila, Mary Ann}, year={2014}, month={Feb}, pages={717–724} }
 @article{george_shankle_main_pecota_arellano_yencho_2014, title={Sweetpotato grown from root pieces displays a significant genotype x environment interaction and yield instability}, volume={49}, number={8}, journal={HortScience}, author={George, N. A. and Shankle, M. and Main, J. and Pecota, K. V. and Arellano, C. and Yencho, G. C.}, year={2014}, pages={984–990} }
 @article{duvernay_chinn_yencho_2013, title={Hydrolysis and fermentation of sweetpotatoes for production of fermentable sugars and ethanol}, volume={42}, ISSN={["1872-633X"]}, DOI={10.1016/j.indcrop.2012.06.028}, abstractNote={Liquefaction, saccharification, and fermentation of FTA-94 industrial sweetpotatoes (ISPs) were examined using α-amylase and glucoamylase for the production of ethanol. Starch degradation and sugars produced over time were examined for (1) α-amylase (Liquozyme SC) at different loading rates (0.045, 0.45, and 4.5% KNU-S/g dry ISP) during liquefaction; and (2) three glucoamylases (Spirizyme Fuel, Spirizyme Plus Tech, and Spirizyme Ultra) at different loading rates (0.5, 1.0, and 5.0 AGU/g dry ISP) during saccharification. The majority of starch, 47.7 and 65.4% of dry matter, was converted during liquefaction of flour and fresh sweetpotato preparations, respectively, with the addition of 0.45 KNU-S/g dry ISP of Liquozyme SC after 2 h (66.4 and 80.1% initial starch in dry matter, respectively). The enzymes used during saccharification increased starch breakdown, but was more effective in conversion of short chain carbohydrates to fermentable sugars. The addition of 5.0 AGU/g of Spirizyme Ultra after 48 h produced 795.4 and 685.3 mg glucose/g starch with flour and fresh preparations, respectively. Yeast fermentation on hydrolyzed starch was examined over time with and without the addition of salt nutrients. Yeast converted all fermentable sugar (e.g. glucose, fructose, maltose) and produced 62.6 and 33.6 g ethanol/L of hydrolysate for flour (25% w/v, substrate loading) and fresh (12.5% w/v, substrate loading) ISP, respectively, after 48 h without salt addition.}, journal={INDUSTRIAL CROPS AND PRODUCTS}, publisher={Elsevier BV}, author={Duvernay, William H. and Chinn, Mari S. and Yencho, G. Craig}, year={2013}, month={Mar}, pages={527–537} }
 @article{mwanga_yencho_gibson_moyer_2013, title={Methodology for Inoculating Sweetpotato Virus Disease: Discovery of Tip Dieback, and Plant Recovery and Reversion in Different Clones}, volume={97}, ISSN={["1943-7692"]}, DOI={10.1094/pdis-12-11-1072-re}, abstractNote={Evaluating sweetpotato (Ipomoea batatas) genotypes for resistance to sweetpotato virus disease (SPVD) has been slow and inefficient. Ipomoea setosa plants, normally used as the source of scions for graft-infecting sweetpotatoes with viral diseases, are often severely stunted and their mortality is 10 to 30% when infected with SPVD, making them unsuitable as scions. Tanzania, a landrace of I. batatas widely grown in East Africa, was found to be a superior host for maintaining and increasing SPVD inoculum (scions) for mass grafting. Modifications to a cleft-grafting technique also increased survival of grafted SPVD-affected scions from 5 to 100%. These modifications, coupled with an efficient SPVD scoring technique, allowed rapid screening of large sweetpotato populations for SPVD resistance. Plant recovery from SPVD is reported here as a component of SPVD resistance. Differences in recovery from SPVD were detected among progenies, indicating its genetic basis. Plant tip dieback, a hypersensitivity response, was observed only in families with cv. Wagabolige as a parent. These findings may open up new opportunities for improved understanding and control of this devastating disease.}, number={1}, journal={PLANT DISEASE}, publisher={Scientific Societies}, author={Mwanga, R. O. M. and Yencho, G. C. and Gibson, R. W. and Moyer, J. W.}, year={2013}, month={Jan}, pages={30–36} }
 @article{joshi_panthee_louws_yencho_sosinski_arellano_2013, title={RAPD Markers Linked to Late Blight Resistance in Tomato}, volume={14}, ISSN={1994-1412}, url={http://dx.doi.org/10.3126/njst.v14i1.8871}, DOI={10.3126/njst.v14i1.8871}, abstractNote={Identification of marker is the prerequisite for marker assisted selection (MAS) and is also very effective for gene pyramiding. Bulked Segregant Analysis (BSA) technique was used to identify RAPD markers linked to the late blight disease (caused by Phytopthora infestans (Mont. de Bary) resistance in tomato using F2 population generated by crossing tomato inbred lines, NC 85L-1W(2007) which is resistant to late blight and NC 839-2(2007)-1 which is susceptible to it. A total of 250 F2 plants, and 10 plants each of the parents and F1 were used for BSA. Transgressive segregation was observed for late blight resistance. The segregation of susceptible and resistance perfectly fit the expected ratio of 3:1, that means resistance is governed by single recessive gene. Only 34 RAPD primers (17.26%) were found polymorphic between parents. Sixteen RAPD primers (47%) out of 34 gave polymorphic bands between resistant and susceptible bulks of the late blight. Four RAPD primers, namely MRTOMR-026, MRTOMR-031, MRTOMR-038 and MRTOMR-046 were identified as linked markers to loci related to late blight disease. Among those, two were linked to susceptible and two to resistance. Because of low reproducibility and dominant nature of RAPD, these markers need to be converted to SCAR markers. Nepal Journal of Science and Technology Vol. 14, No. 1 (2013) 1-14 DOI: http://dx.doi.org/10.3126/njst.v14i1.8871}, number={1}, journal={Nepal Journal of Science and Technology}, publisher={Nepal Journals Online (JOL)}, author={Joshi, Bal K and Panthee, Dilip R and Louws, Frank J and Yencho, G Craig and Sosinski, Bryon and Arellano, Consuelo}, year={2013}, month={Oct}, pages={1–14} }
 @article{haynes_gergela_hutchinson_yencho_clough_henninger_halseth_sandsted_porter_ocaya_et al._2012, title={Early generation selection at multiple locations may identify potato parents that produce more widely adapted progeny}, volume={186}, ISSN={["0014-2336"]}, DOI={10.1007/s10681-012-0685-1}, number={2}, journal={EUPHYTICA}, publisher={Springer Nature}, author={Haynes, K. G. and Gergela, D. M. and Hutchinson, C. M. and Yencho, G. C. and Clough, M. E. and Henninger, M. R. and Halseth, D. E. and Sandsted, E. and Porter, G. A. and Ocaya, P. C. and et al.}, year={2012}, month={Jul}, pages={573–583} }
 @article{haynes_yencho_clough_henninger_sterrett_2012, title={Genetic Variation for Potato Tuber Micronutrient Content and Implications for Biofortification of Potatoes to Reduce Micronutrient Malnutrition}, volume={89}, ISSN={["1874-9380"]}, DOI={10.1007/s12230-012-9242-7}, number={3}, journal={AMERICAN JOURNAL OF POTATO RESEARCH}, publisher={Springer Nature}, author={Haynes, K. G. and Yencho, G. C. and Clough, M. E. and Henninger, M. R. and Sterrett, S. B.}, year={2012}, month={Jun}, pages={192–198} }
 @article{truong_hu_thompson_yencho_pecota_2012, title={Pressurized liquid extraction and quantification of anthocyanins in purple-fleshed sweet potato genotypes}, volume={26}, ISSN={["1096-0481"]}, DOI={10.1016/j.jfca.2012.03.006}, abstractNote={Analysis of anthocyanins responsible for the purple flesh color is important for breeding programs and development of value-added products. This study aimed to optimize the conditions for anthocyanin extraction from purple-fleshed sweet potatoes (PFSP) using pressurized-liquid extraction (PLE) method and quantify anthocyanins in various genotypes. Freeze-dried powders of PFSP genotypes were extracted with acidified methanol using an accelerated solvent extractor. Anthocyanin content of the extract was characterized by (a) pH-differential method and (b) color value protocol measuring absorbance at 530 nm, which is commonly used in Japan as a commercial indicator of total anthocyanin quantity. Highest anthocyanin yields by PLE were with an acetic acid:methanol:water mixture of 7:75:18% (v/v), sample weight of <0.5 g and 80–120 °C. Among 335 genotypes, the anthocyanin content varied widely from 0 to 663 mg cyanidine-3-glucoside equivalent/100 g powder or 0–210 mg/100 g fresh weight. The total monomeric anthocyanin (TMA) contents determined by the pH-differential method were highly correlated with the Japan color value (JCV) protocol, TMA = (0.145) JCV, R2 = 0.943. These results can be useful for sweet potato breeding programs and processing industry in development of PFSP cultivars and processed products with high anthocyanin levels.}, number={1-2}, journal={JOURNAL OF FOOD COMPOSITION AND ANALYSIS}, publisher={Elsevier BV}, author={Truong, V. D. and Hu, Z. and Thompson, R. L. and Yencho, G. C. and Pecota, K. V.}, year={2012}, pages={96–103} }
 @article{mwanga_niringiye_alajo_kigozi_namukula_mpembe_tumwegamire_gibson_yencho_2011, title={'NASPOT 11', a Sweetpotato Cultivar Bred by a Participatory Plant-breeding Approach in Uganda}, volume={46}, ISSN={["2327-9834"]}, DOI={10.21273/hortsci.46.2.317}, abstractNote={The sweetpotato [Ipomoea batatas (L.) Lam.] cultivar NASPOT 11 (Namulonge Sweetpotato 11) was approved for release by the Ugandan Plant Variety Release Committee in Apr. 2010 (Mwanga et al., 2010). This is the fifth time the sweetpotato breeding program in Uganda has officially released sweetpotato cultivars. The program released 19 cultivars between 1995 and 1999 (Mwanga et al., 2009), but to the best of our knowledge, ‘NASPOT 11’ represents the first sweetpotato cultivar bred from segregating populations by participatory plant breeding (PPB) for Africa and perhaps the world (Gibson et al., 2008; Mwanga et al., 2010). ‘NASPOT 11’ has acceptable storage root shape (long elliptic) when grown in light soils, has high dry matter (DM) ( 34%), and good to excellent consumer acceptance, depending on growth conditions. The cultivar has moderate to high field resistance to sweetpotato virus disease (SPVD) and Alternaria bataticola blight. Both diseases can be devastating, causing high storage root yield losses (50% to 90%) in susceptible clones (Gibson et al., 1998; Loebenstein et al., 2009; Osiru et al., 2009). Therefore, in terms of resistance to diseases, ‘NASPOT 11’ is superior to other previously released cultivars (Tables 1 through 3). Storage root yields exceeded 10 t ha on-farm under good growing conditions (Tables 2 and 3) compared with the average national storage root yield of 4.0 t ha (International Potato Center, 1999). Here we report the release of ‘NASPOT 11’, which provides consumers and farmers with a new cultivar to contribute to food security in the farming and food systems of Uganda.}, number={2}, journal={HORTSCIENCE}, author={Mwanga, Robert O. M. and Niringiye, Charles and Alajo, Agnes and Kigozi, Benjamin and Namukula, Joweria and Mpembe, Isaac and Tumwegamire, Silver and Gibson, Richard W. and Yencho, G. Craig}, year={2011}, month={Feb}, pages={317–321} }
 @article{cervantes-flores_sosinski_pecota_mwanga_catignani_truong_watkins_ulmer_yencho_2011, title={Identification of quantitative trait loci for dry-matter, starch, and beta-carotene content in sweetpotato}, volume={28}, ISSN={["1380-3743"]}, DOI={10.1007/s11032-010-9474-5}, number={2}, journal={MOLECULAR BREEDING}, publisher={Springer Nature}, author={Cervantes-Flores, J. C. and Sosinski, B. and Pecota, K. V. and Mwanga, R. O. M. and Catignani, G. L. and Truong, V. D. and Watkins, R. H. and Ulmer, M. R. and Yencho, G. C.}, year={2011}, month={Aug}, pages={201–216} }
 @article{mccord_sosinski_haynes_clough_yencho_2011, title={Linkage Mapping and QTL Analysis of Agronomic Traits in Tetraploid Potato (Solanum tuberosum subsp tuberosum)}, volume={51}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2010.02.0108}, abstractNote={ABSTRACT Potato ( Solanum tuberosum L.) is one of the world's most important crops. Using a tetraploid population, we developed a linkage map using amplified fragment length polymorphism and simple sequence repeat (SSR) markers, and searched for quantitative trait loci (QTL) via interval mapping and single‐marker analysis of variance. Quantitative trait loci were detected for flower color, foliage maturity, tuber skin texture, dry matter content, specific gravity, and yield. Most linkage groups were anchored to Solanum chromosomes using SSRs. The most significant QTL detected was for flower color. It was located on chromosome II and explained over 40% of the variation for this trait. This QTL most likely corresponds to the R locus for red anthocyanin production. We also confirmed the presence of QTL for foliage maturity on chromosomes III and V. For skin texture, a trait that has not been previously mapped in potato, we detected multiple QTL. One of these, found on chromosome III, explained 20% of the variation. By measuring specific gravity and dry matter independently we were able to detect QTL for these traits that did not co‐locate, even though the traits are strongly correlated. Yield QTL were detected on multiple chromosomes, including a novel one on chromosome III. Many QTL could be modeled as simplex or duplex with dominant effects, but a large number displayed additive or interallelic interactive effects. The mapping and modeling of traits in this tetraploid population could be improved by the use of more codominant markers, such as single nucleotide polymorphisms.}, number={2}, journal={CROP SCIENCE}, publisher={Crop Science Society of America}, author={McCord, Per H. and Sosinski, Bryon R. and Haynes, Kathleen G. and Clough, Mark E. and Yencho, G. Craig}, year={2011}, month={Mar}, pages={771–785} }
 @article{mccord_sosinski_haynes_clough_yencho_2011, title={QTL mapping of internal heat necrosis in tetraploid potato}, volume={122}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-010-1429-z}, abstractNote={Internal heat necrosis (IHN) is a physiological disorder of potato tubers. We developed a linkage map of tetraploid potato using AFLP and SSR markers, and mapped QTL for mean severity and percent incidence of IHN. Phenotypic data indicated that the distribution of IHN is skewed toward resistance. Late foliage maturity was slightly but significantly correlated with increased IHN symptoms. The linkage map for 'Atlantic', the IHN-susceptible parent, covered 1034.4 cM and included 13 linkage groups, and the map for B1829-5, the IHN-resistant parent, covered 940.2 cM and contained 14 linkage groups. QTL for increased resistance to IHN were located on chromosomes IV, V, and groups VII and X of 'Atlantic', and on group VII of B1829-5 in at least 2 of 3 years. The QTL explained between 4.5 and 29.4% of the variation for mean severity, and from 3.7 to 14.5% of the variation for percent incidence. Most QTL detected were dominant, and associated with decreased IHN symptoms. One SSR and 13 AFLP markers that were linked to IHN were tested in a second population. One AFLP marker was associated with decreased symptoms in both populations. The SSR marker was not associated with IHN in the second population, but was closely linked in repulsion to another marker that was associated with IHN, and had the same (negative) effect on the trait as the SSR marker did in the first population. The correlation between maturity and IHN may be partially explained by the presence of markers on chromosome V that are linked to both traits. This research represents the first molecular genetic research of IHN in potato.}, number={1}, journal={THEORETICAL AND APPLIED GENETICS}, publisher={Springer Nature}, author={McCord, P. H. and Sosinski, B. R. and Haynes, K. G. and Clough, M. E. and Yencho, G. C.}, year={2011}, month={Jan}, pages={129–142} }
 @misc{george_pecota_bowen_schultheis_yencho_2011, title={Root Piece Planting in Sweetpotato-A Synthesis of Previous Research and Directions for the Future}, volume={21}, ISSN={["1063-0198"]}, DOI={10.21273/horttech.21.6.703}, abstractNote={Sweetpotato ( Ipomoea batatas ) is traditionally grown for fresh consumption, particularly in developed nations, but it is increasingly being used for alternative markets such as processed foods and industrial products. Sweetpotato is well suited for these end uses but its utilization is limited due to high production costs. These costs are primarily the result of high labor inputs. As a vegetatively propagated crop, sweetpotato is typically planted using unrooted plant cuttings, or “slips,” which requires hand labor at several stages. Consequently, planting costs can be as high as 20% of total production costs. As an alternative to slips, sweetpotato can be established using root pieces, similar to the seed piece system used for potato ( Solanum tuberosum ). This system can be readily mechanized and therefore has the potential to reduce labor demands. Root piece planting has been investigated several times since the 1940s but is not reported to be in large-scale commercial use anywhere in the world. In this work, we review the research literature relating to root piece planting in sweetpotato. This literature demonstrates that it is possible for sweetpotato root pieces to produce yields comparable to slips, but that in most cases yields from root pieces are usually lower than from slips. We conclude that given suitable cultural management and appropriate varieties, it may be possible to successfully produce sweetpotato using root pieces. More work is necessary to develop root piece planting as a viable alternative to slips in sweetpotato production. This work should include the selection and breeding of adapted varieties, evaluation of the economics of sweetpotato production using root pieces, development of planting equipment suited to sweetpotato root pieces, and examination of chemical treatments to improve success of root piece planting.}, number={6}, journal={HORTTECHNOLOGY}, author={George, Nicholas A. and Pecota, Kenneth V. and Bowen, Blake D. and Schultheis, Jonathan K. and Yencho, G. Craig}, year={2011}, month={Dec}, pages={703–711} }
 @article{santa-maria_yencho_haigler_thompson_kelly_sosinski_2011, title={Starch Self-Processing in Transgenic Sweet Potato Roots Expressing a Hyperthermophilic alpha-Amylase}, volume={27}, ISSN={["1520-6033"]}, url={http://europepmc.org/abstract/med/21365786}, DOI={10.1002/btpr.573}, abstractNote={Sweet potato is a major crop in the southeastern United States, which requires few inputs and grows well on marginal land. It accumulates large quantities of starch in the storage roots and has been shown to give comparable or superior ethanol yields to corn per cultivated acre in the southeast. Starch conversion to fermentable sugars (i.e., for ethanol production) is carried out at high temperatures and requires the action of thermostable and thermoactive amylolytic enzymes. These enzymes are added to the starch mixture impacting overall process economics. To address this shortcoming, the gene encoding a hyperthermophilic α-amylase from Thermotoga maritima was cloned and expressed in transgenic sweet potato, generated by Agrobacterium tumefaciens-mediated transformation, to create a plant with the ability to self-process starch. No significant enzyme activity could be detected below 40°C, but starch in the transgenic sweet potato storage roots was readily hydrolyzed at 80°C. The transgene did not affect normal storage root formation. The results presented here demonstrate that engineering plants with hyperthermophilic glycoside hydrolases can facilitate cost effective starch conversion to fermentable sugars. Furthermore, the use of sweet potato as an alternative near-term energy crop should be considered.}, number={2}, journal={BIOTECHNOLOGY PROGRESS}, author={Santa-Maria, Monica C. and Yencho, Craig G. and Haigler, Candace H. and Thompson, William F. and Kelly, Robert M. and Sosinski, Bryon}, year={2011}, pages={351–359} }
 @article{truong_avula_pecota_yencho_2011, title={Sweetpotatoes}, DOI={10.1002/9780470958346.ch36}, abstractNote={This chapter contains sections titled: Introduction Production and Consumption Classification and Origin Postharvest Handling Practices Nutritional Composition of Sweetpotatoes Processing and Utilization References}, journal={Handbook of Vegetables and Vegetable Processing}, publisher={Wiley-Blackwell}, author={Truong, V. D. and Avula, R. Y. and Pecota, K. and Yencho, C. G.}, year={2011}, month={Mar}, pages={717–737} }
 @article{clough_yencho_christ_dejong_halseth_haynes_henninger_hutchinson_kleinhenz_porter_et al._2010, title={An Interactive Online Database for Potato Varieties Evaluated in the Eastern United States}, volume={20}, ISSN={["1943-7714"]}, DOI={10.21273/horttech.20.1.250}, abstractNote={Databases are commonly used to coordinate and summarize research from multiple projects. The potato ( Solanum tuberosum ) research community has invested significant resources in collecting data from multiple states and provinces, and we have developed a web-based database format for the use of researchers, farmers, and consumers. The northeast regional potato variety development project (NE1031) is a U.S. Department of Agriculture, Cooperative State Research, Education, and Extension Service (USDA-CSREES) regional project focused on developing and evaluating the suitability of new varieties and advanced clones from multiple breeding programs for a range of environments. This multistate project and its predecessors have been in existence for more than two decades, and they have resulted in the collection of a significant amount of standardized potato trial data. We have developed an interactive potato variety database that allows researchers and end-users to access and obtain potato variety trial results in one centralized site. The database is populated with the results of potato variety trials conducted in eight states (Florida, Maine, New Jersey, New York, North Carolina, Ohio, Pennsylvania, and Virginia) and two Canadian provinces (Prince Edward Island and Quebec). It currently contains over 35 data features and was developed primarily for scientists interested in potato variety development, growers, and allied industry members. Hypertext mark-up language (HTML) and hypertext preprocessor (PHP) were used to develop the database interface.}, number={1}, journal={HORTTECHNOLOGY}, author={Clough, Mark E. and Yencho, George C. and Christ, Barbara and DeJong, Walter and Halseth, Donald and Haynes, Kathleen and Henninger, Melvin and Hutchinson, Chad and Kleinhenz, Matt and Porter, Greg A. and et al.}, year={2010}, month={Feb}, pages={250–256} }
 @article{mwanga_odongo_niringiye_alajo_kigozi_makumbi_lugwana_namukula_mpembe_kapinga_et al._2009, title={'NASPOT 7', 'NASPOT 8', 'NASPOT 9 O', 'NASPOT 10 O', and 'Dimbuka-Bukulula' Sweetpotato}, volume={44}, ISSN={["2327-9834"]}, DOI={10.21273/hortsci.44.3.828}, abstractNote={Five sweetpotato [Ipomoea batatas L. (Lam.)] cultivars named NASPOT 7 (Namulonge Sweetpotato 7), NASPOT 8, NASPOT 9 O (Namulonge Sweetpotato 9 orangefleshed), NASPOT 10 O, and DimbukaBukulula were approved for release by the Ugandan Plant Variety Release Committee in July 2007 (Mwanga et al., 2007a). This is the fourth group of sweetpotato cultivars to be officially released by the Sweetpotato Program in Uganda. The first three groups were released in different years, six in 1995 (Mwanga et al., 2001), six in 1999 (Mwanga et al., 2003), and two in 2004 (Mwanga et al., 2007c). The five cultivars released in 2007, described here, have acceptable storage root shapes when grown in light soils. They also have high dry matter content ( 30%) and good to excellent consumer acceptance, particularly among children younger than 6 years old and women (Mwanga et al., 2007b, Odongo et al., 2002; Potts and Nagujja, 2007; Wamaniala, 2008). The cultivars have low to moderate levels of field resistance to sweetpotato virus disease (SPVD) and Alternaria bataticola blight and high storage root yields compared with the average national storage root yield of 4.0 t ha (International Potato Center, 1999). The release of these five cultivars provides consumers and farmers with high-quality sweetpotatoes with creamand orange-fleshed storage roots and moderate to high provitamin A contents with potential to alleviate widespread vitamin A deficiency in Uganda and other developing countries (Jaarsveld et al., 2005; Low et al., 2007; Ruel, 2001; UDHS, 2001) and contribute to food security (Mwanga et al., 2007a).}, number={3}, journal={HORTSCIENCE}, author={Mwanga, Robert O. M. and Odongo, Benson and Niringiye, Charles and Alajo, Agnes and Kigozi, Benjamin and Makumbi, Rose and Lugwana, Esther and Namukula, Joweria and Mpembe, Isaac and Kapinga, Regina and et al.}, year={2009}, month={Jun}, pages={828–832} }
 @article{truong_deighton_thompson_mcfeeters_dean_pecota_yencho_2009, title={Characterization of Anthocyanins and Anthocyanidins in Purple-Fleshed Sweetpotatoes by HPLC-DAD/ESI-MS/MS}, volume={58}, ISSN={0021-8561 1520-5118}, url={http://dx.doi.org/10.1021/jf902799a}, DOI={10.1021/jf902799a}, abstractNote={Purple-fleshed sweetpotatoes (PFSP) can be a healthy food choice for consumers and a potential source for natural food colorants. This study aimed to identify anthocyanins and anthocyanidins in PFSP, and to evaluate the effect of thermal processing on these polyphenolic compounds. Freeze-dried powder of raw and steamed samples of three PFSP varieties were extracted with acidified methanol using a Dionex ASE 200 accelerated solvent extractor. Seventeen anthocyanins were identified by HPLC-DAD/ESI-MS/MS for Stokes Purple and NC 415 varieties with five major compounds: cyanidin 3-caffeoylsophoroside-5-glucoside, peonidin 3-caffeoylsophoroside-5-glucoside, cyanidin 3-caffeoyl-p-hydroxybenzoylsophoroside-5-glucoside, peonidin 3-caffeoyl-p-hydroxybenzoyl-sophoroside-5-glucoside, and peonidin-caffeoyl-feruloylsophoroside-5-glucoside. Okinawa variety showed 12 pigments with 3 major peaks identified as cyanidin 3-caffeoylsophoroside-5-glucoside, cyanidin 3-(6′′,6′′′-dicaffeoylsophoroside)-5-glucoside and cyanidin 3-(6′′-caffeoyl-6′′′-feruloylsophoroside)-5-glucoside. Steam cooking had no significant effect on total anthocyanin content or the anthocyanin pigments. Cyanidin and peonidin, which were the major anthocyanidins in the acid hydrolyzed extracts, were well separated and quantified by HPLC with external standards. Cyanidin and peonidin, which contribute to the blue and red hues of PFSP, can be simply quantified by HPLC after acid hydrolysis of the anthocyanins.}, number={1}, journal={Journal of Agricultural and Food Chemistry}, publisher={American Chemical Society (ACS)}, author={Truong, Van-Den and Deighton, Nigel and Thompson, Roger T. and McFeeters, Roger F. and Dean, Lisa O. and Pecota, Kenneth V. and Yencho, G. Craig}, year={2009}, month={Dec}, pages={404–410} }
 @article{santa-maria_chou_yencho_haigler_thompson_kelly_sosinski_2009, title={Plant cell calcium-rich environment enhances thermostability of recombinantly produced alpha-amylase from the hyperthermophilic bacterium Thermotoga maritime}, volume={104}, ISSN={1097-0290}, url={http://dx.doi.org/10.1002/bit.22468}, DOI={10.1002/bit.22468}, abstractNote={In the industrial processing of starch for sugar syrup and ethanol production, a liquefaction step is involved where starch is initially solubilized at high temperature and partially hydrolyzed with a thermostable and thermoactive alpha-amylase. Most amylases require calcium as a cofactor for their activity and stability, therefore calcium, along with the thermostable enzyme, are typically added to the starch mixture during enzymatic liquefaction, thereby increasing process costs. An attractive alternative would be to produce the enzyme directly in the tissue to be treated. In a proof of concept study, tobacco cell cultures were used as model system to test in planta production of a hyperthermophilic alpha-amylase from Thermotoga maritima. While comparable biochemical properties to recombinant production in Escherichia coli were observed, thermostability of the plant-produced alpha-amylase benefited significantly from high intrinsic calcium levels in the tobacco cells. The plant-made enzyme retained 85% of its initial activity after 3 h incubation at 100 degrees C, whereas the E. coli-produced enzyme was completely inactivated after 30 min under the same conditions. The addition of Ca(2+) or plant cell extracts from tobacco and sweetpotato to the E. coli-produced enzyme resulted in a similar stabilization, demonstrating the importance of a calcium-rich environment for thermostability, as well as the advantage of producing this enzyme directly in plant cells where calcium is readily available.}, number={5}, journal={Biotechnology and Bioengineering}, publisher={Wiley}, author={Santa-Maria, Monica C. and Chou, Chung-Jung and Yencho, G. Craig and Haigler, Candace H. and Thompson, William F. and Kelly, Robert M. and Sosinski, Bryon}, year={2009}, month={Dec}, pages={947–956} }
 @article{santa-maria_pecota_yencho_allen_sosinski_2009, title={Rapid shoot regeneration in industrial 'high starch' sweetpotato (Ipomoea batatas L.) genotypes}, volume={97}, ISSN={["1573-5044"]}, DOI={10.1007/s11240-009-9504-3}, number={1}, journal={PLANT CELL TISSUE AND ORGAN CULTURE}, author={Santa-Maria, Monica and Pecota, Kenneth V. and Yencho, Craig G. and Allen, George and Sosinski, Bryon}, year={2009}, month={Apr}, pages={109–117} }
 @article{yencho_pecota_schultheis_vanesbroeck_holmes_little_thornton_truong_2008, title={'Covington' sweetpotato}, volume={43}, ISSN={["0018-5345"]}, DOI={10.21273/hortsci.43.6.1911}, abstractNote={‘Covington’ is an orange-fleshed, smooth-skinned, rose-colored, table-stock sweetpotato [ Ipomoea batatas (L.) Lam.] developed by North Carolina State University (NCSU). ‘Covington’, named after the late Henry M. Covington, an esteemed sweetpotato scientist at North Carolina State, was evaluated as NC98-608 in multiple state and regional yield trials during 2001 to 2006. ‘Covington’ produces yields equal to ‘Beauregard’, a dominant sweetpotato variety produced in the United States, but it is typically 5 to 10 days later in maturity. ‘Covington’ typically sizes its storage roots more evenly than ‘Beauregard’ resulting in fewer jumbo class roots and a higher percentage of number one roots. Total yields are similar for the two clones with the dry matter content of ‘Covington’ storage roots typically being 1 to 2 points higher than that of ‘Beauregard’. ‘Covington’ is resistant to fusarium wilt [ Fusarium oxysporum Schlect. f.sp. batatas (Wollenw.) Snyd. & Hans.], southern root-knot nematode [ Meloidogyne incognita (Kofoid & White 1919) Chitwood 1949 race 3], and moderately resistant to streptomyces soil rot [ Streptomyces ipomoeae (Person & W.J. Martin) Wakswan & Henrici]. Symptoms of the russet crack strain of Sweet Potato Feathery Mottle Virus have not been observed in ‘Covington’. The flavor of the baked storage roots of ‘Covington’ has been rated as very good by standardized and informal taste panels and typically scores as well or better in this regard when compared with ‘Beauregard’.}, number={6}, journal={HORTSCIENCE}, author={Yencho, G. Craig and Pecota, Kenneth V. and Schultheis, Jonathan R. and VanEsbroeck, Zvezdana-Pesic and Holmes, Gerald J. and Little, Billy E. and Thornton, Allan C. and Truong, Van-Den}, year={2008}, month={Oct}, pages={1911–1914} }
 @article{cervantes-flores_yencho_pecota_sosinski_mwanga_2008, title={Detection of Quantitative Trait Loci and Inheritance of Root-knot Nematode Resistance in Sweetpotato}, volume={133}, DOI={10.21273/jashs.133.6.844}, abstractNote={Resistance to root-knot nematodes [ Meloidogyne incognita (Kofoid & White) Chitwood] in sweetpotato [ Ipomoea batatas (L.) Lam.] was studied in a mapping population consisting of 240 progeny derived from a cross between ‘Beauregard’, the predominant cultivar in the United States, and ‘Tanzania’, an African landrace. Quantitative trait loci (QTL) analyses to locate markers associated with resistance to root-knot nematodes (RKN) were performed using genetic maps based on parental segregation in ‘Beauregard’ and ‘Tanzania’ consisting of 726 and 947 single-dose amplified fragment length polymorphism (AFLP) markers, respectively. RKN resistance in the progeny was highly skewed with most of the progeny exhibiting medium to high levels of resistance. Single-point analysis of variance and interval mapping revealed seven consistently significant QTL in ‘Tanzania’ and two significant QTL in ‘Beauregard’. In ‘Tanzania’, three QTL were associated with reduction in resistance as measured by the number of RKN egg masses and explained ≈20% of the variation. Another four QTL had positive effects on resistance and explained ≈21% of the variation. Other minor QTL explained ≈2% or less of the variation but were not always consistent across geographical locations. In ‘Beauregard’, two QTL had positive effects on RKN resistance and explained ≈6% of the observed variation. Based on molecular and phenotypic data, RKN resistance in sweetpotato is hypothesized to be conferred by several genes, but at least nine AFLP markers (seven from ‘Tanzania’ and two from ‘Beauregard’) are associated with genomic regions that have the biggest effect in the number of egg masses of RKN produced in the root system.}, number={6}, journal={Journal of the American Society for Horticultural Science}, publisher={American Society for Horticultural Science}, author={Cervantes-Flores, Jim C. and Yencho, G. Craig and Pecota, Kenneth V. and Sosinski, Bryon and Mwanga, Robert O.M.}, year={2008}, month={Nov}, pages={844–851} }
 @article{cervantes-flores_yencho_kriegner_pecota_faulk_mwanga_sosinski_2008, title={Development of a genetic linkage map and identification of homologous linkage groups in sweetpotato using multiple-dose AFLP markers}, volume={21}, ISSN={["1380-3743"]}, DOI={10.1007/s11032-007-9150-6}, number={4}, journal={MOLECULAR BREEDING}, publisher={Springer Nature}, author={Cervantes-Flores, Jim C. and Yencho, G. Craig and Kriegner, Albert and Pecota, Kenneth V. and Faulk, Maria A. and Mwanga, Robert O. M. and Sosinski, Bryon R.}, year={2008}, month={May}, pages={511–532} }
 @misc{yencho_mccord_haynes_sterrett_2008, title={Internal heat necrosis of potato - A review}, volume={85}, ISSN={["1874-9380"]}, DOI={10.1007/s12230-008-9008-4}, number={1}, journal={AMERICAN JOURNAL OF POTATO RESEARCH}, publisher={Springer Nature}, author={Yencho, G. Craig and McCord, Per H. and Haynes, Kathleen G. and Sterrett, S. B. Rikki}, year={2008}, month={Feb}, pages={69–76} }
 @misc{yencho_pecota_2008, title={Ornamental sweetpotato plant named 'Sweet Caroline Bewitched Purple'}, volume={PP18,574}, number={2008 March 1}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Yencho, G. and Pecota, K.}, year={2008} }
 @misc{yencho_pecota_2008, title={Ornamental sweetpotato plant named 'Sweet Caroline Green Yellow'}, volume={PP18,673}, number={2008 Apr. 1}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Yencho, G. and Pecota, K.}, year={2008} }
 @misc{yencho_pecota_hancock_2008, title={Ornamental sweetpotato plant named 'Sweet Caroline Sweetheart Light Green'}, volume={PP18,572}, number={2008 Mar. 11}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Yencho, G. C. and Pecota, K. and Hancock, C. N.}, year={2008} }
 @misc{yencho_pecota_hancock_2008, title={Ornamental sweetpotato plant named 'Sweet Caroline Sweetheart Purple'}, volume={PP18,573}, number={2008 Mar. 11}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Yencho, G. C. and Pecota, K. and Hancock, C. N.}, year={2008} }
 @misc{yencho_pecota_2008, title={Sweetpotato plant named 'Covington'}, volume={PP18,516}, number={2008 Feb. 26}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Yencho, G. C. and Pecota, K.}, year={2008} }
 @article{teow_truong_mcfeeters_thompson_pecota_yencho_2007, title={Antioxidant activities, phenolic and beta-carotene contents of sweet potato genotypes with varying flesh colours}, volume={103}, ISSN={["1873-7072"]}, DOI={10.1016/j.foodchem.2006.09.033}, abstractNote={Antioxidant activities (μmol Trolox equivalent (TE)/g fresh weight) of 19 sweet potato genotypes with distinctive flesh colour (white, cream, yellow, orange and purple) were measured by oxygen radical absorbance capacity (ORAC), 2,2-diphenyl-1-picrylhydrazyl (DPPH), and 2,2′-azinobis(3-ethyl-benzothiazoline-6-sulfonic acid) (ABTS). Total phenolics were measured using the Folin–Ciocalteau method, total anthocyanins by the pH-differential method, and β-carotene by HPLC. The total antioxidant activity (hydrophilic + lipophilic ORAC) was highest (27.2 μmol TE/g fresh weight (fw)) for NC415 (purple-fleshed) and lowest (2.72 μmol TE/g fw) for Xushu 18 (white-fleshed). The hydrophilic-ORAC values were significantly correlated with the DPPH (R2 = 0.859) and ABTS (R2 = 0.761) values. However, the lipophilic-ORAC values were poorly correlated with the β-carotene contents (R2 = 0.480). The total phenolic contents (0.011–0.949 mg chlorogenic acid equivalent/g fw) were highly correlated with the hydrophilic-ORAC (R2 = 0.937) and DPPH (R2 = 0.820) values. Therefore, the total phenolic content can serve as a useful indicator for the antioxidant activities of sweet potatoes.}, number={3}, journal={FOOD CHEMISTRY}, publisher={Elsevier BV}, author={Teow, Choong C. and Truong, Van-Den and McFeeters, Roger F. and Thompson, Roger L. and Pecota, Kenneth V. and Yencho, G. Craig}, year={2007}, pages={829–838} }
 @article{contreras_ranney_milla-lewis_yencho_2007, title={Investigating parentage and hybridity of three azaleodendrons using amplified fragment length polymorphism analysis}, volume={42}, DOI={10.21273/hortsci.42.3.740}, abstractNote={Morphological analysis historically has been used to determine parentage of unknown hybrids. This can be difficult when potential parents have similar appearance, as in the case of three azaleodendron cultivars, Rhododendron L. ‘Fragrans’, ‘Fragrans Affinity’, and ‘Fragrant Affinity’. These cultivars are similar in name and appearance, and all are purported hybrids of R. catawbiense Michx. or R. ponticum L. and R. viscosum (L.) Torr. Amplified fragment length polymorphism (AFLP) analysis was conducted to determine whether the cultivars are synonyms or distinct clones and to elucidate the parental species. The three cultivars, suspected to be hybrids between taxa in subgenera Hymenanthes (Blume) K.Koch (evergreen rhododendrons) and Pentanthera (G.Don) Pojarkova (deciduous azaleas), and related taxa from each subgenus were evaluated using 31 AFLP primer combinations. Genetic similarity, calculated using Jaccard's coefficient, among the hybrids ranged from 53% to 71%, indicating that they are distinct cultivars and not a single clone. Genetic similarity was highest between the hybrids and R. ponticum among the evergreen rhododendrons, and R. viscosum among the deciduous azaleas. A dendrogram generated using the genetic similarity matrix grouped taxa into their respective subgenera, with the three cultivars nested intermediately between subgenera but more closely with subgenus Hymenanthes and particularly R. ponticum , suggesting it is the evergreen rhododendron parent. Furthermore, principle components grouped R. ponticum more closely with the hybrids and there were 18 AFLP fragments unique to R. ponticum and the hybrids. However, no unique AFLP bands were shared exclusively among the hybrids and the purported deciduous azalea parent, R. viscosum , suggesting that the original azalea parents may have been hybrids.}, number={3}, journal={HortScience}, publisher={American Society for Horticultural Science}, author={Contreras, R. N. and Ranney, T. G. and Milla-Lewis, S. R. and Yencho, G. C.}, year={2007}, pages={740–743} }
 @misc{pecota_yencho_hancock_2007, title={Ornamental sweetpotato plant named 'Sweet Caroline Red'}, volume={PP17,483}, number={2007 Mar. 13}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Pecota, K. and Yencho, G. C. and Hancock, C. N., Jr.}, year={2007} }
 @article{villavicencio_blankenship_yencho_thomas_raper_2007, title={Temperature effect on skin adhesion, cell wall enzyme activity, lignin content, anthocyanins, growth parameters, and periderm histochemistry of sweetpotato}, volume={132}, number={5}, journal={Journal of the American Society for Horticultural Science}, author={Villavicencio, L. E. and Blankenship, S. M. and Yencho, G. C. and Thomas, J. F. and Raper, C. D.}, year={2007}, pages={729–738} }
 @article{sterrett_haynes_yencho_henninger_vinyard_2006, title={4x-2x potato clones with resistance or susceptibility to internal heat necrosis differ in tuber mineral status}, volume={46}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2005.06-0093}, abstractNote={Internal heat necrosis (IHN) is a physiological disorder resulting in necrotic tissue in the pith of potato ( Solanum spp.) tubers. Susceptibility is associated with localized Ca deficiency within the tuber, but Ca availability may be influenced by other nutrients. Studies in Virginia, North Carolina, and New Jersey in 2001 and 2002 determined the influence of soil‐applied Ca on tuber yield, specific gravity (SG), IHN, and nutrient concentration. Furrow‐applied Ca sulfate (448 kg ha −1 Ca) was applied to IHN resistant or susceptible interspecific 4×–2× S. tuberosum L. ( tbr ) × S. phureja Juz. & Bukasov– S. stenotomum Juz. & Bukasov hybrids. Tuber yield, SG, incidence and severity of IHN, and pith concentrations of P, K, Mg, Ca, S, Na, Zn, Mn, Cu, and Fe were determined. Clones differed significantly for yield, SG, and IHN expression. Resistant clones were lower in IHN incidence than susceptible clones, but the clone × Ca interaction was not consistently significant within location–years. Incidence was fit with a classification and regression tree (CART) model with the 10 nutrients as regressors, which revealed that IHN‐resistant clones had higher tuber concentrations of Mn and S, but lower P. These results suggest that resistance or susceptibility to IHN is a complex function of tuber tissue mineral status. Mn, S, and P may make a more important contribution to clonal IHN resistance than Ca. Additional work is needed to verify the potential for minimizing IHN by either nutrient management or genetic enhancement.}, number={4}, journal={CROP SCIENCE}, publisher={Crop Science Society of America}, author={Sterrett, S. B. and Haynes, K. G. and Yencho, G. C. and Henninger, M. R. and Vinyard, B. T.}, year={2006}, pages={1471–1478} }
 @misc{yencho_pecota_2006, title={Ornamental sweetpotato plant named 'Sweet Caroline Sweetheart Red'}, volume={PP19,013}, number={2006 Mar 31}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Yencho, G. C. and Pecota, K.}, year={2006} }
 @misc{pecota_yencho_pierce_2004, title={Ornamental sweetpotato plant named 'Sweet Caroline Light Green'}, volume={PP15,028}, number={2004 July 20}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Pecota, K. and Yencho, G. and Pierce, C.}, year={2004} }
 @misc{pecota_yencho_pierce_2004, title={Ornamental sweetpotato plant named 'Sweet Caroline Purple'}, volume={PP14,912}, number={2004 June 15}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Pecota, K. and Yencho, G. C. and Pierce, C.}, year={2004} }
 @article{villavicencio_blankenship_yencho_2004, title={Skin adhesion in sweetpotato and its lack of relationship to polygalacturonase and pectinmethylesterase during storage}, volume={32}, ISSN={["1873-2356"]}, DOI={10.1016/j.postharvbio.2003.10.007}, abstractNote={Sweetpotatoes have a tendency to experience epidermal loss during harvest and postharvest handling. Epidermal detachment from underlying periderm (skin loss) causes weight loss, shriveling of the root surface, increased susceptibility to pathogen attack and inferior appearance. ‘Beauregard’ is very prone to skin loss, while ‘Jewel’ is thought to have stronger skin. Our objective was to determine the variation in skin strength in relation to cell wall enzyme activity and to determine possible correlations among these variables that could explain skin loss on the basis of enzyme activity during storage of the roots. Skin adhesion, polygalacturonase (PG) and pectinmethylesterase (PME) activity were measured during storage of ‘Beauregard’ and ‘Jewel’ roots in 1999 and again in 2000. Skin adhesion varied among years and cultivars. Overall, roots of ‘Beauregard’ were more susceptible than ‘Jewel’ to skin loss after several weeks of storage. Roots of ‘Jewel’ had lower skin adhesion at harvest, which increased after several weeks of storage and decreased again at the end of the storage period. Enzyme activity exhibited a random pattern during the storage period, and skin adhesion did not correlate with PG or PME activity.}, number={2}, journal={POSTHARVEST BIOLOGY AND TECHNOLOGY}, publisher={Elsevier BV}, author={Villavicencio, LE and Blankenship, SM and Yencho, GC}, year={2004}, month={May}, pages={183–192} }
 @article{bryan_pesic-vanesbroeck_schultheis_pecota_swallow_yencho_2003, title={Cultivar decline in sweetpotato: I. Impact of micropropagation on yield, storage root quality, and virus incidence in 'Beauregard'}, volume={128}, number={6}, journal={Journal of the American Society for Horticultural Science}, author={Bryan, A. D. and Pesic-Vanesbroeck, Z. and Schultheis, J. R. and Pecota, K. V. and Swallow, W. H. and Yencho, G. C.}, year={2003}, pages={846–855} }
 @article{bryan_schultheis_pesic-vanesbroeck_yencho_2003, title={Cultivar decline in sweetpotato: II. Impact of virus infection on yield and storage root quality in 'Beauregard' and 'Hernandez'}, volume={128}, number={6}, journal={Journal of the American Society for Horticultural Science}, author={Bryan, A. D. and Schultheis, J. R. and Pesic-Vanesbroeck, Z. and Yencho, G. C.}, year={2003}, pages={856–863} }
 @article{mwanga_odongo_turyamureeba_alajo_yencho_gibson_smit_carey_2003, title={Release of six sweetpotato cultivars ('NASPOT 1' to 'NASPOT 6') in Uganda}, volume={38}, number={3}, journal={HortScience}, author={Mwanga, R. O. M. and Odongo, B. and Turyamureeba, G. and Alajo, A. and Yencho, G. C. and Gibson, R. W. and Smit, N. and Carey, E. E.}, year={2003}, pages={475–476} }
 @article{sterrett_henninger_yencho_lu_vinyard_haynes_2003, title={Stability of Internal Heat Necrosis and Specific Gravity in Tetraploid × Diploid Potatoes}, volume={43}, DOI={10.2135/cropsci2003.7900}, abstractNote={Internal heat necrosis (IHN) is a severe physiological disorder of potato ( Solanum tuberosum L.) tubers, characterized by brown spots that first appear near the apical end of the tuber parenchyma, although most of the parenchyma tissue is involved in severe cases. The purposes of this study were to evaluate 4x‐2x clones of S. tuberosum × S. phureja Juz. & Bukasov –S. stenotomum Juz. & Bukasov ( phu‐stn ) for specific gravity (SG) and incidence and severity of IHN in the mid‐Atlantic states, and identify clones with low incidence and severity of IHN and high SG for future enhancement efforts in S. tuberosum In 1999 and 2000, 26 and 88 4x‐2x clones, respectively, and the check cultivar ‘Atlantic’ were grown in North Carolina, Virginia, and New Jersey, in a randomized complete block design with two replications. At harvest, tubers > 64 mm in diameter were rated for IHN. The SG was also determined. The correlation between incidence and severity of IHN was very high; however, there was no correlation between IHN and SG. There were significant differences among the clones for SG and IHN. There were also significant clone × location interactions for SG and IHN. Several 4x‐2x clones were identified each year with significantly less IHN, and higher SG than Atlantic. The majority of these clones were stable both before and after removal of environmental heterogeneity. These results indicate that phu‐stn has the potential to expand the tetraploid potato breeding base for both high SG and resistance to IHN in the mid‐Atlantic states.}, number={3}, journal={Crop Science}, publisher={Crop Science Society of America}, author={Sterrett, S. B. and Henninger, M. R. and Yencho, G. C. and Lu, W. and Vinyard, B. T. and Haynes, K. G.}, year={2003}, pages={790} }
 @article{sterrett_henninger_yencho_lu_vinyard_haynes_2003, title={Stability of Internal Heat Necrosis and Specific Gravity in Tetraploid × Diploid Potatoes}, volume={43}, DOI={10.2135/cropsci2003.0790}, abstractNote={Internal heat necrosis (IHN) is a severe physiological disorder of potato (Solanum tuberosum L.) tubers, characterized by brown spots that first appear near the apical end of the tuber parenchyma, although most of the parenchyma tissue is involved in severe cases. The purposes of this study were to evaluate 4x-2x clones of S. tuberosum × S. phureja Juz. & Bukasov–S. stenotomum Juz. & Bukasov (phu-stn) for specific gravity (SG) and incidence and severity of IHN in the mid-Atlantic states, and identify clones with low incidence and severity of IHN and high SG for future enhancement efforts in S. tuberosum In 1999 and 2000, 26 and 88 4x-2x clones, respectively, and the check cultivar ‘Atlantic’ were grown in North Carolina, Virginia, and New Jersey, in a randomized complete block design with two replications. At harvest, tubers > 64 mm in diameter were rated for IHN. The SG was also determined. The correlation between incidence and severity of IHN was very high; however, there was no correlation between IHN and SG. There were significant differences among the clones for SG and IHN. There were also significant clone × location interactions for SG and IHN. Several 4x-2x clones were identified each year with significantly less IHN, and higher SG than Atlantic. The majority of these clones were stable both before and after removal of environmental heterogeneity. These results indicate that phu-stn has the potential to expand the tetraploid potato breeding base for both high SG and resistance to IHN in the mid-Atlantic states.}, number={3}, journal={Crop Science}, publisher={Crop Science Society of America}, author={Sterrett, S. B. and Henninger, M. R. and Yencho, G. C. and Lu, W. and Vinyard, B. T. and Haynes, K. G.}, year={2003}, pages={790} }
 @article{mwanga_yencho_moyer_2002, title={Diallel analysis of sweetpotatoes for resistance to sweetpotato virus disease}, volume={128}, ISSN={["0014-2336"]}, DOI={10.1023/A:1020828421757}, number={2}, journal={EUPHYTICA}, author={Mwanga, ROM and Yencho, CGC and Moyer, JW}, year={2002}, pages={237–248} }
 @article{cervantes-flores_yencho_davis_2002, title={Efficient Evaluation of Resistance to Three Root-knot Nematode Species in Selected Sweetpotato Cultivars}, volume={37}, DOI={10.21273/hortsci.37.2.390}, abstractNote={Five sweetpotato [ Ipomoea batatas (L.) Lam.] cultivars (`Beauregard', `Excel', `Jewel', `Hernandez', and `Porto Rico') were evaluated for resistance to three root-knot nematode species: Meloidogyne arenaria (Neal) Chitwood (race 2), M. incognita (Kofoid & White) Chitwood (race 3), and M. javanica (Treub) Chitwood. Resistance screening efficiency was assessed in both 400-cm 3 square pots and 150-cm 3 Conetainers™. Nematode infection was assessed as the percentage of root system galled, percentage of root system necrosis, and the number of nematode eggs produced per gram of root tissue. Means of these dependent variables were not different ( P ≤ 0.05) between container types, with Conetainers™ being more efficient to use. Root necrosis was not related to nematode infection, but was significant among cultivars ( P = 0.0005). The resistance responses of the cultivars differed depending on the nematode species. All five cultivars were resistant to M. arenaria race 2. `Hernandez', `Excel', and `Jewel' were also resistant to M. incognita race 3 and M. javanica .}, number={2}, journal={HortScience}, publisher={American Society for Horticultural Science}, author={Cervantes-Flores, J.C. and Yencho, G.C. and Davis, E.L.}, year={2002}, month={Apr}, pages={390–392} }
 @inproceedings{yencho_pecota_schultheis_sosinski_2002, title={Grower-participatory sweetpotato breeding efforts in North Carolina}, volume={583}, DOI={10.17660/actahortic.2002.583.6}, abstractNote={Sweetpotato, based on area and value, is the most important vegetable crop produced in North Carolina, and NC is the leading supplier of sweetpotatoes in the US producing ca. 218 thousand metric tons per year (ca. 35-40% of the national supply) worth an estimated $55.7 million. In 1997, we initiated a grower-participatory breeding effort to develop improved sweetpotato varieties for NC growers. This highly collaborative project involves researchers and extension specialists from NC State University, county extension agents, growers and industry representatives. Our variety development efforts are supported by the NC Sweetpotato Commission. To date, the project has been highly successful. This manuscript will describe our overall breeding efforts and it will focus on how this project has resulted in: 1) improved two-way learning between the breeding program and our clientele - growers; and 2) increased support and awareness of our conventional and genomics-based sweetpotato breeding and research efforts.}, number={583}, booktitle={Proceedings of the first international conference on sweetpotato food and health: Lima, Peru 26-29 July, 2001}, publisher={Leuven, Belgium: International Society for Horticultural Science}, author={Yencho, G. C. and Pecota, K. V. and Schultheis, J. R. and Sosinski, B. R.}, year={2002}, pages={69–76} }
 @article{cervantes-flores_yencho_davis_2002, title={Host Reactions of Sweetpotato Genotypes to Root-knot Nematodes and Variation in Virulence of Meloidogyne incognita Populations}, volume={37}, DOI={10.21273/hortsci.37.7.1112}, abstractNote={Sweetpotato [ Ipomoea batatas (L.) Lam.] genotypes were evaluated for resistance to North Carolina root-knot nematode populations: Meloidogyne arenaria (Neal) Chitwood races 1 and 2; M. incognita (Kofoid & White) Chitwood races 1, 2, 3, and 4; and M. javanica (Treub) Chitwood. Resistance screening was conducted using 150-cm 3 Conetainers containing 3 sand: 1 soil mix. Nematode infection and reproduction were assessed as the number of egg masses produced by root-knot nematodes per root system. Host suitability for the root-knot nematode populations differed among the 27 sweetpotato genotypes studied. Five genotypes (`Beauregard', L86-33, PDM P6, `Porto Rico', and `Pelican Processor') were selected for further study based on their differential reaction to the different root-knot nematodes tested. Two African landraces (`Tanzania' and `Wagabolige') were also selected because they were resistant to all the nematode species tested. The host status was tested against the four original M. incognita races, and an additional eight populations belonging to four host races, but collected from different geographical regions. The virulence of root-knot nematode populations of the same host race varied among and within sweetpotato genotypes. `Beauregard', L86-33, and PDM P6 were hosts for all 12 M. incognita populations, but differences in the aggressiveness of the isolates were observed. `Porto Rico' and `Pelican Processor' had different reactions to the M. incognita populations, regardless of the host race. Several clones showed resistance to all M. incognita populations tested. These responses suggest that different genes could be involved in the resistance of sweetpotato to root-knot nematodes. The results also suggest that testing Meloidogyne populations against several different sweetpotato hosts may be useful in determining the pathotypes affecting sweetpotato.}, number={7}, journal={HortScience}, publisher={American Society for Horticultural Science}, author={Cervantes-Flores, J.C. and Yencho, G.C. and Davis, E.L.}, year={2002}, pages={1112–1116} }
 @article{mwanga_moyer_zhang_carey_yencho_2002, title={NATURE OF RESISTANCE OF SWEETPOTATO TO SWEETPOTATO VIRUS DISEASE}, volume={8}, DOI={10.17660/actahortic.2002.583.12}, abstractNote={Sweetpotato virus disease (SPVD) is a disease syndrome due to the dual infection and synergistic interaction of sweetpotato chlorotic stunt crinivirus (SPCSV) and sweetpotato feathery mottle potyvirus (SPFMV). SPVD causes up to 98% yield loss in East Africa. Uganda’s sweetpotato breeding program released six sweetpotato cultivars with moderate to high levels of field SPVD resistance in 1995. A multidisciplinary partnership involving Namulonge Agricultural and Animal Production Research Institute in Uganda, North Carolina State University, the US Vegetable laboratory (USV, USDA-ARS) and Clemson University, Charleston, South Carolina, and the International Potato Center (CIP), Lima, Peru, has investigated the genetic basis of SPVD resistance. This paper highlights research findings of the response of sweetpotato to sweetpotato virus disease. General combining ability (GCA) and specific combining ability of (SCA) of 45 sweetpotato diallel families, and the GCA to SCA variance component ratios were high, indicating that additive gene effects are predominant in the inheritance of SPVD and recovery. The distribution of SPVD scores in the promising families was skewed toward highly susceptible categories in Uganda and Peru. In the proposed model for inheritance, two genes are unlinked and they are inherited in a hexosamic or tetradisomic manner. Based on amplified fragment length polymorphism (AFLP) and quantitative trait loci (QTL) analyses, two unlinked AFLP markers were associated with the loci conferring resistance to SPCSV and SPFMV.}, number={583}, journal={Acta Horticulturae}, publisher={International Society for Horticultural Science (ISHS)}, author={Mwanga, R.O.M. and Moyer, J.W. and Zhang, D.P. and Carey, E.E. and Yencho, G.C.}, year={2002}, month={Aug}, pages={113–119} }
 @article{mwanga_kriegner_cervantes-flores_zhang_moyer_yencho_2002, title={Resistance to Sweetpotato Chlorotic Stunt Virus and Sweetpotato Feathery Mottle Virus Is Mediated by Two Separate Recessive Genes in Sweetpotato}, volume={127}, DOI={10.21273/jashs.127.5.798}, abstractNote={When sweetpotato chlorotic stunt crinivirus (SPCSV) and sweetpotato feathery mottle potyvirus (SPFMV) infect sweetpotato [ Ipomoea batatas (L.) Lam.], they interact synergistically and cause sweetpotato virus disease (SPVD), a major constraint to food productivity in east Africa. The genetic basis of resistance to these diseases was investigated in 15 sweetpotato diallel families (1352 genotypes) in Uganda, and in two families of the same diallel at the International Potato Center (CIP), Lima, Peru. Graft inoculation with SPCSV and SPFMV resulted in severe SPVD symptoms in all the families in Uganda. The distribution of SPVD scores was skewed toward highly susceptible categories (SPVD scores 4 and 5), eliminating almost all the resistant genotypes (scores 1 and 2). Likewise, when two promising diallel families (`Tanzania' × `Bikilamaliya' and `Tanzania' × `Wagabolige') were graft inoculated with SPCSV and SPFMV at CIP, severe SPVD was observed in most of the progenies. Individual inoculation of these two families with SPCSV or SPFMV, and Mendelian segregation analysis for resistant vs. susceptible categories led us to hypothesize that resistance to SPCSV and SPFMV was conditioned by two separate recessive genes inherited in a hexasomic or tetradisomic manner. Subsequent molecular marker studies yielded two genetic markers associated with resistance to SPCSV and SPFMV. The AFLP and RAPD markers linked to SPCSV and SPFMV resistance explained 70% and 72% of the variation in resistance, respectively. We propose naming these genes as s pcsv1 and s pfmv1 . Our results also suggest that, in the presence of both of these viruses, additional genes mediate oligogenic or multigenic horizontal (quantitative) effects in the progenies studied for resistance to SPVD.}, number={5}, journal={Journal of the American Society for Horticultural Science}, publisher={American Society for Horticultural Science}, author={Mwanga, R.O.M. and Kriegner, A. and Cervantes-Flores, J.C. and Zhang, D.P. and Moyer, J.W. and Yencho, G.C.}, year={2002}, month={Sep}, pages={798–806} }
 @article{sosinski_he_cervantes-flores_pokrzywa_bruckner_yencho_2002, title={Sweetpotato Genomics at North Carolina State University}, volume={8}, ISBN={["90-6605-985-0"]}, ISSN={["2406-6168"]}, DOI={10.17660/actahortic.2002.583.4}, number={583}, journal={PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON SWEETPOTATO: FOOD AND HEALTH FOR THE FUTURE}, publisher={International Society for Horticultural Science (ISHS)}, author={Sosinski, B and He, L and Cervantes-Flores, J and Pokrzywa, RM and Bruckner, A and Yencho, GC}, year={2002}, pages={51–60} }
 @article{haynes_porter_christ_goth_delong_halseth_sieczka_henninger_sterrett_yencho_et al._2001, title={Amey: A multipurpose, russet-skinned potato cultivar for the eastern United States}, volume={78}, ISSN={["0003-0589"]}, DOI={10.1007/BF02883542}, number={3}, journal={AMERICAN JOURNAL OF POTATO RESEARCH}, author={Haynes, KG and Porter, GA and Christ, BJ and Goth, RW and DeLong, KO and Halseth, DE and Sieczka, JB and Henninger, MR and Sterrett, SB and Yencho, GC and et al.}, year={2001}, pages={175–181} }
 @misc{yencho_cohen_byrne_2000, title={Applications of tagging and mapping insect resistance loci in plants}, volume={45}, ISSN={["1545-4487"]}, DOI={10.1146/annurev.ento.45.1.393}, abstractNote={▪ Abstract This review examines how molecular markers can be used to increase our understanding of the mechanisms of plant resistance to insects and develop insect resistant crops. We provide a brief description of the types of molecular markers currently being employed, and describe how they can be applied to identify and track genes of interest in a marker-assisted breeding program. A summary of the work reported in this field of study, with examples in which molecular markers have been applied to increase understanding of the mechanistic and biochemical bases of resistance in potato and maize plant/pest systems, is provided. We also describe how molecular markers can be applied to develop more durable insect-resistant crops. Finally, we identify key areas in molecular genetics that we believe will provide exciting and productive research opportunities for those working to develop insectresistant crops.}, number={1}, journal={ANNUAL REVIEW OF ENTOMOLOGY}, publisher={Annual Reviews}, author={Yencho, GC and Cohen, MB and Byrne, PF}, year={2000}, pages={393–422} }
 @article{cervantes_davis_yencho_2000, title={Evaluation of Sweetpotato Cultivars to Root-knot Nematodes}, volume={35}, DOI={10.21273/hortsci.35.4.569e}, abstractNote={This study was conducted to determine whether the type of pot used for the evaluation affected the resistance response of the sweetpotato plants, and to assess the resistance response to different root-knot nematode species. Five sweetpotato [ Ipomoea batatas (L.) Lam] cultivars, `Beauregard', `Exce'l, `Jewel', `Hernandez', and `Porto Rico', were screened for M. incognita (race 3), Meloidogyne arenaria (race 2), and M. javanica , in both 10-cm-side, square pots and 4-cm-diameter, cone pots. Gall index, necrosis index, and number of nematode eggs per gram of root were used to estimate nematode-resistance reaction. Mean of all indices between the 2 pot types were not significantly different (α = 0.05). Gall and necrosis indices were not correlated in any of the cultivars. Resistance response depended on cultivars and nematode species for all variables analyzed. `Beauregard' was the most susceptible to Meloidogyne . `Hernandez' and `Excel' were found to be the most resistant cultivars to the Meloidogyne species.}, number={4}, journal={HortScience}, publisher={American Society for Horticultural Science}, author={Cervantes, J.C. and Davis, D.L. and Yencho, G.C.}, year={2000}, month={Jul}, pages={569E–569d} }
 @article{yencho_kowalski_kennedy_sanford_2000, title={Segregation of leptine glycoalkaloids and resistance to Colorado potato beetle (Leptinotarsa decemlineata (Say)) in F2 Solanum tuberosum (4x) x S-chacoense (4x) potato progenies}, volume={77}, ISSN={["1874-9380"]}, DOI={10.1007/BF02853941}, number={3}, journal={AMERICAN JOURNAL OF POTATO RESEARCH}, author={Yencho, GC and Kowalski, SP and Kennedy, GG and Sanford, LL}, year={2000}, pages={167–178} }
 @article{collins_pecota_yencho_1999, title={Carolina Ruby sweetpotato}, volume={34}, number={1}, journal={HortScience}, author={Collins, W. W. and Pecota, K. V. and Yencho, G. C.}, year={1999}, pages={155–156} }
 @article{davies_simko_mueller_yencho_lewis_mcmurry_taylor_ewing_1999, title={Quantitative trait loci for polyamine content in an RFLP-mapped potato population and their relationship to tuberization}, volume={106}, DOI={10.1034/j.1399-3054.1999.106210.x}, abstractNote={DNA‐based genetic markers are now widely used by geneticists to locate genes for quantitative traits, and may also serve as a valuable tool for dissecting complex physiological phenomena. Van den Berg et al. (1996a QTL analysis of potato tuberization. Theor Appl Gen 93: 307–316), using restriction fragment length polymorphism (RFLP)‐mapped populations of potato, detected eleven quantitative trait loci (QTLs) for tuberization. Taylor et al. (1992 Expression and sequence analysis of cDNAs induced during the early stages of tuberisation in different organs of the potato plant [ Solanum tuberosum L.]. Plant Mol Biol 20: 641–651) have identified one of the genes associated with tuberization as that for the enzyme S‐adenosylmethionine decarboxylase (SAMdc), an enzyme of the polyamine biosynthetic pathway. Chromosomal loci for SAMdc and arginine decarboxylase were established on the potato and tomato chromosomal maps, respectively, by hybridizing cDNA probes for these genes to RFLP digests. The polyamine content of leaves from an RFLP‐mapped potato population was analyzed by fluorescence detection following HPLC, with quantitation using an internal standard. The data were analyzed by the ‘qGene’ statistical program, and QTLs for polyamines were detected on seven chromosomes. At least six QTLs were found for spermine, two for spermidine, and two for putrescine. A spermidine QTL was on chromosome 5 linked to marker TG441 , very close to the place where SAMdc mapped. There was some congruence between QTLs for spermine and those previously detected for tuberization and dormancy, but relationships were not consistent.}, number={2}, journal={Physiologia Plantarum}, publisher={Wiley}, author={Davies, Peter J. and Simko, Ivan and Mueller, Suzanne M. and Yencho, G. Craig and Lewis, Candice and McMurry, Susan and Taylor, Mark A. and Ewing, Elmer E.}, year={1999}, month={Jun}, pages={210–218} }
 @article{yencho_kowalski_kobayashi_sinden_bonierbale_deahl_1998, title={QTL mapping of foliar glycoalkaloid aglycones in Solanum tuberosum x S-berthaultii potato progenies: quantitative variation and plant secondary metabolism}, volume={97}, ISSN={["0040-5752"]}, DOI={10.1007/s001220050932}, number={4}, journal={THEORETICAL AND APPLIED GENETICS}, publisher={Springer Nature}, author={Yencho, GC and Kowalski, SP and Kobayashi, RS and Sinden, SL and Bonierbale, MW and Deahl, KL}, year={1998}, month={Sep}, pages={563–574} }
 @article{reyes_yencho_velasco_calvert_1997, title={Análisis de poblaciones de Tagosodes orizicolus (Muir) vector del virus de la hoja blanca en zonas arroceras de Colombia}, volume={23}, ISSN={2665-4385 0120-0488}, url={http://dx.doi.org/10.25100/socolen.v23i2.9899}, DOI={10.25100/socolen.v23i2.9899}, abstractNote={La incidencia del virus de la hoja blanca (RHBV) se está incrementando en Colombia. La habilidad de T orizicolus de transmitir el virus es una característica controlada genéticamente. Debido a que en la naturale­za existen muchos factores que influencian el porcentaje de insectos vectores de T orizicolus, este estudio se realizó para deter­minar el porcentaje de insectos que tienen la capacidad genética de transmitir el RHBV. Se colectaron muestras de T orizicolus en varias regiones arroceras de Colombia, en campos que presentaban diferentes niveles de infesta­ción de RHBV. El porcentaje de insectos con capacidad genética de transmitir el RHBV fue siempre mayor que el porcentaje de insectos que fue­ron vectores virulíferos en el campo. Este método es útil como un indicador y ha sido utilizado para identificar las regiones arroceras de Colombia que están en gran ries­go de presentar epidemias de RHBV.}, number={2}, journal={Revista Colombiana de Entomología}, publisher={Universidad del Valle}, author={Reyes, Luis Antonio and Yencho, Craig and Velasco, Cecilia and Calvert, Lee}, year={1997}, month={Dec}, pages={165–169} }
 @article{yencho_bonierbale_tingey_plaisted_tanksley_1996, title={Molecular markers locate genes for resistance to the Colorado potato beetle, Leptinotarsa decemlineata, in hybrid Solanum tuberosum x S. berthaultii potato progenies}, volume={81}, DOI={10.1111/j.1570-7458.1996.tb02026.x}, abstractNote={Abstract The wild Bolivian potato, Solanum berthaultii Hawkes, has been used as a source of resistance to the Colorado potato beetle (CPB), Leptinotarsa decemlineata Say, one of the most significant pests of potato. In this study, two reciprocal backcross S. tuberosum x S. berthaultii potato progenies, BCB and BCT, were mapped with RFLP markers and screened for resistance to CPB consumption, oviposition and defoliation. The genotypic and phenotypic data were combined and analysed to locate quantitative trait loci (QTLs) for resistance to CPB. Three QTLs on three chromosomes in BCB, and two QTLs on two chromosomes in BCT influenced resistance. The QTLs were generally additive but one instance of epistasis was noted. Each QTL accounted for 4–12% of the phenotypic variation observed in resistance. In the more resistant BCB population, a three QTL model explained ca. 20% of the variation in CPB oviposition. When alleles at the three QTLs were homozygous S. berthaultii , oviposition was reduced ca. 60% compared to the heterozygotes. The QTLs for resistance to CPB were compared to those previously identified for the type A and B glandular trichomes, which have been implicated in resistance in the same progenies. Generally, the QTLs for resistance to CPB coincided with loci associated with the glandular trichomes confirming the importance of the glandular trichomes in mediating resistance. However, a relatively strong and consistent QTL for insect resistance in both BCB and BCT on chromosome 1 was observed that was not associated with any trichome traits, suggesting the trichomes may not account for all of the resistance observed in these progenies.}, number={2}, journal={Entomologia Experimentalis et Applicata}, publisher={Wiley}, author={Yencho, G. Craig and Bonierbale, Meredith W. and Tingey, Ward M. and Plaisted, Robert L. and Tanksley, Steven D.}, year={1996}, month={Nov}, pages={141–154} }
 @article{yencho_tingey_1994, title={Glandular trichomes of Solanum berthaultii alter host preference of the Colorado potato Beetle, Leptinotarsa decemlineata}, volume={70}, DOI={10.1111/j.1570-7458.1994.tb00750.x}, abstractNote={Abstract Choice and no‐choice studies were conducted to determine how the glandular trichomes of the wild potato, Solanum berthaultii Hawkes, affect host preference of the Colorado potato beetle, Leptinotarsa decemlineata (Say). Given a feeding choice between S. tuberosum and S. berthaultii , larvae and adults preferred the foliage of S. tuberosum , but adults were more discriminating. When foliage of S. berthaultii was appressed to S. tuberosum leaflets, fewer adults fed on the appressed leaflets. When given a choice between ‘trichome‐intact’ and ‘trichome‐removed’ S. berthaultii foliage, adults preferred to feed on the latter. The preference for ‘trichome‐removed’ foliage and the percent of adults initiating feeding, increased with the degree of trichome removal. These studies provide evidence that the resistance of S. berthaultii is associated with feeding deterrents localized in the glandular trichomes, that S. berthaultii possesses more than one mechanism of resistance to the Colorado potato beetle, and that the expression of resistance is dependent on the developmental stage of the insect.}, number={3}, journal={Entomologia Experimentalis et Applicata}, publisher={Wiley}, author={Yencho, G. Craig and Tingey, Ward M.}, year={1994}, month={Mar}, pages={217–225} }
 @article{yencho_renwick_steffens_tingey_1994, title={Leaf surface extracts ofSolanum berthaultii hawkes deter colorado potato beetle feeding}, volume={20}, DOI={10.1007/bf02059737}, abstractNote={Leaf rinses ofS. berthaultii PI 473334 with methylene chloride were deterrent to feeding by the Colorado potato beetle when applied toS. tuberosum tuber and leaf disks. When the leaf rinse was separated into its nonvolatile and volatile fractions and applied to tuber disks, the nonvolatile fraction was highly deterrent, while the volatile fraction reduced consumption, but not significantly compared to the controls. A hexane leaf rinse was not deterrent to feeding, while an acetone rinse was approximately twofold more deterrent than the methylene chloride rinse when applied to leaf disks. Three cycles of bioassay-guided, reversed-phase open-column fractionation of an acetone leaf rinse yielded a relatively polar fraction with low deterrent activity, and two nonpolar fractions exhibiting higher specific activity. Reversed-phase preparative HPLC of these fractions yielded seven active fractions among the 10 assayed. Subsequent analytical HPLC indicated that two fractions each contained a single UV-absorbing compound, while another represented a mixture of at least four compounds. The remaining fractions were composed of complex mixtures of possibly ionic or polymeric compounds that were poorly resolved by HPLC.}, number={5}, journal={Journal of Chemical Ecology}, publisher={Springer Nature}, author={Yencho, G. C. and Renwick, J. A. A. and Steffens, J. C. and Tingey, W. M.}, year={1994}, month={May}, pages={991–1007} }
 @article{benedict_treacy_ring_yencho_1992, title={Behavior of Pyrethroid-Susceptible and -Resistant Heliothis Virescens (F.) (Lepidoptera: Noctuidae) Larvae on Cotton Treated with Insecticides}, volume={85}, ISSN={1938-291X 0022-0493}, url={http://dx.doi.org/10.1093/jee/85.6.2058}, DOI={10.1093/jee/85.6.2058}, abstractNote={The behavior of a pyrethroid-resistant strain (R) and a -susceptible strain (S) of Heliothis virescens (F.) was observed on budding (flower buds) cotton plants in the greenhouse. Treatments were plants sprayed with (1) chlordimeform at the LC20 for the S strain; (2) cypermethrin at the LC20 for the S strain; (3) a mixture of chlordimeform and cypermethrin at the LC20 for the S strain (combined LC20s used in treatments 1 and 2); and (4) an unsprayed control. Third-stage Rand S larvae were placed on the plants 1 h after spraying, and their behavior was recorded. Feeding of S larvae was reduced and resting was increased on plants treated with cypermethrin compared with R larvae, or Sand R larvae on unsprayed plants. The chlordimeform treatment caused reduced feeding on flower buds and increased locomotion for Sand R larvae compared with Sand R larvae on untreated plants. The mixture of chlordimeform and cypermethrin Significantly increased locomotion and reduced feeding of R larvae compared with their behavior on plants treated only with cypermethrin. Both Sand R larvae abandoned plants treated with chlordimeform or the mixture more frequently compared with untreated or cypermethrin-treated plants. These results show that chlordimeform can alter behavior of Sand R larvae on plants treated with cypermethrin. Under field conditions, use of behavioral active chemicals like chlordimeform could alter the behavior of wild H. virescens larvae so that flower bud damage is reduced and larval acquisition of insecticide residues is increased.}, number={6}, journal={Journal of Economic Entomology}, publisher={Oxford University Press (OUP)}, author={Benedict, J. H. and Treacy, M. F. and Ring, D. R. and Yencho, G. C.}, year={1992}, month={Dec}, pages={2058–2063} }
 @article{yencho_getzin_lono_1986, title={Economic Injury Level, Action Threshold, and a Yield-loss Model for the Pea Aphid, Acyrthosiphon pisum (Homoptera: Aphididae), on Green Peas, Pisum sativum}, volume={79}, DOI={10.1093/jee/79.6.1681}, abstractNote={Economic injury level, action threshold, and population development studies with the pea aphid (PA), Acyrthosiphon pisum (Harris), were conducted during 1983–85. Pea aphid densities, simulating those in commercial pea fields, were established using insecticides to manipulate infestation levels. Three experiments, incorporating 12 treatments and six replications, were analyzed. A generalized, nonlinear equation relating pea yield to accumulated aphid feeding days (AFD) is described. The model approximates two phases of a sigmoid infestation-yield curve. An upper maximum plateau and a region of rapidly decreasing yield are approximated. Beyond 1,800 AFD, a lower minimum yield plateau is hypothesized. Economic injury levels calculated for the 3 years’ experiments using the generalized model were 22.2, 18.2, and 12.2 AFD, respectively. Action threshold estimates were determined from linear regression estimates of yield versus aphids per plant at bloom. Action thresholds were 3.6, 0.3, and 0.3 aphids per plant for the years 1983, 1984, and 1985, respectively. The pea quality components, tenderometer (TD) and sieve size, were altered by maximum PA densities. High AFD levels increased TD and decreased sieve size significantly when compared with aphid-free controls. Protein content of green peas was not significantly altered by PA feeding.}, number={6}, journal={Journal of Economic Entomology}, publisher={Oxford University Press (OUP)}, author={Yencho, G. C. and Getzin, L. W. and Lono, Garrell E.}, year={1986}, pages={1681–1687} }