@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{mishra_dee_moar_dufner-beattie_baum_dias_alyokhin_buzza_rondon_clough_et al._2021, title={Selection for high levels of resistance to double-stranded RNA (dsRNA) in Colorado potato beetle (Leptinotarsa decemlineata Say) using non-transgenic foliar delivery}, volume={11}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-021-85876-1}, abstractNote={Insecticidal double-stranded RNAs (dsRNAs) silence expression of vital genes by activating the RNA interference (RNAi) mechanism in insect cells. Despite high commercial interest in insecticidal dsRNA, information on resistance to dsRNA is scarce, particularly for dsRNA products with non-transgenic delivery (ex. foliar/topical application) nearing regulatory review. We report the development of the CEAS 300 population of Colorado potato beetle (Leptinotarsa decemlineata Say) (Coleoptera: Chrysomelidae) with > 11,100-fold resistance to a dsRNA targeting the V-ATPase subunit A gene after nine episodes of selection using non-transgenic delivery by foliar coating. Resistance was associated with lack of target gene down-regulation in CEAS 300 larvae and cross-resistance to another dsRNA target (COPI β; Coatomer subunit beta). In contrast, CEAS 300 larvae showed very low (~ 4-fold) reduced susceptibility to the Cry3Aa insecticidal protein from Bacillus thuringiensis. Resistance to dsRNA in CEAS 300 is transmitted as an autosomal recessive trait and is polygenic. These data represent the first documented case of resistance in an insect pest with high pesticide resistance potential using dsRNA delivered through non-transgenic techniques. Information on the genetics of resistance and availability of dsRNA-resistant L. decemlineata guide the design of resistance management tools and allow research to identify resistance alleles and estimate resistance risks.}, number={1}, journal={SCIENTIFIC REPORTS}, author={Mishra, Swati and Dee, James and Moar, William and Dufner-Beattie, Jodi and Baum, James and Dias, Nayma Pinto and Alyokhin, Andrei and Buzza, Aaron and Rondon, Silvia I. and Clough, Mark and et al.}, year={2021}, month={Mar} }
 @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={There are many challenges involved with the genetic analyses of autopolyploid species, such as the tetraploid potato, Solanum tuberosum (2n = 4x = 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 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{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{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 ", {:sup=>"®"}, " 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", {:sup=>"®"}, " 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{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{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{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{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={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} }
 @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} }