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Title: A community resource for exploring and utilizing genetic diversity in the USDA Pea Single Plant Plus Collection

Author
item HOLDSWORTH, WILLIAM - Cornell University
item GAZAVE, ELODIE - Cornell University
item CHENG, PENG - University Of Missouri
item MYERS, JAMES - Oregon State University
item GORE, MICHAEL - Cornell University
item Coyne, Clarice - Clare
item McGee, Rebecca
item MAZOUREK, MICHAEL - Cornell University

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/6/2017
Publication Date: 4/8/2017
Citation: Holdsworth, W.L., Gazave, E., Cheng, P., Myers, J.R., Gore, M.A., Coyne, C.J., McGee, R.J., Mazourek, M. 2017. A community resource for exploring and utilizing genetic diversity in the USDA Pea Single Plant Plus Collection. Horticulture Research. doi: 10.1038/hortres.2017.17.

Interpretive Summary: Pea (Pisum sativum L.) is a globally important food, feed, and cover crop in temperate environments. In 2013, green and dry peas had a worldwide production of 17.4 and 11.5 MMT, respectively, collectively making pea the fourth largest legume crop after soybean, groundnut, and common bean. As a rotation or cover crop, pea can fix nitrogen at levels sufficient to produce subsequent vegetable and cereal crops with reduced application of additional fertilizers. Plant breeding is improving yields and disease resistances in all market classes of pea. The USDA core collection represents a valuable source of traits for pea breeding programs. Collectively, the genetic bottleneck associated with pea improvement through breeding is not as severe as in some crops and much diversity has been retained, presumably because alleles critical for different end-uses and growing environments are maintained in their respective breeding programs. Tthis research used DNA sequencing to generate a publicly available, high-density marker data set for the USDA core collection for breeders and pea researchers to use for discovery of genes associated with needed trait improvement like yield and plant disease resistances.

Technical Abstract: Globally, pea (Pisum sativum L.) is an important temperate legume crop for food, feed, and fodder, and many breeding programs exist to develop cultivars adapted to these end uses. In order to conserve genetic diversity useful to researchers, large pea collections have been constructed by numerous national institutions. To this end, the United States Department of Agriculture Pisum Diversity Collection consists of 431 pea accessions selected to represent global morphological, geographic, and taxonomic diversity within the Pisum genus. To enhance the value of this collection for trait mapping and genomics-assisted breeding, detailed genetic characterization is needed. In this study, genotyping-by-sequencing'a cost-effective method for de novo SNP marker discovery'was used to comprehensively analyze the UPDC, resulting in 66 591 high-quality SNPs. This data allowed us to identify accessions divergent from mainstream breeding germplasm that could serve as sources of novel, favorable alleles. In particular, a group of peas from Central Asia appear as diverse as a sister species, P. fulvum, and subspecies, P. sativum subsp. elatius. These SNP data can be paired with existing phenotype data for trait mapping; as proof-of-concept, the A gene controlling flower color was localized to its previously identified position. SNP data were also used to define a smaller core collection of 108 accessions with similar levels of genetic diversity as the entire UPDC, resulting in a smaller germplasm set for research screening and evaluation under limited resources. SNP data are publicly available to serve as a community resource to inform diverse pea breeding and genetics programs.