@article{hislop_luby_loarca_humann_hummer_bassil_zhao_sheehan_casa_billings_et al._2024, title={A Blueberry (<i> Vaccinium</i> L.) Crop Ontology to Enable Standardized Phenotyping for Blueberry Breeding and Research}, volume={59}, ISSN={["2327-9834"]}, DOI={10.21273/HORTSCI17676-23}, abstractNote={Breeding programs around the world continually collect data on large numbers of individuals. To be able to combine data collected across regions, years, and experiments, research communities develop standard operating procedures for data collection and measurement. One such method is a crop ontology, or a standardized vocabulary for collecting data on commonly measured traits. The ontology is also computer readable to facilitate the use of data management systems such as databases. Blueberry breeders and researchers across the United States have come together to develop the first standardized crop ontology in blueberry ( Vaccinium spp.). We provide an overview and report on the construction of the first blueberry crop ontology and the 178 traits and methods included within. Researchers of Vaccinium species—such as other blueberry species, cranberry, lingonberry, and bilberry—can use the described crop ontology to collect phenotypic data of greater quality and consistency, interoperability, and computer readability. Crop ontologies, as a shared data language, benefit the entire worldwide research community by enabling collaborative meta-analyses that can be used with genomic data for quantitative trait loci, genome-wide association studies, and genomic selection analysis.}, number={10}, journal={HORTSCIENCE}, author={Hislop, Lillian M. and Luby, Claire H. and Loarca, Jenyne and Humann, Jodi and Hummer, Kim E. and Bassil, Nahla and Zhao, Dongyan and Sheehan, Moira J. and Casa, Alexandra M. and Billings, Grant T. and et al.}, year={2024}, month={Oct}, pages={1433–1442} }
 @article{abdelhamid_omri_araouki_chehab_garcia-ruiz_ashrafi_2024, title={Application of RAPD and ISSR markers tools for commercial monovarietal Tunisian extra virgin olive oils (EVOO) authenticity and traceability}, volume={8}, ISSN={["2365-7448"]}, DOI={10.1007/s41207-024-00614-z}, journal={EURO-MEDITERRANEAN JOURNAL FOR ENVIRONMENTAL INTEGRATION}, author={Abdelhamid, Sofiane and Omri, Amal and Araouki, Amira and Chehab, Hechmi and Garcia-Ruiz, Roberto and Ashrafi, Hudson}, year={2024}, month={Aug} }
 @article{chizk_clark_johns_nelson_ashrafi_aryal_worthington_2023, title={Genome-wide association identifies key loci controlling blackberry postharvest quality}, volume={14}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2023.1182790}, abstractNote={IntroductionBlackberry (Rubus subgenus Rubus) is a soft-fruited specialty crop that often suffers economic losses due to degradation in the shipping process. During transportation, fresh-market blackberries commonly leak, decay, deform, or become discolored through a disorder known as red drupelet reversion (RDR). Over the past 50 years, breeding programs have achieved better fruit firmness and postharvest quality through traditional selection methods, but the underlying genetic variation is poorly understood.MethodsWe conducted a genome-wide association of fruit firmness and RDR measured in 300 tetraploid fresh-market blackberry genotypes from 2019-2021 with 65,995 SNPs concentrated in genic regions of the R. argutus reference genome.ResultsFruit firmness and RDR had entry-mean broad sense heritabilities of 68% and 34%, respectively. Three variants on homologs of polygalacturonase (PG), pectin methylesterase (PME), and glucan endo-1,3-β-glucosidase explained 27% of variance in fruit firmness and were located on chromosomes Ra06, Ra01, and Ra02, respectively. Another PG homolog variant on chromosome Ra02 explained 8% of variance in RDR, but it was in strong linkage disequilibrium with 212 other RDR-associated SNPs across a 23 Mb region. A large cluster of six PME and PME inhibitor homologs was located near the fruit firmness quantitative trait locus (QTL) identified on Ra01. RDR and fruit firmness shared a significant negative correlation (r = -0.28) and overlapping QTL regions on Ra02 in this study.DiscussionOur work demonstrates the complex nature of postharvest quality traits in blackberry, which are likely controlled by many small-effect QTLs. This study is the first large-scale effort to map the genetic control of quantitative traits in blackberry and provides a strong framework for future GWAS. Phenotypic and genotypic datasets may be used to train genomic selection models that target the improvement of postharvest quality.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Chizk, T. Mason and Clark, John R. R. and Johns, Carmen and Nelson, Lacy and Ashrafi, Hamid and Aryal, Rishi and Worthington, Margaret L. L.}, year={2023}, month={Jun} }
 @article{brůna_aryal_dudchenko_sargent_mead_buti_cavallini_hytönen_andrés_pham_et al._2022, title={A chromosome-length genome assembly and annotation of blackberry (<i>Rubus argutus</i>, cv. “Hillquist”)}, volume={11}, ISSN={2160-1836}, url={http://dx.doi.org/10.1093/g3journal/jkac289}, DOI={10.1093/g3journal/jkac289}, abstractNote={Abstract
               Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R. occidentalis), red raspberry (R. idaeus), and R. chingii, but very few genomic resources exist for blackberries and their relatives in subgenus Rubus. Here we present a chromosome-length assembly and annotation of the diploid blackberry germplasm accession “Hillquist” (R. argutus). “Hillquist” is the only known source of primocane-fruiting (annual-fruiting) in tetraploid fresh-market blackberry breeding programs and is represented in the pedigree of many important cultivars worldwide. The “Hillquist” assembly, generated using Pacific Biosciences long reads scaffolded with high-throughput chromosome conformation capture sequencing, consisted of 298 Mb, of which 270 Mb (90%) was placed on 7 chromosome-length scaffolds with an average length of 38.6 Mb. Approximately 52.8% of the genome was composed of repetitive elements. The genome sequence was highly collinear with a novel maternal haplotype-resolved linkage map of the tetraploid blackberry selection A-2551TN and genome assemblies of R. chingii and red raspberry. A total of 38,503 protein-coding genes were predicted, of which 72% were functionally annotated. Eighteen flowering gene homologs within a previously mapped locus aligning to an 11.2 Mb region on chromosome Ra02 were identified as potential candidate genes for primocane-fruiting. The utility of the “Hillquist” genome has been demonstrated here by the development of the first genotyping-by-sequencing-based linkage map of tetraploid blackberry and the identification of possible candidate genes for primocane-fruiting. This chromosome-length assembly will facilitate future studies in Rubus biology, genetics, and genomics and strengthen applied breeding programs.}, number={ue 2}, journal={G3 Genes|Genomes|Genetics}, publisher={Oxford University Press (OUP)}, author={Brůna, Tomáš and Aryal, Rishi and Dudchenko, Olga and Sargent, Daniel James and Mead, Daniel and Buti, Matteo and Cavallini, Andrea and Hytönen, Timo and Andrés, Javier and Pham, Melanie and et al.}, editor={Pyhäjärvi, TEditor}, year={2022}, month={Nov} }
 @article{crowl_fritsch_tiley_lynch_ranney_ashrafi_manos_2022, title={A first complete phylogenomic hypothesis for diploid blueberries (Vaccinium section Cyanococcus)}, volume={10}, ISSN={["1537-2197"]}, DOI={10.1002/ajb2.16065}, abstractNote={AbstractPremiseThe true blueberries (Vaccinium sect. Cyanococcus; Ericaceae), endemic to North America, have been intensively studied for over a century. However, with species estimates ranging from nine to 24 and much confusion regarding species boundaries, this ecologically and economically valuable group remains inadequately understood at a basic evolutionary and taxonomic level. As a first step toward understanding the evolutionary history and taxonomy of this species complex, we present the first phylogenomic hypothesis of the known diploid blueberries.MethodsWe used flow cytometry to verify the ploidy of putative diploid taxa and a target‐enrichment approach to obtain a genomic data set for phylogenetic analyses.ResultsDespite evidence of gene flow, we found that a primary phylogenetic signal is present. Monophyly for all morphospecies was recovered, with two notable exceptions: one sample of V. boreale was consistently nested in the V. myrtilloides clade and V. caesariense was nested in the V. fuscatum clade. One diploid taxon, Vaccinium pallidum, is implicated as having a homoploid hybrid origin.ConclusionsThis foundational study represents the first attempt to elucidate evolutionary relationships of the true blueberries of North America with a phylogenomic approach and sets the stage for multiple avenues of future study such as a taxonomic revision of the group, the verification of a homoploid hybrid taxon, and the study of polyploid lineages within the context of a diploid phylogeny.}, journal={AMERICAN JOURNAL OF BOTANY}, author={Crowl, Andrew A. and Fritsch, Peter W. and Tiley, George P. and Lynch, Nathan P. and Ranney, Thomas G. and Ashrafi, Hamid and Manos, Paul S.}, year={2022}, month={Oct} }
 @article{mengist_bostan_de paola_teresi_platts_cremona_qi_mackey_bassil_ashrafi_et al._2022, title={Autopolyploid inheritance and a heterozygous reciprocal translocation shape chromosome genetic behavior in tetraploid blueberry (Vaccinium corymbosum)}, volume={9}, ISSN={["1469-8137"]}, url={https://doi.org/10.1111/nph.18428}, DOI={10.1111/nph.18428}, abstractNote={Summary


Understanding chromosome recombination behavior in polyploidy species is key to advancing genetic discoveries. In blueberry, a tetraploid species, the line of evidences about its genetic behavior still remain poorly understood, owing to the inter‐specific, and inter‐ploidy admixture of its genome and lack of in depth genome‐wide inheritance and comparative structural studies.

Here we describe a new high‐quality, phased, chromosome‐scale genome of a diploid blueberry, clone W85. The genome was integrated with cytogenetics and high‐density, genetic maps representing six tetraploid blueberry cultivars, harboring different levels of wild genome admixture, to uncover recombination behavior and structural genome divergence across tetraploid and wild diploid species.

Analysis of chromosome inheritance and pairing demonstrated that tetraploid blueberry behaves as an autotetraploid with tetrasomic inheritance. Comparative analysis demonstrated the presence of a reciprocal, heterozygous, translocation spanning one homolog of chr‐6 and one of chr‐10 in the cultivar Draper. The translocation affects pairing and recombination of chromosomes 6 and 10. Besides the translocation detected in Draper, no other structural genomic divergences were detected across tetraploid cultivars and highly inter‐crossable wild diploid species.

These findings and resources will facilitate new genetic and comparative genomic studies in Vaccinium and the development of genomic assisted selection strategy for this crop.

}, journal={NEW PHYTOLOGIST}, author={Mengist, Molla F. and Bostan, Hamed and De Paola, Domenico and Teresi, Scott J. and Platts, Adrian E. and Cremona, Gaetana and Qi, Xinpeng and Mackey, Ted and Bassil, Nahla V and Ashrafi, Hamid and et al.}, year={2022}, month={Sep} }
 @article{sullenberger_jia_gao_ashrafi_foolad_2022, title={Identification of late blight resistance quantitative trait loci in Solanum pimpinellifolium accession PI 270441}, volume={8}, ISSN={["1940-3372"]}, DOI={10.1002/tpg2.20251}, abstractNote={AbstractLate blight (LB), caused by the oomycete Phytophthora infestans, is one of the most destructive diseases of the cultivated tomato (Solanum lycopersicum L.) and potato (Solanum tuberosum L.) worldwide. Genetic changes in the pathogen have resulted in the emergence of new genotypes, overcoming formerly effective fungicides or host resistance genes. We previously reported the identification of a LB‐resistant accession (PI 270441) of the wild tomato species S. pimpinellifolium L. and the high heritability of its resistance. In the present study, an F2 population (n = 1,209), derived from a cross between PI 270441 and a LB‐susceptible tomato breeding line (Fla. 8059), was screened for response to LB infection. Extreme resistant (n = 44) and susceptible (n = 39) F2 individuals were selected and used in a trait‐based marker analysis (TBA; a.k.a selective genotyping) to identify and map quantitative trait loci (QTLs) conferring LB resistance. Reduced representation libraries (RRLs) of Fla. 8059 and PI 270441 were constructed, sequenced, and mapped to the tomato genome. A total of 13,054 single‐nucleotide polymorphisms (SNPs) were identified, of which, 200 were used to construct a genetic linkage map and locate QTLs. Four LB resistance QTLs were identified on chromosomes 1, 10, and 11 of PI 270441. The markers associated with these QTLs can be used to transfer LB resistance from PI 270441 into new tomato cultivars and to develop near‐isogenic lines for fine mapping of the QTL.}, journal={PLANT GENOME}, author={Sullenberger, Matthew T. and Jia, Mengyuan and Gao, Sihui and Ashrafi, Hamid and Foolad, Majid R.}, year={2022}, month={Aug} }
 @article{redpath_aryal_lynch_spencer_hulse-kemp_ballington_green_bassil_hummer_ranney_et al._2022, title={Nuclear DNA contents and ploidy levels of North American Vaccinium species and interspecific hybrids}, volume={297}, ISSN={["1879-1018"]}, DOI={10.1016/j.scienta.2022.110955}, abstractNote={Breeding strategies for improving blueberry (Vaccinium corymbosum and V. virgatum) cultivars often include introgressing regionally adapted species into the cultivated gene pools through interspecific hybridization. However, these approaches are complicated by variation in ploidy, triploid blocks and infertility, production of unreduced gametes, and aneuploidy. The objective of this study was to use flow cytometry, k-mer distribution analysis, and known pedigree information to evaluate genome sizes (2C nuclear and 1Cx monoploid), and ploidy of diverse accessions from Vaccinium sections and species. A total of 369 accessions, including a diversity panel (DP) of 251 inter- and intra-specific hybrid Vaccinium accessions, as well as 118 non-hybrid Vaccinium species across multiple sections, were sampled from the North Carolina State University blueberry breeding program and the National Clonal Germplasm Repository. The nuclear DNA content was analyzed via flow cytometry. The mean (range) DNA content of diploid, tetraploid, and hexaploid reference species were 1.20 pg (0.99 pg in V. crassifolium 'Well's Delight' to 1.41 pg in V. caesariense NC79–24), 2.37 pg (2.11 pg in V. corymbosum 'Concord' to 3.01 pg in V. corymbosum DE599), and 3.64 pg (3.24 in V. constablaei NC83–21–2 to 3.80 in V. virgatum 'Premier' and NC4790), respectively. Of the 369 unique accessions analyzed for ploidy, 259 were tetraploid, 46 were diploid, one was triploid, 51 were pentaploid or aneuploid with 2C values between tetraploid and hexaploid values, and 12 were hexaploid. Tetraploid hybrid pedigrees, which involved hexaploid crosses within three prior generations, had a 2C value range between 2.22 pg and 2.59 pg. Interspecific pentaploid and aneuploid progeny 2C DNA content ranged from 2.61 pg to 3.15 pg. We speculate some of these progeny to be near tetraploids with extra chromosomes from hexaploid progenitors. Further karyotyping of these individuals is necessary to ascertain aneuploidy anomalies. This research provides an expanded knowledge base of genome sizes, ploidy, and reproductive pathways for diverse species and hybrids to enhance future breeding, improvement, and the genomic study of blueberry.}, journal={SCIENTIA HORTICULTURAE}, author={Redpath, Lauren E. and Aryal, Rishi and Lynch, Nathan and Spencer, Jessica A. and Hulse-Kemp, Amanda M. and Ballington, James R. and Green, Jaimie and Bassil, Nahla and Hummer, Kim and Ranney, Thomas and et al.}, year={2022}, month={Apr} }
 @article{adhikari_aryal_redpath_broeck_ashrafi_philbrick_jacobs_sozzani_louws_2022, title={RNA-Seq and Gene Regulatory Network Analyses Uncover Candidate Genes in the Early Defense to Two Hemibiotrophic Colletorichum spp. in Strawberry}, volume={12}, ISSN={["1664-8021"]}, DOI={10.3389/fgene.2021.805771}, abstractNote={Two hemibiotrophic pathogens, Colletotrichum acutatum (Ca) and C. gloeosporioides (Cg), cause anthracnose fruit rot and anthracnose crown rot in strawberry (Fragaria × ananassa Duchesne), respectively. Both Ca and Cg can initially infect through a brief biotrophic phase, which is associated with the production of intracellular primary hyphae that can infect host cells without causing cell death and establishing hemibiotrophic infection (HBI) or quiescent (latent infections) in leaf tissues. The Ca and Cg HBI in nurseries and subsequent distribution of asymptomatic infected transplants to fruit production fields is the major source of anthracnose epidemics in North Carolina. In the absence of complete resistance, strawberry varieties with good fruit quality showing rate-reducing resistance have frequently been used as a source of resistance to Ca and Cg. However, the molecular mechanisms underlying the rate-reducing resistance or susceptibility to Ca and Cg are still unknown. We performed comparative transcriptome analyses to examine how rate-reducing resistant genotype NCS 10-147 and susceptible genotype ‘Chandler’ respond to Ca and Cg and identify molecular events between 0 and 48 h after the pathogen-inoculated and mock-inoculated leaf tissues. Although plant response to both Ca and Cg at the same timepoint was not similar, more genes in the resistant interaction were upregulated at 24 hpi with Ca compared with those at 48 hpi. In contrast, a few genes were upregulated in the resistant interaction at 48 hpi with Cg. Resistance response to both Ca and Cg was associated with upregulation of MLP-like protein 44, LRR receptor-like serine/threonine-protein kinase, and auxin signaling pathway, whereas susceptibility was linked to modulation of the phenylpropanoid pathway. Gene regulatory network inference analysis revealed candidate transcription factors (TFs) such as GATA5 and MYB-10, and their downstream targets were upregulated in resistant interactions. Our results provide valuable insights into transcriptional changes during resistant and susceptible interactions, which can further facilitate assessing candidate genes necessary for resistance to two hemibiotrophic Colletotrichum spp. in strawberry.}, journal={FRONTIERS IN GENETICS}, author={Adhikari, Tika B. and Aryal, Rishi and Redpath, Lauren E. and Broeck, Lisa and Ashrafi, Hamid and Philbrick, Ashley N. and Jacobs, Raymond L. and Sozzani, Rosangela and Louws, Frank J.}, year={2022}, month={Mar} }
 @article{edger_iorizzo_bassil_benevenuto_ferrao_giongo_hummer_lawas_leisner_li_et al._2022, title={There and back again; historical perspective and future directions for Vaccinium breeding and research studies}, volume={9}, ISSN={["2052-7276"]}, DOI={10.1093/hr/uhac083}, abstractNote={Abstract
               The genus Vaccinium L. (Ericaceae) contains a wide diversity of culturally and economically important berry crop species. Consumer demand and scientific research in blueberry (Vaccinium spp.) and cranberry (Vaccinium macrocarpon) have increased worldwide over the crops’ relatively short domestication history (~100 years). Other species, including bilberry (Vaccinium myrtillus), lingonberry (Vaccinium vitis-idaea), and ohelo berry (Vaccinium reticulatum) are largely still harvested from the wild but with crop improvement efforts underway. Here, we present a review article on these Vaccinium berry crops on topics that span taxonomy to genetics and genomics to breeding. We highlight the accomplishments made thus far for each of these crops, along their journey from the wild, and propose research areas and questions that will require investments by the community over the coming decades to guide future crop improvement efforts. New tools and resources are needed to underpin the development of superior cultivars that are not only more resilient to various environmental stresses and higher yielding, but also produce fruit that continue to meet a variety of consumer preferences, including fruit quality and health related traits.}, journal={HORTICULTURE RESEARCH}, author={Edger, Patrick P. and Iorizzo, Massimo and Bassil, Nahla V and Benevenuto, Juliana and Ferrao, Luis Felipe V and Giongo, Lara and Hummer, Kim and Lawas, Lovely Mae F. and Leisner, Courtney P. and Li, Changying and et al.}, year={2022}, month={Jan} }
 @article{hulse-kemp_bostan_chen_ashrafi_stoffel_sanseverino_li_cheng_schatz_garvin_et al._2021, title={An anchored chromosome-scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids}, volume={6}, ISSN={["1940-3372"]}, DOI={10.1002/tpg2.20101}, abstractNote={AbstractSpinach (Spinacia oleracea L.) is a member of the Caryophyllales family, a basal eudicot asterid that consists of sugar beet (Beta vulgaris L. subsp. vulgaris), quinoa (Chenopodium quinoa Willd.), and amaranth (Amaranthus hypochondriacus L.). With the introduction of baby leaf types, spinach has become a staple food in many homes. Production issues focus on yield, nitrogen‐use efficiency and resistance to downy mildew (Peronospora effusa). Although genomes are available for the above species, a chromosome‐level assembly exists only for quinoa, allowing for proper annotation and structural analyses to enhance crop improvement. We independently assembled and annotated genomes of the cultivar Viroflay using short‐read strategy (Illumina) and long‐read strategies (Pacific Biosciences) to develop a chromosome‐level, genetically anchored assembly for spinach. Scaffold N50 for the Illumina assembly was 389 kb, whereas that for Pacific BioSciences was 4.43 Mb, representing 911 Mb (93% of the genome) in 221 scaffolds, 80% of which are anchored and oriented on a sequence‐based genetic map, also described within this work. The two assemblies were 99.5% collinear. Independent annotation of the two assemblies with the same comprehensive transcriptome dataset show that the quality of the assembly directly affects the annotation with significantly more genes predicted (26,862 vs. 34,877) in the long‐read assembly. Analysis of resistance genes confirms a bias in resistant gene motifs more typical of monocots. Evolutionary analysis indicates that Spinacia is a paleohexaploid with a whole‐genome triplication followed by extensive gene rearrangements identified in this work. Diversity analysis of 75 lines indicate that variation in genes is ample for hypothesis‐driven, genomic‐assisted breeding enabled by this work.}, journal={PLANT GENOME}, author={Hulse-Kemp, Amanda M. and Bostan, Hamed and Chen, Shiyu and Ashrafi, Hamid and Stoffel, Kevin and Sanseverino, Walter and Li, Linzhou and Cheng, Shifeng and Schatz, Michael C. and Garvin, Tyler and et al.}, year={2021}, month={Jun} }
 @article{zhao_maren_kosentka_liao_lu_duduit_huang_ashrafi_zhao_huerta_et al._2021, title={An optimized protocol for stepwise optimization of real-time RT-PCR analysis}, volume={8}, ISSN={["2052-7276"]}, url={https://doi.org/10.1038/s41438-021-00616-w}, DOI={10.1038/s41438-021-00616-w}, abstractNote={AbstractComputational tool-assisted primer design for real-time reverse transcription (RT) PCR (qPCR) analysis largely ignores the sequence similarities between sequences of homologous genes in a plant genome. It can lead to false confidence in the quality of the designed primers, which sometimes results in skipping the optimization steps for qPCR. However, the optimization of qPCR parameters plays an essential role in the efficiency, specificity, and sensitivity of each gene’s primers. Here, we proposed an optimized approach to sequentially optimizing primer sequences, annealing temperatures, primer concentrations, and cDNA concentration range for each reference (and target) gene. Our approach started with a sequence-specific primer design that should be based on the single-nucleotide polymorphisms (SNPs) present in all the homologous sequences for each of the reference (and target) genes under study. By combining the efficiency calibrated and standard curve methods with the 2−ΔΔCt method, the standard cDNA concentration curve with a logarithmic scale was obtained for each primer pair for each gene. As a result, an R2 ≥ 0.9999 and the efficiency (E) = 100 ± 5% should be achieved for the best primer pair of each gene, which serve as the prerequisite for using the 2−ΔΔCt method for data analysis. We applied our newly developed approach to identify the best reference genes in different tissues and at various inflorescence developmental stages of Tripidium ravennae, an ornamental and biomass grass, and validated their utility under varying abiotic stress conditions. We also applied this approach to test the expression stability of six reference genes in soybean under biotic stress treatment with Xanthomonas axonopodis pv. glycines (Xag). Thus, these case studies demonstrated the effectiveness of our optimized protocol for qPCR analysis.}, number={1}, journal={HORTICULTURE RESEARCH}, author={Zhao, Fangzhou and Maren, Nathan A. and Kosentka, Pawel Z. and Liao, Ying-Yu and Lu, Hongyan and Duduit, James R. and Huang, Debao and Ashrafi, Hamid and Zhao, Tuanjie and Huerta, Alejandra I and et al.}, year={2021}, month={Dec} }
 @article{kraft_sit_diepenbrock_ashrafi_aryal_fernandez_burrack_2021, title={Detection of Fruit Meals Within Laboratory-Raised and Field-Trapped Adult Drosophila suzukii (Diptera: Drosophilidae) Guts}, volume={9}, ISSN={2296-701X}, url={http://dx.doi.org/10.3389/fevo.2021.719645}, DOI={10.3389/fevo.2021.719645}, abstractNote={The feeding habits of adult Brachycera are understudied and may provide important context for understanding invasive pest biology, as with the polyphagous small fruit pest Drosophila suzukii. We developed molecular methods to study adult D. suzukii gut content in order to understand its feeding habits. We designed and verified two primer pairs specific for either blueberries or blackberries and used a qPCR melt curve analysis to determine whether we can detect the presence or absence of berry feeding by adult flies. In a laboratory assay, the blueberry fly meal DNA can be detected for longer periods than the blackberry meal DNA. Generally, female gut contents are less variable than male gut contents. We also tested recently emerged flies that were not fed as adults but developed as larvae in either blueberries or blackberries. Some adult flies from each fruit had detectable fruit DNA in their gut, which could be due to pupal meconium feeding after emergence. Next, we aimed to test the primers in the field to develop techniques to track fruit feeding by D. suzukii in its natural field environment. First, to identify the most appropriate collection method, we determined how long we could detect fruit DNA, using previously developed primers within D. suzukii gut preserved in four types of trap fluid in the laboratory. The likelihood of detecting blackberry DNA differed by day, trap fluid, and between sexes. For the blueberry primer, the possibility of detecting blueberry DNA differed by trap fluid only. Based on those results, we used RV antifreeze with a Scentry SWD lure in field trials at two research station locations, one containing blackberries and one with blueberries. We established transects away from each fruit planting and collected up to 120 total flies at each point along transects. There were no significant differences in the number of flies containing berry DNA among collection points along the transect in both locations. These results suggest that adult flies move between crop and non-crop habitats and may not be highly dependent on fruit food resources.}, journal={Frontiers in Ecology and Evolution}, publisher={Frontiers Media SA}, author={Kraft, Laura J. and Sit, Tim L. and Diepenbrock, Lauren M. and Ashrafi, Hamid and Aryal, Rishi and Fernandez, Gina E. and Burrack, Hannah J.}, year={2021}, month={Aug} }
 @article{yow_zhang_bansal_eacker_sullivan_liachko_cubeta_rollins_ashrafi_2021, title={Genome sequence of Monilinia vaccinii-corymbosi sheds light on mummy berry disease infection of blueberry and mating type}, volume={11}, ISSN={["2160-1836"]}, url={https://doi.org/10.1093/g3journal/jkaa052}, DOI={10.1093/g3journal/jkaa052}, abstractNote={Abstract
               Mummy berry disease, caused by the fungal pathogen Monilinia vaccinii-corymbosi (Mvc), is one of the most economically important diseases of blueberries in North America. Mvc is capable of inducing two separate blighting stages during its life cycle. Infected fruits are rendered mummified and unmarketable. Genomic data for this pathogen is lacking, but could be useful in understanding the reproductive biology of Mvc and the mechanisms it deploys to facilitate host infection. In this study, PacBio sequencing and Hi-C interaction data were utilized to create a chromosome-scale reference genome for Mvc. The genome comprises nine chromosomes with a total length of 30 Mb, an N50 length of 4.06 Mb, and an average 413X sequence coverage. A total of 9399 gene models were predicted and annotated, and BUSCO analysis revealed that 98% of 1,438 searched conserved eukaryotic genes were present in the predicted gene set. Potential effectors were identified, and the mating-type (MAT) locus was characterized. Biotrophic effectors allow the pathogen to avoid recognition by the host plant and evade or mitigate host defense responses during the early stages of fruit infection. Following locule colonization, necrotizing effectors promote the mummification of host tissues. Potential biotrophic effectors utilized by Mvc include chorismate mutase for reducing host salicylate and necrotrophic effectors include necrosis-inducing proteins and hydrolytic enzymes for macerating host tissue. The MAT locus sequences indicate the potential for homothallism in the reference genome, but a deletion allele of the MAT locus, characterized in a second isolate, indicates heterothallism. Further research is needed to verify the roles of individual effectors in virulence and to determine the role of the MAT locus in outcrossing and population genotypic diversity.}, number={2}, journal={G3-GENES GENOMES GENETICS}, publisher={Oxford University Press (OUP)}, author={Yow, Ashley G. and Zhang, Yucheng and Bansal, Kamaldeep and Eacker, Stephen M. and Sullivan, Shawn and Liachko, Ivan and Cubeta, Marc A. and Rollins, Jeffrey A. and Ashrafi, Hamid}, editor={Baltrus, DEditor}, year={2021}, month={Feb} }
 @article{redpath_gumpertz_ballington_bassil_ashrafi_2021, title={Genotype, Environment, Year, and Harvest Effects on Fruit Quality Traits of Five Blueberry (Vaccinium corymbosum L.) Cultivars}, volume={11}, ISSN={["2073-4395"]}, url={https://doi.org/10.3390/agronomy11091788}, DOI={10.3390/agronomy11091788}, abstractNote={Blueberries (Vaccinium spp.) comprise a broad range of perennial woody species. Introgression of native species into cultivated germplasm has adapted Vaccinium germplasm to a range of climates and growing conditions for cultivated blueberry. Genetic differences signify phenotypic variance that is observed among blueberry accessions. In addition, variability in geographic and climatic growing conditions between environments or within the same environment across different years may further affect fruit and plant phenotypic expression. As a result, a phenotype is a function of genetic background (G), environment (E), and their interaction (G × E). In addition, other temporally regulated factors such as year (Y) and harvest time (H) impact plant and fruit quality phenotypic variation. Our research aimed to assess the genotypic performance of five blueberry cultivars, including ‘Echota’, ‘O’Neal’, ‘Reveille’, ‘Summit’, and ‘Sunrise’. The selected cultivars were phenotyped for various fruit quality-related traits over two sequential harvests in two years and two locations. Our results indicated that genotype was a significant source of variation for most phenotypic characteristics. Further, the effect of Y × H and G × Y × H significantly affected the majority of studied phenotypic traits. Within the studied genotypes, ‘Reveille’ and ‘O’Neal’ phenotypic stability were consistent across locations and years; additionally, ‘Summit’ phenotypic characteristics were stable across years, environments, and harvests. Clonal plant replicates within a genotype, harvest, and environment, in addition to individual fruit measures, were the most significant sources of variability.}, number={9}, journal={AGRONOMY-BASEL}, author={Redpath, Lauren E. and Gumpertz, Marcia and Ballington, James R. and Bassil, Nahla and Ashrafi, Hamid}, year={2021}, month={Sep} }
 @article{mengist_bostan_young_kay_gillitt_ballington_kay_ferruzzi_ashrafi_lila_et al._2021, title={High-density linkage map construction and identification of loci regulating fruit quality traits in blueberry}, volume={8}, ISSN={["2052-7276"]}, url={https://doi.org/10.1038/s41438-021-00605-z}, DOI={10.1038/s41438-021-00605-z}, abstractNote={AbstractFruit quality traits play a significant role in consumer preferences and consumption in blueberry (Vaccinium corymbosumL). The objectives of this study were to construct a high-density linkage map and to identify the underlying genetic basis of fruit quality traits in blueberry. A total of 287 F1individuals derived from a cross between two southern highbush blueberry cultivars, ‘Reveille’ and ‘Arlen’, were phenotyped over three years (2016–2018) for fruit quality-related traits, including titratable acidity, pH, total soluble solids, and fruit weight. A high-density linkage map was constructed using 17k single nucleotide polymorphisms markers. The linkage map spanned a total of 1397 cM with an average inter-loci distance of 0.08 cM. The quantitative trait loci interval mapping based on the hidden Markov model identified 18 loci for fruit quality traits, including seven loci for fruit weight, three loci for titratable acidity, five loci for pH, and three loci for total soluble solids. Ten of these loci were detected in more than one year. These loci explained phenotypic variance ranging from 7 to 28% for titratable acidity and total soluble solid, and 8–13% for pH. However, the loci identified for fruit weight did not explain more than 10% of the phenotypic variance. We also reported the association between fruit quality traits and metabolites detected by Proton nuclear magnetic resonance analysis directly responsible for these fruit quality traits. Organic acids, citric acid, and quinic acid were significantly (P < 0.05) and positively correlated with titratable acidity. Sugar molecules showed a strong and positive correlation with total soluble solids. Overall, the study dissected the genetic basis of fruit quality traits and established an association between these fruit quality traits and metabolites.}, number={1}, journal={HORTICULTURE RESEARCH}, author={Mengist, Molla F. and Bostan, Hamed and Young, Elisheba and Kay, Kristine L. and Gillitt, Nicholas and Ballington, James and Kay, Colin D. and Ferruzzi, Mario G. and Ashrafi, Hamid and Lila, Mary Ann and et al.}, year={2021}, month={Dec} }
 @article{maren_zhao_aryal_touchell_liu_ranney_ashrafi_2021, title={Reproductive developmental transcriptome analysis of Tripidium ravennae (Poaceae)}, volume={22}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-021-07641-y}, abstractNote={AbstractBackgroundTripidium ravennaeis a cold-hardy, diploid species in the sugarcane complex (PoaceaesubtribeSaccharinae) with considerable potential as a genetic resource for developing improved bioenergy and ornamental grasses. An improved understanding of the genetic regulation of reproductive processes (e.g., floral induction, inflorescence development, and seed development) will enable future applications of precision breeding and gene editing of floral and seed development. In particular, the ability to silence reproductive processes would allow for developing seedless forms of valuable but potentially invasive plants. The objective of this research was to characterize the gene expression environment of reproductive development inT. ravennae.ResultsDuring the early phases of inflorescence development, multiple key canonical floral integrators and pathways were identified. Annotations of type II subfamily of MADS-box transcription factors, in particular, were over-represented in the GO enrichment analyses and tests for differential expression (FDRp-value < 0.05). The differential expression of floral integrators observed in the early phases of inflorescence development diminished prior to inflorescence determinacy regulation. Differential expression analysis did not identify many unique genes at mid-inflorescence development stages, though typical biological processes involved in plant growth and development expressed abundantly. The increase in inflorescence determinacy regulatory elements and putative homeotic floral development unigenes at mid-inflorescence development coincided with the expression of multiple meiosis annotations and multicellular organism developmental processes. Analysis of seed development identified multiple unigenes involved in oxidative-reductive processes.ConclusionReproduction in grasses is a dynamic system involving the sequential coordination of complex gene regulatory networks and developmental processes. This research identified differentially expressed transcripts associated with floral induction, inflorescence development, and seed development inT. ravennae. These results provide insights into the molecular regulation of reproductive development and provide a foundation for future investigations and analyses, including genome annotation, functional genomics characterization, gene family evolutionary studies, comparative genomics, and precision breeding.}, number={1}, journal={BMC GENOMICS}, author={Maren, Nathan and Zhao, Fangzhou and Aryal, Rishi and Touchell, Darren and Liu, Wusheng and Ranney, Thomas and Ashrafi, Hamid}, year={2021}, month={Jun} }
 @article{zurn_driskill_jung_main_yin_clark_cheng_ashrafi_aryal_clark_et al._2020, title={A Rosaceae Family-Level Approach To Identify Loci Influencing Soluble Solids Content in Blackberry for DNA-Informed Breeding}, volume={10}, ISSN={["2160-1836"]}, DOI={10.1534/g3.120.401449}, abstractNote={Abstract
               A Rosaceae family-level candidate gene approach was used to identify genes associated with sugar content in blackberry (Rubus subgenus Rubus). Three regions conserved among apple (Malus × domestica), peach (Prunus persica), and alpine strawberry (Fragaria vesca) were identified that contained previously detected sweetness-related quantitative trait loci (QTL) in at least two of the crops. Sugar related genes from these conserved regions and 789 sugar-associated apple genes were used to identify 279 Rubus candidate transcripts. A Hyb-Seq approach was used in conjunction with PacBio sequencing to generate haplotype level sequence information of sugar-related genes for 40 cultivars with high and low soluble solids content from the University of Arkansas and USDA blackberry breeding programs. Polymorphisms were identified relative to the ‘Hillquist’ blackberry (R. argutus) and ORUS 4115-3 black raspberry (R. occidentalis) genomes and tested for their association with soluble solids content (SSC). A total of 173 alleles were identified that were significantly (α = 0.05) associated with SSC. KASP genotyping was conducted for 92 of these alleles on a validation set of blackberries from each breeding program and 48 markers were identified that were significantly associated with SSC. One QTL, qSSC-Ruh-ch1.1, identified in both breeding programs accounted for an increase of 1.5 °Brix and the polymorphisms were detected in the intron space of a sucrose synthase gene. This discovery represents the first environmentally stable sweetness QTL identified in blackberry. The approach demonstrated in this study can be used to develop breeding tools for other crops that have not yet benefited directly from the genomics revolution.}, number={10}, journal={G3-GENES GENOMES GENETICS}, author={Zurn, Jason D. and Driskill, Mandie and Jung, Sook and Main, Dorrie and Yin, Melinda H. and Clark, Melissa C. and Cheng, Lailiang and Ashrafi, Hamid and Aryal, Rishi and Clark, John R. and et al.}, year={2020}, month={Oct}, pages={3729–3740} }
 @article{maren_touchell_ranney_ashrafi_whitfield_chinn_2020, title={Biomass yields, cytogenetics, fertility, and compositional analyses of novel bioenergy grass hybrids (Tripidium spp.)}, volume={12}, ISSN={["1757-1707"]}, url={https://doi.org/10.1111/gcbb.12676}, DOI={10.1111/gcbb.12676}, abstractNote={AbstractHigh biomass yields have been documented for Tripidium spp. (Erianthus spp., Saccharum spp.), but targeted breeding for bioenergy applications has been limited. Advanced, interspecific hybrids between Tripidium ravennae and T. arundinaceum were planted in replicated field plots in 2016. Comparative feedstock evaluations examined biomass yields, cytogenetics, plant fertility, and compositional analyses relative to Miscanthus × giganteus. Dry biomass yields varied as a function of year and accession and increased each year ranging from 3.4 to 10.6, 8.6 to 37.3, and 23.7 to 60.6 Mg/ha for Tripidium hybrids compared to 2.3, 16.2 and 27.9 Mg/ha for M. × giganteus in 2016, 2017, and 2018, respectively. Cytology and cytometry confirmed that Tripidium hybrids were tetraploid with 2n = 4x = 40 (2C genome size = 5.06 pg) and intermediate between T. ravennae with 2n = 2x = 20 (2C genome size = 2.55 pg) and T. arundinaceum with 2n = 6x = 60 (2C genome size = 7.61 pg). Plant fertility characteristics varied considerably with some accessions producing no viable seeds or fewer than that observed for M. × giganteus. Accessions varied significantly for flowering culm number and height and dates of peak anthesis ranging from 14 September to 2 October. Variations in yield and compositional analyses contributed to variations in theoretical ethanol yields ranging from 10,181 to 27,546 L/ha for Tripidium accessions compared to 13,095 L/ha for M. × giganteus. Relative feed value (RFV) indices for winter‐harvested Tripidium accessions varied from 52.8 to 60.0 compared to M. × giganteus with 45.4. RFV for summer‐harvested Tripidium accessions varied from 71.6 to 80.5 compared to M. × giganteus with 61.0. These initial findings for Tripidium hybrids, including high biomass yields, cold hardiness, and desirable traits for multiple markets (e.g., forage, bioenergy, bioproducts), are promising and warrant further development of Tripidium as a temperate bioenergy feedstock.}, number={5}, journal={GLOBAL CHANGE BIOLOGY BIOENERGY}, author={Maren, Nathan A. and Touchell, Darren H. and Ranney, Thomas G. and Ashrafi, Hamid and Whitfield, Matthew B. and Chinn, Mari}, year={2020}, month={May}, pages={361–373} }
 @article{jiang_li_takeda_kramer_ashrafi_hunter_2019, title={3D point cloud data to quantitatively characterize size and shape of shrub crops}, volume={6}, ISSN={["2052-7276"]}, DOI={10.1038/s41438-019-0123-9}, abstractNote={Size and shape are important properties of shrub crops such as blueberries, and they can be particularly useful for evaluating bush architecture suited to mechanical harvesting. The overall goal of this study was to develop a 3D imaging approach to measure size-related traits and bush shape that are relevant to mechanical harvesting. 3D point clouds were acquired for 367 bushes from five genotype groups. Point cloud data were preprocessed to obtain clean bush points for characterizing bush architecture, including bush morphology (height, width, and volume), crown size, and shape descriptors (path curve λ and five shape indices). One-dimensional traits (height, width, and crown size) had high correlations (R2 = 0.88-0.95) between proposed method and manual measurements, whereas bush volume showed relatively lower correlations (R2 = 0.78-0.85). These correlations suggested that the present approach was accurate in measuring one-dimensional size traits and acceptable in estimating three-dimensional bush volume. Statistical results demonstrated that the five genotype groups were statistically different in crown size and bush shape. The differences matched with human evaluation regarding optimal bush architecture for mechanical harvesting. In particular, a visualization tool could be generated using crown size and path curve λ, which showed great potential of determining bush architecture suitable for mechanical harvesting quickly. Therefore, the processing pipeline of 3D point cloud data presented in this study is an effective tool for blueberry breeding programs (in particular for mechanical harvesting) and farm management.}, journal={HORTICULTURE RESEARCH}, author={Jiang, Yu and Li, Changying and Takeda, Fumiomi and Kramer, Elizabeth A. and Ashrafi, Hamid and Hunter, Jamal}, year={2019}, month={Apr} }
 @article{jahnke_dole_ashrafi_2020, title={Simulated storage causes carbohydrate loss and rooting differences in two poinsettia cultivars}, volume={100}, ISSN={["1918-1833"]}, DOI={10.1139/cjps-2019-0232}, abstractNote={ Unrooted cuttings of ‘Prestige Red’ and ‘White Star’ poinsettias (Euphorbia pulcherrima Willd. ex Klotzsch) were stored in a box at 10 °C for 0, 2, 4, 6 or 8 d to simulate shipping and holding. Visual root ratings decreased following ≥4 d of storage but did not differ from the non-stored cuttings. Root rating of ‘White Star’ was 0.5 higher and cuttings maintained higher fructose and glucose concentrations compared to ‘Prestige Red’. Glucose (r2 = 0.4824) followed by fructose plus glucose (r2 = 0.4222) were the best predictors of rooting. Carbohydrate maintenance may be an indicator of storage tolerant and better-rooting cultivars. }, number={4}, journal={CANADIAN JOURNAL OF PLANT SCIENCE}, author={Jahnke, Nathan J. and Dole, John M. and Ashrafi, Hamid}, year={2020}, month={Aug}, pages={459–462} }
 @article{gallardo_zhang_dossett_polashock_rodriguez-saona_vorsa_edger_ashrafi_babiker_finn_et al._2018, title={Breeding Trait Priorities of the Blueberry Industry in the United States and Canada}, volume={53}, DOI={10.21273/hortsci12964-18}, abstractNote={Developing new blueberry cultivars requires plant breeders to be aware of current and emerging needs throughout the supply chain, from producer to consumer. Because breeding perennial crop plants (such as blueberry) is time- and resource-intensive, understanding and targeting priority traits is critical to enhancing the efficiency of breeding programs. This study assesses blueberry industry breeding priorities for fruit and plant quality traits based on a survey conducted at commodity group meetings across nine U.S. states and in British Columbia (Canada) between Nov. 2016 and Mar. 2017. In general, industry responses signaled that the most important trait cluster was fruit quality including the firmness, flavor, and shelf life. Fruit quality traits affect price premiums received by producers; influence consumer’s preferences; and have the potential to increase the feasibility of mechanical harvesting, all critical to the economic viability of the industry. There were differences across regions in the relative importance assigned to traits for disease resistance, arthropod resistance, and tolerance to abiotic stresses. Our findings will be useful to researchers seeking solutions for challenges to the North American blueberry industry including development of new cultivars with improved traits using accelerated DNA-based selection strategies.}, number={7}, journal={HortScience}, publisher={American Society for Horticultural Science}, author={Gallardo, R. Karina and Zhang, Qi and Dossett, Michael and Polashock, James J. and Rodriguez-Saona, Cesar and Vorsa, Nicholi and Edger, Patrick P. and Ashrafi, Hamid and Babiker, Ebrahiem and Finn, Chad E. and et al.}, year={2018}, month={Jul}, pages={1021–1028} }
 @misc{aryal_yow_ashrafi_2018, title={Developing the Genomic Resources for a Tetraploid Blueberry cv "O'Neal"}, note={Poster #6}, author={Aryal, Rishi and Yow, Ashley and Ashrafi, Hamid}, year={2018}, month={Aug} }
 @misc{aryal_ashrafi_2018, title={Differential Gene Expression during Blueberry Fruits Ripening}, note={Poster 300-011}, author={Aryal, Rishi and Ashrafi, Hamid}, year={2018}, month={Jul} }
 @misc{aryal_bostan_yow_tseng_iorizzo_ashrafi_Januaary 13-17, 2018, title={Differential Gene Expression during Flower and Fruit Development of the Blueberry Cv. "O'Neal"}, note={Poster P0203}, author={Aryal, Rishi and Bostan, Hamed and Yow, Ashley G. and Tseng, Elizabeth and Iorizzo, Massimo and Ashrafi, Hamid}, year={Januaary 13-17, 2018}, month={Januaary 13-17, 2018} }
 @misc{redpath_yow_aryal_hulse-kemp_franks_whetten_ashrafi_2018, title={Differential Gene Expression of Southern Highbush Blueberry cv. ‘O’Neal’ Floral Buds in Response to Freeze Treatment and Recovery Periods}, note={Poster 279}, author={Redpath, Lauren E. and Yow, Ashley G. and Aryal, Rishi and Hulse-Kemp, Amanda M. and Franks, Robert G. and Whetten, Ross and Ashrafi, Hamid}, year={2018}, month={Jul} }
 @misc{redpath_ashrafi_2018, title={Differential Gene Expression of ‘O’Neal’ Blueberry Floral Buds in Response to Freeze Treatment and Recovery Periods}, author={Redpath, Lauren E. and Ashrafi, Hamid}, year={2018}, month={Apr} }
 @misc{redpath_bland_ballington_jiang_li_ashrafi_2018, title={Evaluation of Mechanically Harvested Southern Highbush Blueberries (Vaccinium corymbosum) Advanced Selections for Fresh Market}, author={Redpath, Lauren E. and Bland, Terry W. and Ballington, James R. and Jiang, Yu and Li, Changying and Ashrafi, Hamid}, year={2018}, month={Jul} }
 @misc{young_redpath_iorizzo_ashrafi_2018, title={Fruit Quality Related Trait Evaluation in a Segregating F1 Population of Blueberry from a Cross Between "Reveille" and "Arlen" Cultivars}, note={Poster 117-SII}, author={Young, Elisheba and Redpath, Lauren and Iorizzo, Massimo and Ashrafi, Hamid}, year={2018}, month={Aug} }
 @article{ohlson_ashrafi_foolad_2018, title={Identification and Mapping of Late Blight Resistance Quantitative Trait Loci in Tomato Accession PI 163245}, volume={0}, DOI={10.3835/plantgenome2018.01.0007}, abstractNote={Late blight (LB), caused by the oomycete Phytophthora infestans (Mont.) de Bary, is one of the most devastating diseases of tomato (Solanum lycopersicum L.) and potato (S. tuberosum L.) worldwide. The importance of LB on tomato has increased due to the occurrence of aggressive and fungicide‐resistant clonal lineages of P. infestans. Consequently, identification and characterization of new sources of genetic resistance to LB has become a priority in tomato breeding. Previously, we reported accession PI 163245 as a promising source of highly heritable LB resistance for tomato breeding. The purpose of this study was to identify and map quantitative trait loci (QTLs) associated with LB resistance in this accession using a trait‐based marker analysis (a.k.a. selective genotyping). An F2 mapping population (n = 560) derived from a cross between a LB‐susceptible tomato breeding line (Fla. 8059) and PI 163245 was screened for LB resistance, and the most resistant (n = 39) and susceptible (n = 35) individuals were selected for genotyping. Sequencing and comparison of the reduced representation libraries (RRLs) derived from genomic DNA of the two parents resulted in the identification of 33,541 putative single nucleotide polymorphism (SNP) markers, of which, 233 genome‐wide markers were used to genotype the 74 selected F2 individuals. The marker analysis resulted in the identification of four LB resistance QTLs conferred by PI 163245, located on chromosomes 2, 3, 10, and 11. Research is underway to develop near‐isogenic lines (NILs) for fine mapping the QTLs and develop tomato breeding lines with LB resistance introduced from PI 163245.}, number={0}, journal={The Plant Genome}, publisher={Crop Science Society of America}, author={Ohlson, Erik W. and Ashrafi, Hamid and Foolad, Majid R.}, year={2018}, pages={0} }
 @misc{redpath_yow_aryal_hulse-kemp_franks_whetten_ashrafi_2018, title={RNA-Seq Analysis of Floral Bud Response to Freeze Treatments in Southern Highbush Blueberry CV "O’Neal"}, note={Poster 81}, author={Redpath, Lauren E. and Yow, Ashley G. and Aryal, Rishi and Hulse-Kemp, Amanda M. and Franks, Robert G. and Whetten, Ross and Ashrafi, Hamid}, year={2018}, month={Aug} }
 @article{gonda_ashrafi_lyon_strickler_hulse-kemp_ma_sun_stoffel_powell_futrell_et al._2019, title={Sequencing-Based Bin Map Construction of a Tomato Mapping Population, Facilitating High-Resolution Quantitative Trait Loci Detection}, volume={12}, ISSN={["1940-3372"]}, DOI={10.3835/plantgenome2018.02.0010}, abstractNote={Genotyping‐by‐sequencing (GBS) was employed to construct a highly saturated genetic linkage map of a tomato (Solanum lycopersicum L.) recombinant inbred line (RIL) population, derived from a cross between cultivar NC EBR‐1 and the wild tomato S. pimpinellifolium L. accession LA2093. A pipeline was developed to convert single nucleotide polymorphism (SNP) data into genomic bins, which could be used for fine mapping of quantitative trait loci (QTL) and identification of candidate genes. The pipeline, implemented in a python script named SNPbinner, adopts a hidden Markov model approach for calculation of recombination breakpoints followed by genomic bins construction. The total length of the newly developed high‐resolution genetic map was 1.2‐fold larger than previously estimated based on restriction fragment length polymorphism (RFLP) and polymerase chain reaction (PCR)–based markers. The map was used to verify and refine QTL previously identified for two fruit quality traits in the RIL population, fruit weight (FW) and fruit lycopene content (LYC). Two well‐described FW QTL (fw2.2 and fw3.2) were localized precisely at their known underlying causative genes, and the QTL intervals were decreased by two‐ to tenfold. A major QTL for LYC content (Lyc12.1) was verified at high resolution and its underlying causative gene was determined to be ζ‐carotene isomerase (SlZISO). The RIL population, the high resolution genetic map, and the easy‐to‐use genotyping pipeline, SNPbinner, are made publicly available.}, number={1}, journal={PLANT GENOME}, author={Gonda, Itay and Ashrafi, Hamid and Lyon, David A. and Strickler, Susan R. and Hulse-Kemp, Amanda M. and Ma, Qiyue and Sun, Honghe and Stoffel, Kevin and Powell, Adrian F. and Futrell, Stephanie and et al.}, year={2019}, month={Mar} }
 @misc{young._ballington_ashrafi_2018, title={Single Nucleotide Polymorphic (SNP) Marker Discovery in a Diverse Panel of Blueberry (Vaccinium sp.) Species}, note={Abstract pp. 42}, author={Young., Elisheba and Ballington, James R. and Ashrafi, Hamid}, year={2018}, month={Jul} }
 @misc{yow_burchhardt_rollins_cubeta_ashrafi_2017, title={Differential Gene Expression Analysis of Blueberry Cultivar “Arlen” in Response to Mummy Berry (Monilinia vaccinii-corymbosi) Disease Infection}, author={Yow, Ashley G. and Burchhardt, Kathleen and Rollins, Jeffrey A. and Cubeta, Marc A. and Ashrafi, Hamid}, year={2017}, month={Sep} }
 @article{naegele_granke_fry_hill_ashrafi_van deynze_hausbeck_2017, title={Disease Resistance to Multiple Fungal and Oomycete Pathogens Evaluated Using a Recombinant Inbred Line Population in Pepper}, volume={107}, ISSN={["1943-7684"]}, DOI={10.1094/phyto-02-17-0040-r}, abstractNote={ Incorporating disease resistance into cultivars is a primary focus of modern breeding programs. Resistance to pathogens is often introgressed from landrace or wild individuals with poor fruit quality into commercial-quality cultivars. Sites of multiple disease resistance (MDR) are regions or “hot spots” of the genome with closely linked genes for resistance to different pathogens that could enable rapid incorporation of resistance. An F2-derived F6 recombinant inbred line population from a cross between ‘Criollo de Morelos 334’ (CMM334) and ‘Early Jalapeno’ was evaluated in inoculated fruit studies for susceptibility to oomycete and fungal pathogens: Phytophthora capsici, P. nicotianae, Botrytis cinerea, Fusarium oxysporum, F. solani, Sclerotinia sclerotiorum, Alternaria spp., Rhizopus oryzae, R. stolonifer, and Colletotrichum acutatum. All isolates evaluated were virulent on pepper. Significant differences in disease susceptibility were identified among lines for each of the pathogens evaluated. P. capsici was the most virulent pathogen, while R. oryzae and one Sclerotinia isolate were the least virulent. Quantitative trait loci associated with resistance were identified for Alternaria spp. and S. sclerotiorum. Positive correlations in disease incidence were detected between Alternaria spp. and F. oxysporum, F. solani, and C. acutatum, as well as between C. acutatum and Botrytis spp., F. oxysporum, F. solani, and P. capsici. No sites of MDR were identified for pathogens tested; however, positive correlations in disease incidence were detected among pathogens suggesting there may be genetic linkage among resistance genes in CM334 and Early Jalapeno. }, number={12}, journal={PHYTOPATHOLOGY}, publisher={Scientific Societies}, author={Naegele, R. P. and Granke, L. L. and Fry, J. and Hill, T. A. and Ashrafi, H. and Van Deynze, A. and Hausbeck, M. K.}, year={2017}, month={Dec}, pages={1522–1531} }
 @misc{yow_burchhardt_cubeta_ashrafi_2017, title={Identification of Candidate Genes for Mummy Berry Disease Resistance in Blueberry}, note={Poster 205}, author={Yow, Ashley G. and Burchhardt, Kathleen and Cubeta, Marc A. and Ashrafi, Hamid}, year={2017}, month={Mar} }
 @misc{yow_burchhardt_cubeta_ashrafi_2017, title={Identification of Candidate Genes for Mummy Berry Disease Resistance in Blueberry}, note={Poster P0244}, author={Yow, Ashley G. and Burchhardt, Kathleen and Cubeta, Marc A. and Ashrafi, Hamid}, year={2017}, month={Jan} }
 @article{hill_chunthawodtiporn_ashrafi_stoffel_weir_deynze_2017, title={Regions Underlying Population Structure and the Genomics of Organ Size Determination in }, volume={10}, DOI={10.3835/plantgenome2017.03.0026}, abstractNote={Fruits, as an important part of the human diet, have been under strong selection during domestication. In general, continued directed selection has led to varieties having larger fruit with greater shape variation and tremendous increases in fruit mass. Common cultivated peppers (Capsicum annuum L.) are found in a wide range of sizes and shapes. Analysis of genetic relatedness and population structure has shown that the large‐fruited, nonpungent types have reduced diversity and comprise a highly structured group. To explore this population structure, a statistical method for detecting fixation within subpopulations was applied to a set of 21 pungent and 19 nonpungent lines that represent the pepper breeding germplasm. We have identified 17 blocks within the pepper genome that are conserved among nonpungent large‐fruited varieties. To determine if these regions were fixed by selection on fruit size or pungency, quantitative trait loci (QTLs) from seven studies along with capsaicin biosynthesis genes and homologs of organ size regulatory genes were mapped onto the current pepper genome assembly. Of the 17 fixed regions, 14 overlapped with fruit size or shape QTLs. There were seven putative organ size regulators and seven capsaicin biosynthetic genes within these regions. This work defines genomic regions that underly structure within the nonpungent pepper germplasm and QTLs or genes that may have been selected for during the development of large‐fruited nonpungent pepper varieties.}, number={3}, journal={The Plant Genome}, publisher={Crop Science Society of America}, author={Hill, Theresa A. and Chunthawodtiporn, Jareerat and Ashrafi, Hamid and Stoffel, Kevin and Weir, Allyson and Deynze, Allen Van}, year={2017}, pages={0} }
 @article{hulse-kemp_ashrafi_plieske_lemm_stoffel_hill_luerssen_pethiyagoda_lawley_ganal_et al._2016, title={A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding}, volume={3}, ISSN={["2052-7276"]}, url={https://doi.org/10.1038/hortres.2016.36}, DOI={10.1038/hortres.2016.36}, abstractNote={The Capsicum genus (Pepper) is a part of the Solanacae family. It has been important in many cultures worldwide for its key nutritional components and uses as spices, medicines, ornamentals and vegetables. Worldwide population growth is associated with demand for more nutritionally valuable vegetables while contending with decreasing resources and available land. These conditions require increased efficiency in pepper breeding to deal with these imminent challenges. Through resequencing of inbred lines we have completed a valuable haplotype map (HapMap) for the pepper genome based on single-nucleotide polymorphisms (SNP). The identified SNPs were annotated and classified based on their gene annotation in the pepper draft genome sequence and phenotype of the sequenced inbred lines. A selection of one marker per gene model was utilized to create the PepperSNP16K array, which simultaneously genotyped 16 405 SNPs, of which 90.7% were found to be informative. A set of 84 inbred and hybrid lines and a mapping population of 90 interspecific F2 individuals were utilized to validate the array. Diversity analysis of the inbred lines shows a distinct separation of bell versus chile/hot pepper types and separates them into five distinct germplasm groups. The interspecific population created between Tabasco (C. frutescens chile type) and P4 (C. annuum blocky type) produced a linkage map with 5546 markers separated into 1361 bins on twelve 12 linkage groups representing 1392.3 cM. This publically available genotyping platform can be used to rapidly assess a large number of markers in a reproducible high-throughput manner for pepper. As a standardized tool for genetic analyses, the PepperSNP16K can be used worldwide to share findings and analyze QTLs for important traits leading to continued improvement of pepper for consumers. Data and information on the array are available through the Solanaceae Genomics Network.}, number={1}, journal={HORTICULTURE RESEARCH}, publisher={Springer Science and Business Media LLC}, author={Hulse-Kemp, Amanda M. and Ashrafi, Hamid and Plieske, Joerg and Lemm, Jana and Stoffel, Kevin and Hill, Theresa and Luerssen, Hartmut and Pethiyagoda, Charit L. and Lawley, Cindy T. and Ganal, Martin W. and et al.}, year={2016}, month={Jul} }
 @article{iorizzo_ellison_senalik_zeng_satapoomin_huang_bowman_iovene_sanseverino_cavagnaro_et al._2016, title={A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution}, volume={48}, ISSN={["1546-1718"]}, DOI={10.1038/ng.3565}, abstractNote={Philipp Simon, Massimo Iorizzo, Allen Van Deynze and colleagues report the high-quality assembly of the carrot genome, providing an important resource for crop improvement. They find a candidate gene that regulates carotenoid accumulation and gain further insights into asterid genome evolution, including characterization of two new polyploidization events. We report a high-quality chromosome-scale assembly and analysis of the carrot (Daucus carota) genome, the first sequenced genome to include a comparative evolutionary analysis among members of the euasterid II clade. We characterized two new polyploidization events, both occurring after the divergence of carrot from members of the Asterales order, clarifying the evolutionary scenario before and after radiation of the two main asterid clades. Large- and small-scale lineage-specific duplications have contributed to the expansion of gene families, including those with roles in flowering time, defense response, flavor, and pigment accumulation. We identified a candidate gene, DCAR_032551, that conditions carotenoid accumulation (Y) in carrot taproot and is coexpressed with several isoprenoid biosynthetic genes. The primary mechanism regulating carotenoid accumulation in carrot taproot is not at the biosynthetic level. We hypothesize that DCAR_032551 regulates upstream photosystem development and functional processes, including photomorphogenesis and root de-etiolation.}, number={6}, journal={NATURE GENETICS}, publisher={Springer Nature}, author={Iorizzo, Massimo and Ellison, Shelby and Senalik, Douglas and Zeng, Peng and Satapoomin, Pimchanok and Huang, Jiaying and Bowman, Megan and Iovene, Marina and Sanseverino, Walter and Cavagnaro, Pablo and et al.}, year={2016}, month={Jun}, pages={657-+} }
 @article{page_liechty_alexander_clemons_hulse-kemp_ashrafi_van deynze_stelly_udall_2016, title={DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton}, volume={12}, ISSN={["1553-7404"]}, url={http://europepmc.org/abstract/med/27168520}, DOI={10.1371/journal.pgen.1006012}, abstractNote={Allotetraploid cotton species are a vital source of spinnable fiber for textiles. The polyploid nature of the cotton genome raises many evolutionary questions as to the relationships between duplicated genomes. We describe the evolution of the cotton genome (SNPs and structural variants) with the greatly improved resolution of 34 deeply re-sequenced genomes. We also explore the evolution of homoeologous regions in the AT- and DT-genomes and especially the phenomenon of conversion between genomes. We did not find any compelling evidence for homoeologous conversion between genomes. These findings are very different from other recent reports of frequent conversion events between genomes. We also identified several distinct regions of the genome that have been introgressed between G. hirsutum and G. barbadense, which presumably resulted from breeding efforts targeting associated beneficial alleles. Finally, the genotypic data resulting from this study provides access to a wealth of diversity sorely needed in the narrow germplasm of cotton cultivars.}, number={5}, journal={PLOS GENETICS}, publisher={Public Library of Science (PLoS)}, author={Page, Justin T. and Liechty, Zach S. and Alexander, Rich H. and Clemons, Kimberly and Hulse-Kemp, Amanda M. and Ashrafi, Hamid and Van Deynze, Allen and Stelly, David M. and Udall, Joshua A.}, editor={Bomblies, KirstenEditor}, year={2016}, month={May} }
 @misc{yow_burchhardt_cubeta_ashrafi_2016, title={Identification of Differentially Expressed Genes for Mummy Berry (Monilinia vaccinii-corymbosi) Resistance in Blueberry}, note={Poster 120}, author={Yow, Ashley G. and Burchhardt, Kathleen and Cubeta, Marc A. and Ashrafi, Hamid}, year={2016}, month={Aug} }
 @misc{santiago_hulse-kemp_resende_neves_ashrafi_gill_stelly_2016, title={Major CNV Detection by Read-Depth Analysis Using Capture-Based GBS in Cotton}, note={Poster 0563}, author={Santiago, Luis M.De and Hulse-Kemp, Amanda M. and Resende, Marcio and Neves, Leandro G. and Ashrafi, Hamid and Gill, Clare A. and Stelly, David M.}, year={2016}, month={Jan} }
 @article{rinaldi_deynze_portis_rotino_toppino_hill_ashrafi_barchi_lanteri_2016, title={New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL}, volume={7}, DOI={10.3389/fpls.2016.01031}, abstractNote={Eggplant, pepper, and tomato are the most exploited berry-producing vegetables within the Solanaceae family. Their genomes differ in size, but each has 12 chromosomes which have undergone rearrangements causing a redistribution of loci. The genome sequences of all three species are available but differ in coverage, assembly quality and percentage of anchorage. Determining their syntenic relationship and QTL orthology will contribute to exploit genomic resources and genetic data for key agronomic traits. The syntenic analysis between tomato and pepper based on the alignment of 34,727 tomato CDS to the pepper genome sequence, identified 19,734 unique hits. The resulting synteny map confirmed the 14 inversions and 10 translocations previously documented, but also highlighted 3 new translocations and 4 major new inversions. Furthermore, each of the 12 chromosomes exhibited a number of rearrangements involving small regions of 0.5–0.7 Mbp. Due to high fragmentation of the publicly available eggplant genome sequence, physical localization of most eggplant QTL was not possible, thus, we compared the organization of the eggplant genetic map with the genome sequence of both tomato and pepper. The eggplant/tomato syntenic map confirmed all the 10 translocations but only 9 of the 14 known inversions; on the other hand, a newly detected inversion was recognized while another one was not confirmed. The eggplant/pepper syntenic map confirmed 10 translocations and 8 inversions already detected and suggested a putative new translocation. In order to perform the assessment of eggplant and pepper QTL orthology, the eggplant and pepper sequence-based markers located in their respective genetic map were aligned onto the pepper genome. GBrowse in pepper was used as reference platform for QTL positioning. A set of 151 pepper QTL were located as well as 212 eggplant QTL, including 76 major QTL (PVE ≥ 10%) affecting key agronomic traits. Most were confirmed to cluster in orthologous chromosomal regions. Our results highlight that the availability of genome sequences for an increasing number of crop species and the development of “ultra-dense” physical maps provide new and key tools for detailed syntenic and orthology studies between related plant species.}, journal={Frontiers in Plant Science}, publisher={Frontiers Media SA}, author={Rinaldi, Riccardo and Deynze, Allen Van and Portis, Ezio and Rotino, Giuseppe L. and Toppino, Laura and Hill, Theresa and Ashrafi, Hamid and Barchi, Lorenzo and Lanteri, Sergio}, year={2016}, month={Jul} }
 @misc{hill_afnan_ray_chaverri_ashrafi_deynze_bradford_2016, title={QTL Underlying Androgenic Haploid Production in Pepper (Capsicum annuum)}, note={Poster 0819}, author={Hill, Theresa and Afnan, Khalis and Ray, Tui and Chaverri, Alddo and Ashrafi, Hamid and Deynze, Allen Van and Bradford, Kent}, year={2016}, month={Jan} }
 @misc{fernandez_carter_yow_ashrafi_2016, title={Toward Deciphering of Mechanisms Underlying White Drupelet and Reversion Disorders of Blackberry}, note={Poster 0245}, author={Fernandez, Gina and Carter, Johanna R. and Yow, Ashley G. and Ashrafi, Hamid}, year={2016}, month={Jan} }
 @misc{yow_burchhardt_cubeta_ashrafi_2016, title={Using RNA-Seq for the Identification of Candidate Genes for Mummy Berry Disease Resistance in Blueberry}, author={Yow, Ashley G. and Burchhardt, Kathleen and Cubeta, Marc A. and Ashrafi, Hamid}, year={2016}, month={Sep} }
 @article{ashrafi_hulse-kemp_wang_yang_guan_jones_matvienko_mockaitis_chen_stelly_et al._2015, title={A Long-Read Transcriptome Assembly of Cotton (Gossypium hirsutum L.) and Intraspecific Single Nucleotide Polymorphism Discovery}, volume={8}, DOI={10.3835/plantgenome2014.10.0068}, abstractNote={Upland cotton (Gossypium hirsutum L.) has a narrow germplasm base, which constrains marker development and hampers intraspecific breeding. A pressing need exists for high‐throughput single nucleotide polymorphism (SNP) markers that can be readily applied to germplasm in breeding and breeding‐related research programs. Despite progress made in developing new sequencing technologies during the past decade, the cost of sequencing remains substantial when one is dealing with numerous samples and large genomes. Several strategies have been proposed to lower the cost of sequencing for multiple genotypes of large‐genome species like cotton, such as transcriptome sequencing and reduced‐representation DNA sequencing. This paper reports the development of a transcriptome assembly of the inbred line Texas Marker‐1 (TM‐1), a genetic standard for cotton, its usefulness as a reference for RNA sequencing (RNA‐seq)‐based SNP identification, and the availability of transcriptome sequences of four other cotton cultivars. An assembly of TM‐1 was made using Roche 454 transcriptome reads combined with an assembly of all available public expressed sequence tag (EST) sequences of TM‐1. The TM‐1 assembly consists of 72,450 contigs with a total of 70 million bp. Functional predictions of the transcripts were estimated by alignment to selected protein databases. Transcriptome sequences of the five lines, including TM‐1, were obtained using an Illumina Genome Analyzer‐II, and the short reads were mapped to the TM‐1 assembly to discover SNPs among the five lines. We identified >14,000 unfiltered allelic SNPs, of which ∼3,700 SNPs were retained for assay development after applying several rigorous filters. This paper reports availability of the reference transcriptome assembly and shows its utility in developing intraspecific SNP markers in upland cotton.}, number={2}, journal={The Plant Genome}, publisher={Crop Science Society of America}, author={Ashrafi, H. and Hulse-Kemp, A.M. and Wang, F. and Yang, S.S. and Guan, X. and Jones, Don C. and Matvienko, Marta and Mockaitis, Keithanne and Chen, Z. Jeffrey and Stelly, David M. and et al.}, year={2015}, pages={0} }
 @article{hulse-kemp_ashrafi_stoffel_zheng_saski_scheffler_fang_chen_van deynze_stelly_et al._2015, title={BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences, and Perspectives for Genetic Mapping}, volume={5}, url={http://europepmc.org/abstract/med/25858960}, DOI={10.1534/g3.115.017749}, abstractNote={Abstract
               A bacterial artificial chromosome library and BAC-end sequences for cultivated cotton (Gossypium hirsutum L.) have recently been developed. This report presents genome-wide single nucleotide polymorphism (SNP) mining utilizing resequencing data with BAC-end sequences as a reference by alignment of 12 G. hirsutum L. lines, one G. barbadense L. line, and one G. longicalyx Hutch and Lee line. A total of 132,262 intraspecific SNPs have been developed for G. hirsutum, whereas 223,138 and 470,631 interspecific SNPs have been developed for G. barbadense and G. longicalyx, respectively. Using a set of interspecific SNPs, 11 randomly selected and 77 SNPs that are putatively associated with the homeologous chromosome pair 12 and 26, we mapped 77 SNPs into two linkage groups representing these chromosomes, spanning a total of 236.2 cM in an interspecific F2 population (G. barbadense 3-79 × G. hirsutum TM-1). The mapping results validated the approach for reliably producing large numbers of both intraspecific and interspecific SNPs aligned to BAC-ends. This will allow for future construction of high-density integrated physical and genetic maps for cotton and other complex polyploid genomes. The methods developed will allow for future Gossypium resequencing data to be automatically genotyped for identified SNPs along the BAC-end sequence reference for anchoring sequence assemblies and comparative studies.}, number={6}, journal={G3&#58; Genes|Genomes|Genetics}, publisher={Genetics Society of America}, author={Hulse-Kemp, A.M. and Ashrafi, H. and Stoffel, K. and Zheng, X. and Saski, C.A. and Scheffler, B.E. and Fang, D.D. and Chen, Z.J. and Van Deynze, A. and Stelly, D.M. and et al.}, year={2015}, month={Apr}, pages={1095–1105} }
 @article{foolad_ashrafi_2015, title={Characterization of early blight resistance in a recombinant inbred line population of tomato: I. Heritability and trait correlations}, volume={7}, ISSN={13147668}, url={http://www.m-hikari.com/asb/asb2015/asb1-4-2015/41162.html}, DOI={10.12988/asb.2015.41162}, abstractNote={Most commercial cultivars of tomato (Solanum lycopersicum) are susceptible to early blight (EB), a devastating fungal (Alternaria solani and A. tomatophila) disease of tomato in the US and elsewhere. Common measures of disease control currently include sanitation, crop rotation and heavy use of fungicides. Use of resistant cultivars, however, is the most economically acceptable and environmentally sound approach to controlling EB disease in tomato. Sources of genetic resistance to EB have been identified within the related wild species of tomato, including S. habrochaites, S. peruvianum and S. pimpinellifolium. Characterization of genetic resistance to EB would facilitate transfer of resistance to elite breeding lines and hybrid cultivars of tomato. We used a recombinant inbred line (RIL) population of tomato, previously developed from a cross between S. pimpinellifolium accession LA 2093 and S. lycopersicum tomato breeding line NCEBR-1, to determine the inheritance of EB resistance as well as}, journal={Advanced Studies in Biology}, publisher={Hikari, Ltd.}, author={Foolad, Majid R. and Ashrafi, Hamid}, year={2015}, pages={131–148} }
 @article{ashrafi_foolad_2015, title={Characterization of early blight resistance in a recombinant inbred line population of tomato: II. Identification of QTLs and their co-localization with candidate resistance genes}, volume={7}, DOI={10.12988/asb.2015.41163}, abstractNote={Early blight (EB), caused by fungi Alternaria solani and A. tomatophila, is a major foliar disease of the tomato in many growing regions. Sources of resistance have been identified within the related wild species of tomato, including S. habrochaites, S. peruvianum and S. pimpinellifolium. Breeding for EB resistance via traditional protocols has been difficult due to the complexity of resistance and influence of several plant physiological and morphological characteristics on tomato response to EB. Identification of genetic markers associated with EB resistance and application of marker-assisted selection (MAS) would facilitate development of elite tomato breeding lines and hybrid cultivars with EB resistance. The goals of this study were to identify quantitative trait loci (QTLs) conferring resistance to EB in a resistant accession (LA 2093) of the tomato wild 150 Hamid Ashrafi and Majid R. Foolad species S. pimpinellifolium, and discover putative candidate resistance genes and expressed sequence tags (ESTs) that co-localize with the QTLs. Previously, a recombinant inbred line (RIL) population of tomato was developed from a cross between LA 2093 and S. lycopersicum breeding line NCEBR-1 and a genetic linkage map with 294 molecular markers spanning the 12 tomato chromosomes constructed. In the present study, the RIL population was grown and evaluated for EB resistance under field conditions in four successive years and generations (F7, F8, F9 and F10). Early blight disease severity, measured as the final % defoliation as well as the area under disease progress curve (AUDPC), was subjected to QTL analysis using simple interval mapping (SIM) and composite interval mapping (CIM). The SIM and CIM analyses resulted in identification of the same QTLs, though CIM detected QTLs with substantially more accuracy. Across the four generations, 5 major QTLs (LOD ≥ 2.4, P ≤ 0.001) were identified for EB resistance on tomato chromosomes 2 (2 QTLs), 5, 6 and 9. Three QTLs on chromosomes 2 and 6 were contributed from LA 2093 with individual phenotypic effects ranging from 8% to 16%, and two QTLs on chromosomes 5 and 9 were contributed from NCEBR-1 with individual phenotypic effects ranging from 7% to 18%. The QTLs on chromosomes 5 and 6 exhibited largest effects (10% to 18%) among all QTLs and were identified in three of the four generations. These two QTLs should be most useful for MAS and improvement of tomato EB resistance using LA 2093 and NCEBR-1 as resistant resources. The identified QTLs showed co-localization with several resistance genes and candidate ESTs, including Mi-1, ethylene response factor-5, lipoxygenase B, wound-induced protein-1, and phosphoenolpyruvate carboxylase kinase-2. With the genome sequence of tomato available, further investigation of these QTLs may lead to the identification of candidate genes underlying EB resistance in tomato.}, journal={Advanced Studies in Biology}, publisher={Hikari, Ltd.}, author={Ashrafi, Hamid and Foolad, Majid R.}, year={2015}, pages={149–168} }
 @article{hulse-kemp_lemm_plieske_ashrafi_buyyarapu_2015, title={Development of a 63K SNP array for Gossypium and high-density mapping of intra- and inter-specific populations of cotton (G. hirsutum L)}, volume={5}, journal={G3 Gene| Genomes| Genetics}, author={Hulse-Kemp, A. and Lemm, J. and Plieske, J. and Ashrafi, H. and Buyyarapu, R.}, year={2015}, pages={1187–1209} }
 @misc{yow_guo_ashrafi_2015, title={Full-Length Transcriptome Sequencing Using PacBio Sequencing in Blueberry}, author={Yow, Ashley G. and Guo, Weiwen and Ashrafi, Hamid}, year={2015}, month={Nov} }
 @article{hill_ashrafi_chin-wo_stoffel_truco_kozik_michelmore_van deynze_2015, title={Ultra-High Density, Transcript-Based Genetic Maps of Pepper Define Recombination in the Genome and Synteny Among Related Species}, volume={5}, ISSN={["2160-1836"]}, DOI={10.1534/g3.115.020040}, abstractNote={AbstractOur ability to assemble complex genomes and construct ultradense genetic maps now allows the determination of recombination rates, translocations, and the extent of genomic collinearity between populations, species, and genera. We developed two ultradense genetic linkage maps for pepper from single-position polymorphisms (SPPs) identified de novo with a 30,173 unigene pepper genotyping array. The Capsicum frutescens × C. annuum interspecific and the C. annuum intraspecific genetic maps were constructed comprising 16,167 and 3,878 unigene markers in 2108 and 783 genetic bins, respectively. Accuracies of marker groupings and orders are validated by the high degree of collinearity between the two maps. Marker density was sufficient to locate the chromosomal breakpoint resulting in the P1/P8 translocation between C. frutescens and C. annuum to a single bin. The two maps aligned to the pepper genome showed varying marker density along the chromosomes. There were extensive chromosomal regions with suppressed recombination and reduced intraspecific marker density. These regions corresponded to the pronounced nonrecombining pericentromeric regions in tomato, a related Solanaceous species. Similar to tomato, the extent of reduced recombination appears to be more pronounced in pepper than in other plant species. Alignment of maps with the tomato and potato genomes shows the presence of previously known translocations and a translocation event that was not observed in previous genetic maps of pepper.}, number={11}, journal={G3-GENES GENOMES GENETICS}, publisher={Genetics Society of America}, author={Hill, Theresa and Ashrafi, Hamid and Chin-Wo, Sebastian Reyes and Stoffel, Kevin and Truco, Maria-Jose and Kozik, Alexander and Michelmore, Richard and Van Deynze, Allen}, year={2015}, month={Nov}, pages={2341–2355} }
 @misc{ashrafi_2015, title={Using spinach to compare technologies for whole genome assemblies}, author={Ashrafi, H}, year={2015} }
 @article{rehrig_ashrafi_hill_prince_deynze_2014, title={Cosegregates with QTL for Resistance to in Pepper ()}, volume={7}, DOI={10.3835/plantgenome2014.03.0011}, abstractNote={A major problem for the pepper (Capsicum annuum) industry is the root rot disease caused by Phytophthora capsici (Pc), to which all commercial varieties suffer yield losses despite good management practices and available landraces with high levels of resistance. A high‐density map with 3887 markers was generated in a set of recombinant inbred lines (RIL) derived from the highly resistant Capsicum annuum accession Criollo de Morelos‐334 and Early Jalapeño. These lines have been systematically screened for Pc resistance against a set of isolates collected from Mexico, New Mexico, New Jersey, California, Michigan and Tennessee. Quantitative trait loci (QTL) associated with effective resistance across isolates have been identified and validated with SNP markers across additional segregating populations. By leveraging transcriptomic and genomic information, we describe CaDMR1, a homoserine kinase (HSK), as a candidate gene responsible for the major QTL on chromosome P5 for resistance to Pc. SNP markers for the resistant allele were validated to facilitate gene pyramiding schemes for recurrent selection in pepper.}, number={2}, journal={The Plant Genome}, publisher={Crop Science Society of America}, author={Rehrig, William Z. and Ashrafi, Hamid and Hill, Theresa and Prince, James and Deynze, Allen Van}, year={2014}, pages={0} }
 @misc{deynze_hill_ashrafi_kozik_chin-wo_rehrig_2014, title={Deciphering Resistance to Phytophthora capsici in Pepper}, note={Poster P0413}, author={Deynze, Allen Van and Hill, Theresa and Ashrafi, Hamid and Kozik, Alexander and Chin-Wo, Sebastian Reyes and Rehrig, William Zebulun}, year={2014}, month={Jan} }
 @article{foolad_sullenberger_ashrafi_2015, title={Detached-Leaflet Evaluation of Tomato Germplasm for Late Blight Resistance and Its Correspondence to Field and Greenhouse Screenings}, volume={99}, DOI={10.1094/pdis-08-14-0794-re}, abstractNote={ Breeding for disease resistance requires efficient techniques for screening large plant populations. Late blight (LB), caused by the oomycete Phytophthora infestans, is one of the most devastating diseases of tomato (Solanum lycopersicum) worldwide, and there is a great interest in developing cultivars with resistance to this pathogen. Screening for LB resistance is commonly conducted under field or greenhouse conditions using whole plants. In a previous study, we demonstrated correspondence between field and greenhouse screening of tomato for LB resistance. Here, we report the use of a detached-leaflet assay for such screening. Seventy-two genotypes from two tomato species, varying in degree of resistance and susceptibility to LB, were evaluated in two replicated experiments for response to LB in a detached-leaflet assay, and the results were compared with those previously obtained from field and greenhouse screening of the same genotypes. There were significant (P < 0.001) positive correlations between replications (average r = 0.75) and experiments (average r = 0.72), suggesting that the detached-leaflet experiments were consistent. Further, there were significant (P < 0.001) positive correlations between responses in the detached-leaflet assay and those from field (r = 0.82) and greenhouse screenings (r = 0.84), suggesting reliability of the detached-leaflet assay. The results indicate the utility of the detached-leaflet assay for evaluating tomato for LB resistance, which may facilitate screening of large breeding populations. }, number={5}, journal={Plant Disease}, publisher={Scientific Societies}, author={Foolad, Majid R. and Sullenberger, Matthew T. and Ashrafi, Hamid}, year={2015}, month={May}, pages={718–722} }
 @article{hulse-kemp_ashrafi_zheng_wang_hoegenauer_maeda_yang_stoffel_matvienko_clemons_et al._2014, title={Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts}, volume={15}, url={http://europepmc.org/abstract/med/25359292}, DOI={10.1186/1471-2164-15-945}, abstractNote={Cotton (Gossypium spp.) is the largest producer of natural fibers for textile and is an important crop worldwide. Crop production is comprised primarily of G. hirsutum L., an allotetraploid. However, elite cultivars express very small amounts of variation due to the species monophyletic origin, domestication and further bottlenecks due to selection. Conversely, wild cotton species harbor extensive genetic diversity of prospective utility to improve many beneficial agronomic traits, fiber characteristics, and resistance to disease and drought. Introgression of traits from wild species can provide a natural way to incorporate advantageous traits through breeding to generate higher-producing cotton cultivars and more sustainable production systems. Interspecific introgression efforts by conventional methods are very time-consuming and costly, but can be expedited using marker-assisted selection. Using transcriptome sequencing we have developed the first gene-associated single nucleotide polymorphism (SNP) markers for wild cotton species G. tomentosum, G. mustelinum, G. armourianum and G. longicalyx. Markers were also developed for a secondary cultivated species G. barbadense cv. 3–79. A total of 62,832 non-redundant SNP markers were developed from the five wild species which can be utilized for interspecific germplasm introgression into cultivated G. hirsutum and are directly associated with genes. Over 500 of the G. barbadense markers have been validated by whole-genome radiation hybrid mapping. Overall 1,060 SNPs from the five different species have been screened and shown to produce acceptable genotyping assays. This large set of 62,832 SNPs relative to cultivated G. hirsutum will allow for the first high-density mapping of genes from five wild species that affect traits of interest, including beneficial agronomic and fiber characteristics. Upon mapping, the markers can be utilized for marker-assisted introgression of new germplasm into cultivated cotton and in subsequent breeding of agronomically adapted types, including cultivar development.}, number={1}, journal={BMC Genomics}, publisher={Springer Nature}, author={Hulse-Kemp, Amanda M and Ashrafi, Hamid and Zheng, Xiuting and Wang, Fei and Hoegenauer, Kevin A and Maeda, Andrea BV and Yang, S Samuel and Stoffel, Kevin and Matvienko, Marta and Clemons, Kimberly and et al.}, year={2014}, pages={945} }
 @article{kim_park_yeom_kim_lee_lee_seo_choi_cheong_kim_et al._2014, title={Genome sequence of the hot pepper provides insights into the evolution of pungency in <i>Capsicum</i> species}, volume={46}, ISSN={1546-1718}, url={https://www.nature.com/articles/ng.2877}, DOI={10.1038/ng.2877}, abstractNote={Doil Choi and colleagues report the genome sequence of the hot pepper, Capsicum annuum, as well as the resequencing of two cultivated peppers and a wild species, Capsicum chinense. Comparative genomic analysis across Solanaceae provides insights into genome expansion, pungency, ripening and disease resistance in hot peppers. Hot pepper (Capsicum annuum), one of the oldest domesticated crops in the Americas, is the most widely grown spice crop in the world. We report whole-genome sequencing and assembly of the hot pepper (Mexican landrace of Capsicum annuum cv. CM334) at 186.6× coverage. We also report resequencing of two cultivated peppers and de novo sequencing of the wild species Capsicum chinense. The genome size of the hot pepper was approximately fourfold larger than that of its close relative tomato, and the genome showed an accumulation of Gypsy and Caulimoviridae family elements. Integrative genomic and transcriptomic analyses suggested that change in gene expression and neofunctionalization of capsaicin synthase have shaped capsaicinoid biosynthesis. We found differential molecular patterns of ripening regulators and ethylene synthesis in hot pepper and tomato. The reference genome will serve as a platform for improving the nutritional and medicinal values of Capsicum species.}, number={3}, journal={Nature Genetics}, publisher={Springer Nature}, author={Kim, Seungill and Park, Minkyu and Yeom, Seon-In and Kim, Yong-Min and Lee, Je Min and Lee, Hyun-Ah and Seo, Eunyoung and Choi, Jaeyoung and Cheong, Kyeongchae and Kim, Ki-Tae and et al.}, year={2014}, month={Mar}, pages={270–278} }
 @misc{deynze_stelly_ashrafi_hulse_jones_2014, title={Increasing Gossypium hirsutum Intraspecific SNPs via Genomic Sequencing}, note={Poster P0413}, author={Deynze, Allen Van and Stelly, David and Ashrafi, Hamid and Hulse, Amanda M. and Jones, Don C.}, year={2014}, month={Jan} }
 @misc{ashrafi_ohlson_sullenberger_stoffel_masoudi_deynze_foolad_2014, title={SNP marker discovery for tomato breeding using Genotyping-by-Sequencing (GBS)}, note={Abstract pp. 12-13}, author={Ashrafi, Hamid and Ohlson, Erik W. and Sullenberger, Matthew T. and Stoffel, Kevin and Masoudi, Mark and Deynze, Allen Van and Foolad, Majid}, year={2014}, month={Sep} }
 @article{truco_ashrafi_kozik_leeuwen_bowers_wo_stoffel_xu_hill_deynze_et al._2013, title={An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce}, volume={3}, DOI={10.1534/g3.112.004929}, abstractNote={Abstract
               We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa. The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species.}, number={4}, journal={G3&#58; Genes|Genomes|Genetics}, publisher={Genetics Society of America}, author={Truco, Maria José and Ashrafi, Hamid and Kozik, Alexander and Leeuwen, Hans and Bowers, John and Wo, Sebastian Reyes Chin and Stoffel, Kevin and Xu, Huaqin and Hill, Theresa and Deynze, Allen Van and et al.}, year={2013}, month={Mar}, pages={617–631} }
 @article{hill_ashrafi_reyes-chin-wo_yao_stoffel_truco_kozik_michelmore_deynze_2013, title={Characterization of Capsicum annuum Genetic Diversity and Population Structure Based on Parallel Polymorphism Discovery with a 30K Unigene Pepper GeneChip}, volume={8}, DOI={10.1371/journal.pone.0056200}, abstractNote={The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in Capsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs). Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP). Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens) detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA) and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and application of genome-wide transcript-based markers to assess genetic and genomic features among Capsicum annuum.}, number={2}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Hill, Theresa A. and Ashrafi, Hamid and Reyes-Chin-Wo, Sebastian and Yao, JiQiang and Stoffel, Kevin and Truco, Maria-Jose and Kozik, Alexander and Michelmore, Richard W. and Deynze, Allen Van}, editor={Zhang, JianweiEditor}, year={2013}, month={Feb}, pages={e56200} }
 @misc{hulse_hoegenauer_ashrafi_wang_stelly_deynze_hinze_yu_fang_pepper_et al._2013, title={Genome-wide SNP Development and Validation for Intraspecific SNPs in Upland Cotton}, note={Poster P0761}, author={Hulse, Amanda M. and Hoegenauer, Kevin A. and Ashrafi, Hamid and Wang, Fei and Stelly, David and Deynze, Allen Van and Hinze, Lori and Yu, John Z. and Fang, David and Pepper, Alan E. and et al.}, year={2013}, month={Jan} }
 @article{page_huynh_liechty_grupp_stelly_hulse_ashrafi_deynze_wendel_udall_2013, title={Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Re-sequencing}, volume={3}, DOI={10.1534/g3.113.007229}, abstractNote={Abstract
               Understanding the composition, evolution, and function of the Gossypium hirsutum (cotton) genome is complicated by the joint presence of two genomes in its nucleus (AT and DT genomes). These two genomes were derived from progenitor A-genome and D-genome diploids involved in ancestral allopolyploidization. To better understand the allopolyploid genome, we re-sequenced the genomes of extant diploid relatives that contain the A1 (Gossypium herbaceum), A2 (Gossypium arboreum), or D5 (Gossypium raimondii) genomes. We conducted a comparative analysis using deep re-sequencing of multiple accessions of each diploid species and identified 24 million SNPs between the A-diploid and D-diploid genomes. These analyses facilitated the construction of a robust index of conserved SNPs between the A-genomes and D-genomes at all detected polymorphic loci. This index is widely applicable for read mapping efforts of other diploid and allopolyploid Gossypium accessions. Further analysis also revealed locations of putative duplications and deletions in the A-genome relative to the D-genome reference sequence. The approximately 25,400 deleted regions included more than 50% deletion of 978 genes, including many involved with starch synthesis. In the polyploid genome, we also detected 1,472 conversion events between homoeologous chromosomes, including events that overlapped 113 genes. Continued characterization of the Gossypium genomes will further enhance our ability to manipulate fiber and agronomic production of cotton.}, number={10}, journal={G3&#58; Genes|Genomes|Genetics}, publisher={Genetics Society of America}, author={Page, Justin T. and Huynh, Mark D. and Liechty, Zach S. and Grupp, Kara and Stelly, David and Hulse, Amanda M. and Ashrafi, Hamid and Deynze, Allen Van and Wendel, Jonathan F. and Udall, Joshua A.}, year={2013}, month={Aug}, pages={1809–1818} }
 @article{naegele_ashrafi_hill_chin-wo_deynze_hausbeck_2014, title={QTL Mapping of Fruit Rot Resistance to the Plant Pathogen Phytophthora capsici in a Recombinant Inbred Line Capsicum annuum Population}, volume={104}, DOI={10.1094/phyto-05-13-0143-r}, abstractNote={ Phytophthora capsici is an important pepper (Capsicum annuum) pathogen causing fruit and root rot, and foliar blight in field and greenhouse production. Previously, an F6 recombinant inbred line population was evaluated for fruit rot susceptibility. Continuous variation among lines and partial and isolate-specific resistance were found. In this study, Phytophthora fruit rot resistance was mapped in the same F6 population between Criollo del Morelos 334 (CM334), a landrace from Mexico, and ‘Early Jalapeno’ using a high-density genetic map. Isolate-specific resistance was mapped independently in 63 of the lines evaluated and the two parents. Heritability of the resistance for each isolate at 3 and 5 days postinoculation (dpi) was high (h2 = 0.63 to 0.68 and 0.74 to 0.83, respectively). Significant additive and epistatic quantitative trait loci (QTL) were identified for resistance to isolates OP97 and 13709 (3 and 5 dpi) and 12889 (3 dpi only). Mapping of fruit traits showed potential linkage with few disease resistance QTL. The partial fruit rot resistance from CM334 suggests that this may not be an ideal source for fruit rot resistance in pepper. }, number={5}, journal={Phytopathology}, publisher={Scientific Societies}, author={Naegele, R. P. and Ashrafi, H. and Hill, T. A. and Chin-Wo, S. Reyes and Deynze, A. E. Van and Hausbeck, M. K.}, year={2014}, month={May}, pages={479–483} }
 @misc{zheng_wang_hoegenauer_quintana_ashrafi_stelly_bell_deynze_jones_nichols_2013, title={Resolving Tight Linkages Around Renlon by MAS for High-resolution Recombination in Chromosome-11}, note={Poster P4053}, author={Zheng, Xiuting and Wang, Fei and Hoegenauer, Kevin A. and Quintana, Jose and Ashrafi, Hamid and Stelly, David and Bell, Alois A. and Deynze, Allen Van and Jones, Don C. and Nichols, Robert L.}, year={2013}, month={Jan} }
 @article{deynze_hill_ashrafi_2013, title={Structural Genomics}, DOI={10.1201/b14578-10}, abstractNote={Traditionally, traits are divided into two categories: 1) qualitative or Mendelian traits, and 2) quantitative traits. Qualitative traits are those traits controlled by one or two (and rarely a few) genes, none of which is signifi cantly infl uenced by the environment. The effect of each gene is typically "large" and discernable in nature and overall, will result in discrete, observable, phenotypic classes. For qualitative traits, the individual's phenotype is usually a clear representation of its genotype. These traits are also referred to as simply inherited traits and the genetic discipline that focuses on these traits is known as Mendelian genetics. Traits such as seed color, seed shape, pod shape, pod color and petal color observed by Gregor Mendel among pea plants are good examples of such traits. These traits enabled Mendel to formulate the two basic laws of genetics: the law of segregation and the law of independent assortment. These two laws, formulated between 1856 and 1863, are still fundamental in predicting the mode of genetic inheritance of traits.}, journal={Genetics, Genomics, and Breeding of Tomato}, publisher={Science Publishers}, author={Deynze, Allen Van and Hill, Theresa and Ashrafi, Hamid}, year={2013}, month={Jan}, pages={327–344} }
 @misc{wang_hulse_hoegenauer_stelly_ashrafi_deynze_yu_2012, title={Collaborative Development of SNPs for Cotton Research, Introgression, MAS and Breeding. Genome-Wide Gossypium SNP Development and Validation}, url={http://www.cotton.org/beltwide/index.cfm?page=beltwide_overview}, author={Wang, Fei and Hulse, Amanda M. and Hoegenauer, Kevin and Stelly, David M. and Ashrafi, Hamid and Deynze, Allen Van and Yu, John Z.}, year={2012}, month={Jan} }
 @misc{ashrafi_2012, title={Comparison and evaluation of cotton SNPs developed by transcriptome, genome reduction on restriction site conservation and RAD-based sequencing}, author={Ashrafi, H.}, year={2012}, month={Oct} }
 @misc{hill_ashrafi_reyes-chin-wo_romero_kozik_deynze_2012, title={Comparisons of high-density EST-based maps in pepper species}, note={Poster P0479}, author={Hill, Theresa and Ashrafi, Hamid and Reyes-Chin-Wo, Sebastian and Romero, Marcelo Solano and Kozik, Alexander and Deynze, Allen Van}, year={2012}, month={Jan} }
 @article{ashrafi_hill_stoffel_kozik_yao_chin-wo_deynze_2012, title={De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes}, volume={13}, DOI={10.1186/1471-2164-13-571}, abstractNote={Molecular breeding of pepper (Capsicum spp.) can be accelerated by developing DNA markers associated with transcriptomes in breeding germplasm. Before the advent of next generation sequencing (NGS) technologies, the majority of sequencing data were generated by the Sanger sequencing method. By leveraging Sanger EST data, we have generated a wealth of genetic information for pepper including thousands of SNPs and Single Position Polymorphic (SPP) markers. To complement and enhance these resources, we applied NGS to three pepper genotypes: Maor, Early Jalapeño and Criollo de Morelos-334 (CM334) to identify SNPs and SSRs in the assembly of these three genotypes. Two pepper transcriptome assemblies were developed with different purposes. The first reference sequence, assembled by CAP3 software, comprises 31,196 contigs from >125,000 Sanger-EST sequences that were mainly derived from a Korean F1-hybrid line, Bukang. Overlapping probes were designed for 30,815 unigenes to construct a pepper Affymetrix GeneChip® microarray for whole genome analyses. In addition, custom Python scripts were used to identify 4,236 SNPs in contigs of the assembly. A total of 2,489 simple sequence repeats (SSRs) were identified from the assembly, and primers were designed for the SSRs. Annotation of contigs using Blast2GO software resulted in information for 60% of the unigenes in the assembly. The second transcriptome assembly was constructed from more than 200 million Illumina Genome Analyzer II reads (80–120 nt) using a combination of Velvet, CLC workbench and CAP3 software packages. BWA, SAMtools and in-house Perl scripts were used to identify SNPs among three pepper genotypes. The SNPs were filtered to be at least 50 bp from any intron-exon junctions as well as flanking SNPs. More than 22,000 high-quality putative SNPs were identified. Using the MISA software, 10,398 SSR markers were also identified within the Illumina transcriptome assembly and primers were designed for the identified markers. The assembly was annotated by Blast2GO and 14,740 (12%) of annotated contigs were associated with functional proteins. Before availability of pepper genome sequence, assembling transcriptomes of this economically important crop was required to generate thousands of high-quality molecular markers that could be used in breeding programs. In order to have a better understanding of the assembled sequences and to identify candidate genes underlying QTLs, we annotated the contigs of Sanger-EST and Illumina transcriptome assemblies. These and other information have been curated in a database that we have dedicated for pepper project.}, number={1}, journal={BMC Genomics}, publisher={Springer Nature}, author={Ashrafi, Hamid and Hill, Theresa and Stoffel, Kevin and Kozik, Alexander and Yao, JiQiang and Chin-Wo, Sebastian and Deynze, Allen Van}, year={2012}, pages={571} }
 @article{stoffel_leeuwen_kozik_caldwell_ashrafi_cui_tan_hill_reyes-chin-wo_truco_et al._2012, title={Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.)}, volume={13}, DOI={10.1186/1471-2164-13-185}, abstractNote={Abstract
          
            Background
            High-resolution genetic maps are needed in many crops to help characterize the genetic diversity that determines agriculturally important traits. Hybridization to microarrays to detect single feature polymorphisms is a powerful technique for marker discovery and genotyping because of its highly parallel nature. However, microarrays designed for gene expression analysis rarely provide sufficient gene coverage for optimal detection of nucleotide polymorphisms, which limits utility in species with low rates of polymorphism such as lettuce (Lactuca sativa).
          
          
            Results
            We developed a 6.5 million feature Affymetrix GeneChip® for efficient polymorphism discovery and genotyping, as well as for analysis of gene expression in lettuce. Probes on the microarray were designed from 26,809 unigenes from cultivated lettuce and an additional 8,819 unigenes from four related species (L. serriola, L. saligna, L. virosa and L. perennis). Where possible, probes were tiled with a 2 bp stagger, alternating on each DNA strand; providing an average of 187 probes covering approximately 600 bp for each of over 35,000 unigenes; resulting in up to 13 fold redundancy in coverage per nucleotide. We developed protocols for hybridization of genomic DNA to the GeneChip® and refined custom algorithms that utilized coverage from multiple, high quality probes to detect single position polymorphisms in 2 bp sliding windows across each unigene. This allowed us to detect greater than 18,000 polymorphisms between the parental lines of our core mapping population, as well as numerous polymorphisms between cultivated lettuce and wild species in the lettuce genepool. Using marker data from our diversity panel comprised of 52 accessions from the five species listed above, we were able to separate accessions by species using both phylogenetic and principal component analyses. Additionally, we estimated the diversity between different types of cultivated lettuce and distinguished morphological types.
          
          
            Conclusion
            By hybridizing genomic DNA to a custom oligonucleotide array designed for maximum gene coverage, we were able to identify polymorphisms using two approaches for pair-wise comparisons, as well as a highly parallel method that compared all 52 genotypes simultaneously.
          }, number={1}, journal={BMC Genomics}, publisher={Springer Nature}, author={Stoffel, Kevin and Leeuwen, Hans and Kozik, Alexander and Caldwell, David and Ashrafi, Hamid and Cui, Xinping and Tan, Xiaoping and Hill, Theresa and Reyes-Chin-Wo, Sebastian and Truco, Maria-Jose and et al.}, year={2012}, pages={185} }
 @misc{wang_hulse_hoegenauer_stelly_ashrafi_deynze_yu_2012, title={Genome-Wide Gossypium SNP Development and Validation}, url={http://www.cotton.org/beltwide/index.cfm?page=beltwide_overview}, author={Wang, Fei and Hulse, Amanda M. and Hoegenauer, Kevin and Stelly, David M. and Ashrafi, Hamid and Deynze, Allen Van and Yu, John}, year={2012}, month={Jan} }
 @misc{hulse_wang_hoegenauer_stelly_ashrafi_deynze_yu_chen_udall_jones_2012, title={Genome-wide SNP development and validation for allotetraploid Gossypium}, note={Poster P0199}, author={Hulse, Amanda M. and Wang, Fei and Hoegenauer, Kevin and Stelly, David M. and Ashrafi, Hamid and Deynze, Allen Van and Yu, John Z. and Chen, Jeffrey Z. and Udall, Joshua A. and Jones, Dan C.}, year={2012}, month={Jan} }
 @misc{ashrafi_yao_stoffel_reyes-chin-wo_hill_kozik_van deynze_2012, title={Genome-wide SNP discovery from de novo assemblies of pepper (Capsicum annuum) transcriptomes}, note={Poster P0480}, author={Ashrafi, Hamid and Yao, Jiqiang and Stoffel, Kevin and Reyes-Chin-Wo, Sebastian and Hill, Theresa and Kozik, Alexander and Van Deynze, Allen}, year={2012}, month={Jan} }
 @article{yarnes_ashrafi_reyes-chin-wo_hill_stoffel_deynze_2013, title={Identification of QTLs for capsaicinoids, fruit quality, and plant architecture-related traits in an interspecific Capsicum RIL population}, volume={56}, DOI={10.1139/gen-2012-0083}, abstractNote={ Quantitative trait loci (QTL) analyses in pepper are common for horticultural, disease resistance, and fruit quality traits; although none of the studies to date have used sequence-based markers associated with genes. In this study we measured plant architectural, phenological, and fruit quality traits in a pepper mapping population consisting of 92 recombinant inbred lines derived from a cross between Capsicum frutescens acc. 2814-6 and C. annuum var. NuMexRNAKY. Phenotypic measurements were correlated to loci in a high-density EST-based genetic map. In total, 96 QTL were identified for 38 traits, including 12 QTL associated with capsaicinoid levels. Twenty-one loci showed correlation among seemingly unrelated phenotypic categories, highlighting tight linkage or shared genetics between previously unassociated traits in pepper. }, number={1}, journal={Genome}, publisher={Canadian Science Publishing}, author={Yarnes, Shawn C. and Ashrafi, Hamid and Reyes-Chin-Wo, Sebastian and Hill, Theresa A. and Stoffel, Kevin M. and Deynze, Allen Van}, editor={Gulick, P.Editor}, year={2013}, month={Jan}, pages={61–74} }
 @article{paterson_wendel_gundlach_guo_jenkins_jin_llewellyn_showmaker_shu_udall_et al._2012, title={Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres}, volume={492}, ISSN={0028-0836 1476-4687}, url={http://dx.doi.org/10.1038/nature11798}, DOI={10.1038/nature11798}, abstractNote={The Gossypium genus is used to investigate emergent consequences of polyploidy in cotton species; comparative genomic analyses reveal a complex evolutionary history including interactions among subgenomes that result in genetic novelty in elite cottons and provide insight into the evolution of spinnable fibres. A phylogenetic and genomic study of plants of the cotton genus Gossypium provides insights into the role of polyploidy in the angiosperm evolution, and specifically, in the emergence of spinnable fibres in domesticated cottons. The authors show that an abrupt five- to sixfold ploidy increase about 60 million years ago, and allopolyploidy reuniting divergent genomes approximately 1–2 million years ago, conferred a roughly 30-fold duplication of ancestral flowering plant genes in the 'elite' cottons G. hirsutum and G. barbadense compared to their presumed progenitor G. raimondii. Polyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same environments1. Here we show that an abrupt five- to sixfold ploidy increase approximately 60 million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1–2 Myr ago2, conferred about 30–36-fold duplication of ancestral angiosperm (flowering plant) genes in elite cottons (Gossypium hirsutum and Gossypium barbadense), genetic complexity equalled only by Brassica3 among sequenced angiosperms. Nascent fibre evolution, before allopolyploidy, is elucidated by comparison of spinnable-fibred Gossypium herbaceum A and non-spinnable Gossypium longicalyx F genomes to one another and the outgroup D genome of non-spinnable Gossypium raimondii. The sequence of a G. hirsutum AtDt (in which ‘t’ indicates tetraploid) cultivar reveals many non-reciprocal DNA exchanges between subgenomes that may have contributed to phenotypic innovation and/or other emergent properties such as ecological adaptation by polyploids. Most DNA-level novelty in G. hirsutum recombines alleles from the D-genome progenitor native to its New World habitat and the Old World A-genome progenitor in which spinnable fibre evolved. Coordinated expression changes in proximal groups of functionally distinct genes, including a nuclear mitochondrial DNA block, may account for clusters of cotton-fibre quantitative trait loci affecting diverse traits. Opportunities abound for dissecting emergent properties of other polyploids, particularly angiosperms, by comparison to diploid progenitors and outgroups.}, number={7429}, journal={Nature}, publisher={Springer Science and Business Media LLC}, author={Paterson, Andrew H. and Wendel, Jonathan F. and Gundlach, Heidrun and Guo, Hui and Jenkins, Jerry and Jin, Dianchuan and Llewellyn, Danny and Showmaker, Kurtis C. and Shu, Shengqiang and Udall, Joshua and et al.}, year={2012}, month={Dec}, pages={423–427} }
 @article{merk_ashrafi_foolad_2012, title={Selective genotyping to identify late blight resistance genes in an accession of the tomato wild species Solanum pimpinellifolium}, volume={187}, DOI={10.1007/s10681-012-0729-6}, number={1}, journal={Euphytica}, publisher={Springer Nature}, author={Merk, Heather L. and Ashrafi, Hamid and Foolad, Majid R.}, year={2012}, month={Jun}, pages={63–75} }
 @article{powell_nguyen_hill_cheng_figueroa-balderas_aktas_ashrafi_pons_fernandez-munoz_vicente_et al._2012, title={Uniform ripening Encodes a Golden 2-like Transcription Factor Regulating Tomato Fruit Chloroplast Development}, volume={336}, DOI={10.1126/science.1222218}, abstractNote={Pretty or Sweet
          
            The grocery-store tomato that looks beautiful but tastes like tart cardboard arises from selection processes favoring phenotypes that make commercial production more reliable. Significant in that selection process was a mutation that reduced the mottled color variations of unripe green tomatoes, leaving them a uniform, pale, green.
            
              Powell
              et al.
            
            (p.
            1711
            ) analyzed the molecular biology of the mutation. The
            uniform ripening
            mutation turns out to disable a transcription factor called
            Golden 2-like
            (
            GLK2
            ).
            GLK2
            expression increases the fruit's photosynthetic capacity, resulting in higher sugar content.
          }, number={6089}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Powell, A. L. T. and Nguyen, C. V. and Hill, T. and Cheng, K. L. and Figueroa-Balderas, R. and Aktas, H. and Ashrafi, H. and Pons, C. and Fernandez-Munoz, R. and Vicente, A. and et al.}, year={2012}, month={Jun}, pages={1711–1715} }
 @misc{deynze_hill_yarnes_rehrig_chin-wo_ashrafi_adamchak_kozik_prince_2011, title={An Integrated approach to breeding resistance to Phytophthora capsici In Pepper}, note={Poster 450}, author={Deynze, Allen Van and Hill, Theresa A. and Yarnes, Shawn and Rehrig, William Z. and Chin-Wo, Sebastian Reyes and Ashrafi, Hamid and Adamchak, Raoul and Kozik, Alex and Prince, Jim}, year={2011}, month={Jan} }
 @misc{hill_ashrafi_chin-wo_romero_deynze_kozik_Aug. 6-10, 2011, title={Comparisons of high-density EST-based maps in pepper species}, author={Hill, Theresa and Ashrafi, Hamid and Chin-Wo, Sebastian Reyes- and Romero, Marcelo Solano and Deynze, Allen Van and Kozik, Alexander}, year={Aug. 6-10, 2011}, month={Aug. 6-10, 2011} }
 @article{iorizzo_senalik_grzebelus_bowman_cavagnaro_matvienko_ashrafi_deynze_simon_2011, title={De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity}, volume={12}, DOI={10.1186/1471-2164-12-389}, abstractNote={Abstract
          
            Background
            Among next generation sequence technologies, platforms such as Illumina and SOLiD produce short reads but with higher coverage and lower cost per sequenced nucleotide than 454 or Sanger. A challenge now is to develop efficient strategies to use short-read length platforms for de novo assembly and marker development. The scope of this study was to develop a de novo assembly of carrot ESTs from multiple genotypes using the Illumina platform, and to identify polymorphisms.
          
          
            Results
            A de novo assembly of transcriptome sequence from four genetic backgrounds produced 58,751 contigs and singletons. Over 50% of these assembled sequences were annotated allowing detection of transposable elements and new carrot anthocyanin genes. Presence of multiple genetic backgrounds in our assembly allowed the identification of 114 computationally polymorphic SSRs, and 20,058 SNPs at a depth of coverage of 20× or more. Polymorphisms were predominantly between inbred lines except for the cultivated x wild RIL pool which had high intra-sample polymorphism. About 90% and 88% of tested SSR and SNP primers amplified a product, of which 70% and 46%, respectively, were of the expected size. Out of verified SSR and SNP markers 84% and 82% were polymorphic. About 25% of SNPs genotyped were polymorphic in two diverse mapping populations.
          
          
            Conclusions
            This study confirmed the potential of short read platforms for de novo EST assembly and identification of genetic polymorphisms in carrot. In addition we produced the first large-scale transcriptome of carrot, a species lacking genomic resources.
          }, number={1}, journal={BMC Genomics}, publisher={Springer Nature}, author={Iorizzo, Massimo and Senalik, Douglas A and Grzebelus, Dariusz and Bowman, Megan and Cavagnaro, Pablo F and Matvienko, Marta and Ashrafi, Hamid and Deynze, Allen Van and Simon, Philipp W}, year={2011}, month={Aug} }
 @misc{deynze_hill_prince_yarnes_chunthawodtiporn_rehrig_reyes-chin-wo_ashrafi_kozik_2011, title={Development and Application of Genomic Tools in Pepper}, note={Workshop 531}, author={Deynze, Allen Van and Hill, Theresa and Prince, Jim and Yarnes, Shawn and Chunthawodtiporn, Jareerat and Rehrig, William and Reyes-Chin-wo, Sebastian and Ashrafi, Hamid and Kozik, Alexander}, year={2011}, month={Jan} }
 @article{ashrafi_kinkade_merk_foolad_2011, title={Identification of novel quantitative trait loci for increased lycopene content and other fruit quality traits in a tomato recombinant inbred line population}, volume={30}, DOI={10.1007/s11032-011-9643-1}, number={1}, journal={Molecular Breeding}, publisher={Springer Nature}, author={Ashrafi, Hamid and Kinkade, Matthew P. and Merk, Heather L. and Foolad, Majid R.}, year={2011}, month={Oct}, pages={549–567} }
 @misc{deynze_hill_prince_yarnes_chunthawodtiporn_rehrig_reyes-chin-wo_ashrafi_kozik_2011, title={The Genetic Map and Genome Sequencing of Lettuce}, note={Workshop 531}, author={Deynze, Allen Van and Hill, Theresa and Prince, Jim and Yarnes, Shawn and Chunthawodtiporn, Jareerat and Rehrig, William and Reyes-Chin-wo, Sebastian and Ashrafi, Hamid and Kozik, Alexander}, year={2011}, month={Jan} }
 @misc{hill_ashrafi_kozik_deynze_2010, title={Ultra High Density EST-Based Maps Reveal Genome Differences Between C. frutescence And C. annuum}, author={Hill, Theresa and Ashrafi, Hamid and Kozik, Alex and Deynze, Allen Van}, year={2010}, month={Jan} }
 @article{ashrafi_kinkade_foolad_2009, title={A new genetic linkage map of tomato based on a Solanum lycopersicum × S. pimpinellifolium RIL population displaying locations of candidate pathogen response genes}, volume={52}, DOI={10.1139/g09-065}, abstractNote={The narrow genetic base of the cultivated tomato, Solanum lycopersicum L., necessitates introgression of new variation from related species. Wild tomato species represent a rich source of useful genes and traits. Exploitation of genetic variation within wild species can be facilitated by the use of molecular markers and genetic maps. Recently we identified an accession (LA2093) within the red-fruited wild tomato species Solanum pimpinellifolium L. with exceptionally desirable characteristics, including disease resistance, abiotic stress tolerance, and high fruit lycopene content. To facilitate genetic characterization of such traits and their exploitation in tomato crop improvement, we developed a new recombinant inbred line (RIL) population from a cross between LA2093 and an advanced tomato breeding line (NCEBR-1). Furthermore, we constructed a medium-density molecular linkage map of this population using 294 polymorphic markers, including standard RFLPs, EST sequences (used as RFLP probes), CAPS, and SSRs. The map spanned 1091 cM of the tomato genome with an average marker spacing of 3.7 cM. A majority of the EST sequences, which were mainly chosen based on the putative role of their unigenes in disease resistance, defense-related response, or fruit quality, were mapped onto the tomato chromosomes for the first time. Co-localizations of relevant EST sequences with known disease resistance genes in tomato were also examined. This map will facilitate identification, genetic exploitation, and positional cloning of important genes or quantitative trait loci in LA2093. It also will allow the elucidation of the molecular mechanism(s) underlying important traits segregating in the RIL population. The map may further facilitate characterization and exploitation of genetic variation in other S. pimpinellifolium accessions as well as in modern cultivars of tomato.}, number={11}, journal={Genome}, publisher={Canadian Science Publishing}, author={Ashrafi, Hamid and Kinkade, Matthew and Foolad, Majid R.}, editor={Gulick, PatrickEditor}, year={2009}, month={Nov}, pages={935–956} }
 @misc{kozik_leeuwen_truco_stoffel_mchale_ashrafi_lavelle_cui_deynze_michelmore_2009, title={Construction of an Ultra High Density Genetic Map of Lettuce using an Affymetrix GeneChip}, note={Poster 68}, author={Kozik, Alexander and Leeuwen, Hans and Truco, Maria Jose and Stoffel, Kevin and McHale, Leah and Ashrafi, Hamid and Lavelle, Dean and Cui, Xinping and Deynze, Allen Van and Michelmore, Richard W.}, year={2009}, month={Jan} }
 @misc{leeuwen_stoffel_truco_ashrafi_cui_kozik_michelmore_deynze_2009, title={Development and Utilization of a High Density 6.6 Million Feature Affymetrix GeneChip for Marker Discovery and Genotyping in Lettuce}, note={Poster 69}, author={Leeuwen, Hans and Stoffel, Kevin and Truco, María José and Ashrafi, Hamid and Cui, Xinping and Kozik, Alexander and Michelmore, Richard W. and Deynze, Allen Van}, year={2009}, month={Jan} }
 @misc{leeuwen_stoffel_kozik_cui_ashrafi_mchale_lavelle_wong_chen_truco_et al._2009, title={High-Density Mapping of the Lettuce Genome with SFP Markers in over 15,000 Unigenes}, note={Workshop 126}, author={Leeuwen, Hans and Stoffel, Kevin and Kozik, Alexander and Cui, Xinping and Ashrafi, Hamid and McHale, Leah and Lavelle, Dean and Wong, Gene and Chen, Fallon and Truco, María José and et al.}, year={2009}, month={Jan} }
 @misc{ashrafi_hill_yao_leeuwen_michelmore_kozik_deynze_2009, title={The Application of a Whole Genome Pepper Array to Identify SFPs in a Diversity Panel}, note={Workshop 459}, author={Ashrafi, Hamid and Hill, Theresa and Yao, Jiqiang and Leeuwen, Hans and Michelmore, Richard and Kozik, Alexander and Deynze, Allen Van}, year={2009}, month={Jan} }
 @misc{hill_ashrafi_yao_jong_francis_kozik_deynze_2009, title={The Application of a Whole Genome Pepper Array to Solanaceae Crops}, author={Hill, Theresa and Ashrafi, Hamid and Yao, Jiqiang and Jong, Walter De and Francis, David and Kozik, Alex and Deynze, Allen Van}, year={2009}, month={Oct} }
 @article{sharma_zhang_niño-liu_ashrafi_foolad_2008, title={A Solanum lycopersicum × Solanum pimpinellifolium Linkage Map of Tomato Displaying Genomic Locations of R-Genes, RGAs, and Candidate Resistance/Defense-Response ESTs}, volume={2008}, DOI={10.1155/2008/926090}, abstractNote={We have identified an accession (LA2093) within the tomato wild species Solanum pimpinellifolium with many desirable characteristics, including biotic and abiotic stress tolerance and good fruit quality. To utilize the full genetic potential of LA2093 in tomato breeding, we have developed a linkage map based on anF2population of a cross between LA2093 and a tomato breeding line, using 115 RFLP, 94 EST, and 41 RGA markers. The map spanned 1002.4 cM of the 12 tomato chromosomes with an average marker distance of 4.0 cM. The length of the map and linear order of the markers were in good agreement with the published maps of tomato. The ESTs were chosen based on their sequence similarities with known resistance or defense-response genes, signal-transduction factors, transcriptional regulators, and genes encoding pathogenesis-related proteins. Locations of several ESTs and RGAs coincided with locations of several known tomato resistance genes and quantitative resistance loci (QRLs), suggesting that candidate-gene approach may be effective in identifying and mapping new R genes. This map will be useful for marker-assisted exploitation of desirable traits in LA2093 and otherS. pimpinellifoliumaccessions, and possibly for utilization of genetic variation withinS. lycopersicum.}, journal={International Journal of Plant Genomics}, publisher={Hindawi Limited}, author={Sharma, Arun and Zhang, Liping and Niño-Liu, David and Ashrafi, Hamid and Foolad, Majid R.}, year={2008}, pages={1–18} }
 @article{foolad_merk_ashrafi_2008, title={Genetics, Genomics and Breeding of Late Blight and Early Blight Resistance in Tomato}, volume={27}, DOI={10.1080/07352680802147353}, abstractNote={Late blight (LB), caused by the oomycete Phytophthora infestans, and early blight (EB), caused by the fungi Alternaria solani and A. tomatophila, are two common and destructive foliar diseases of the cultivated tomato (Solanum lycopersicum) and potato (Solanum tuberosum) in the United States and elsewhere in the world. While LB can infect and devastate tomato plants at any developmental stages, EB infection is usually associated with plant physiological maturity and fruit load where older senescing plants exhibit greater susceptibility and a heavy fruit set enhances the disease. At present, cultural practices and heavy use of fungicides are the most common measures for controlling LB and EB. Genetic resources for resistance have been identified for both diseases, largely within the tomato wild species, in particular the red-fruited species S. pimpinellifolium and the green-fruited species S. habrochaites. A few race-specific major resistance genes (e.g., Ph-1, Ph-2 and Ph-3) and several race-nonspecific resistance QTLs have been reported for LB. Ph-3 is a strong resistance gene and has been incorporated into many breeding lines of fresh market and processing tomato. However, new P. infestans isolates have been identified which overcome Ph-3 resistance. Recently, a new resistance gene (Ph-5) has been identified, which confers resistance to several pathogen isolates including those overcoming the previous resistance genes. Advanced breeding lines including Ph-5 alone and in combinations with Ph-2 and Ph-3 are being developed. Genetic controls of EB resistance have been studied and advanced breeding lines and cultivars with improved resistance have been developed through traditional breeding. Additionally, QTLs for EB resistance have been identified, which can be utilized for marker-assisted resistance breeding. Currently, new inbred lines and cultivars of tomato with good levels of EB resistance and competitive yield performance are being developed at the Pennsylvania State University. This review will focus on the current knowledge of both LB and EB with respect to the causal pathogens, host resistances, and genetics and breeding progresses.}, number={2}, journal={Critical Reviews in Plant Sciences}, publisher={Informa UK Limited}, author={Foolad, Majid R. and Merk, Heather L. and Ashrafi, Hamid}, year={2008}, month={Jun}, pages={75–107} }
 @misc{ashrafi_kinkade_foolad_2007, title={HPLC and spectrophotometer analyses of fruit carotenoids In a Lycopersicon esculentum X L. pimpinellifolium RIL population reveals several new QTLs for lycopene content}, note={Abstract published in the Proceedings for the meeting, p. 210}, author={Ashrafi, H. and Kinkade, M.R. and Foolad, M.R.}, year={2007}, month={Jan} }
 @misc{merk_ashrafi_kinkade_foolad_2007, title={Identification and molecular mapping of a new dominant gene (Ph5) conferring broad-spectrum resistance against tomato late blight}, note={Abstract published in the Proceedings for the meeting, p. 210}, author={Merk, H.L. and Ashrafi, H. and Kinkade, M.P. and Foolad, M.R.}, year={2007}, month={Jan} }
 @misc{ashrafi_lin_foolad_2006, title={A molecular linkage map of tomato based on RFLP markers and candidate disease-resistance/defense-response genes in an F7 RIL population}, author={Ashrafi, H. and Lin, G.Y. and Foolad, M.R.}, year={2006}, month={Mar} }
 @misc{ashrafi_lin_foolad_2006, title={Identification of QTLs for tomato early blight resistance in a RIL population of a cross between Lycopersicon esculentum and L. pimpinellifolium}, author={Ashrafi, H. and Lin, G.Y. and Foolad, M.R.}, year={2006}, month={Apr} }
 @inproceedings{foolad_merk_ashrafi_kinkade_Nov. 9-10, 2006, place={Fletcher, NC}, title={Identification of new sources of late blight resistance in tomato and mapping of a new resistance gene}, booktitle={Proc. 21st Annual Tomato Disease Workshop}, publisher={NC State University}, author={Foolad, M.R. and Merk, H.L. and Ashrafi, H. and Kinkade, M.P.}, year={Nov. 9-10, 2006}, month={Nov. 9-10, 2006} }
 @misc{ashrafi_sharma_kole_merk_lin_foolad_2006, title={Mapping of early blight resistance QTLs and candidate resistance genes in a RIL population of tomato}, note={Abstract published in the Proceedings for the meeting, p. 218}, author={Ashrafi, H. and Sharma, A. and Kole, C. and Merk, H. and Lin, G.Y. and Foolad, M.R.}, year={2006}, month={Jan} }
 @misc{merk_ashrafi_kole_kinkade_lin_foolad_2006, title={Toward identification and mapping of new late blight resistance genes in tomato}, note={Poster 0245}, author={Merk, H.L. and Ashrafi, H. and Kole, C. and Kinkade, M. and Lin, G.Y. and Foolad, M.R.}, year={2006}, month={Apr} }
 @article{ashrafi_sharma_niño-liu_zhang_foolad_2005, title={(13) Comparative Mapping of Early Blight Resistance QTLs and Candidate Resistance Genes in F2, F3, F4 and a RIL Population of Tomato}, volume={40}, number={4}, journal={HortScience}, author={Ashrafi, H. and Sharma, A. and Niño-Liu, D. and Zhang, L. and Foolad, M.}, year={2005}, pages={1040} }
 @misc{ashrafi_sharma_niño-liu_zhang_foolad_2005, title={Comparative mapping of early blight resistance QTLs and candidate resistance genes in F2, F3, F4 and a RIL population of Tomato}, author={Ashrafi, H. and Sharma, A. and Niño-Liu, D. and Zhang, L. and Foolad, M.R.}, year={2005} }
 @misc{ashrafi_sharma_niño-liu_foolad_2005, title={Genetic mapping of candidate resistance genes in tomato using an F2 and a RIL population of a Lycopersicon esculentum × L. pimpinellifolium cross}, author={Ashrafi, H. and Sharma, A. and Niño-Liu, D. and Foolad, M.R.}, year={2005}, month={Mar} }
 @article{foolad_sharma_ashrafi_lin_2005, title={Genetics and Breeding of Early Blight Resistance in Tomato}, volume={40}, journal={HortScience}, author={Foolad, M.R. and Sharma, A. and Ashrafi, H. and Lin, G.}, year={2005}, pages={1114–1114} }
 @misc{sharma_ashrafi_foolad_2005, title={Genetics of early blight resistance in tomato}, note={Abstract published in the Proceedings for the meeting, p. 191}, author={Sharma, A. and Ashrafi, H. and Foolad, M.R.}, year={2005}, month={Jan} }
 @misc{r._sharma_ashrafi_2004, title={Early blight resistance in tomato: genetics, breeding and accelerated breeding}, author={R., Foolad M. and Sharma, A. and Ashrafi, H.}, year={2004}, month={Jun} }
 @article{samaee_shobbar_ashrafi_hosseini-mazinani_sheidai_2003, title={MOLECULAR CHARACTERIZATION OF OLIVE GERMPLASM IN IRAN BY USE OF RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD) AND CORRELATION WITH PHENOTYPIC STUDIES: PRELIMINARY RESULTS}, volume={7}, DOI={10.17660/actahortic.2003.623.18}, abstractNote={ISHS XXVI International Horticultural Congress: Plant Genetic Resources, The Fabric of Horticultures Future MOLECULAR CHARACTERIZATION OF OLIVE GERMPLASM IN IRAN BY USE OF RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD) AND CORRELATION WITH PHENOTYPIC STUDIES: PRELIMINARY RESULTS}, number={623}, journal={Acta Horticulturae}, publisher={International Society for Horticultural Science (ISHS)}, author={Samaee, S.M. and Shobbar, Z.S. and Ashrafi, H. and Hosseini-Mazinani, M. and Sheidai, M.}, year={2003}, month={Jul}, pages={169–175} }