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United States Department of Agriculture

Agricultural Research Service

Research Project: RESEARCH, ACQUISITION, MANAGEMENT, AND DOCUMENTATION OF PLANT GENETIC RESOURCES

Location: Plant Germplasm Introduction and Testing

Title: Genetic diversity, population structure and genome-wide marker-trait association analysis of the USDA pea (Pisum sativum L.) core collection

Authors
item Kwon, Soon
item Brown, Allan -
item Hu, Jinguo
item McGee, Rebecca
item Watt, Chasity -
item Kisha, Theodore
item Timmerman-Vaughan, Gail -
item Grusak, Michael
item Mcphee, Kevin -
item Coyne, Clarice

Submitted to: Genes and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 6, 2012
Publication Date: May 20, 2012
Citation: Kwon, S.J., Brown, A.F., Hu, J., Mcgee, R.J., Watt, C., Kisha, T.J., Timmerman-Vaughan, G., Grusak, M.A., Mcphee, K., Coyne, C.J. 2012. Genetic diversity, population structure and genome-wide marker-trait association analysis of the USDA pea (Pisum sativum L.) core collection. Genes and Genomics. 10.1007/s13258-011-0213-z.

Interpretive Summary: In this study, the USDA pea core collection was analyzed to unravel marker-traits association to generate useful information for pea improvement. This core collection, containing 285 accessions with diverse phenotypic and geographic origins, was characterized with 137 DNA-based markers of different types and evaluated for twelve seed nutrient concentrations, six disease/pest resistance scores, and 31 morphological/agronomic traits. We investigated the genetic diversity and the population structure using 137 polymorphic DNA markers and analyzed associations between individual markers and each of the 49 quantitative/qualitative traits. Fifteen pairs of associations were at the significant levels of P= 0.01 when tested using all three different statistical models. This is the first report of genetic structure and association study of a global pea core collection. The reported information of marker-traits associations is useful to breeders to implement marker-assisted selection, which will expedite the process of breeding superior pea cultivars.

Technical Abstract: Genetic diversity, population structure and genome-wide marker-trait association analysis was conducted for the USDA pea (Pisum sativum L.) core collection. The core collection contained 285 accessions with diverse phenotypes and geographic origins. The 137 DNA markers included 102 polymorphic fragments amplified by 15 microsatellite primer pairs, 36 RAPD loci and one SCAR (sequence characterized amplified region) marker. The 49 phenotypic traits fall into the categories of seed macro- and micro-nutrients, disease resistance, agronomic traits and seed characteristics. Genetic diversity, population structure and marker-trait association were analyzed with the software packages PowerMarker, STUCTURE and TASSEL, respectively. A great amount of variation was revealed by the DNA markers at the molecular level. Identified were three sub-populations that constituted 56.1%, 13.0% and 30.9%, respectively, of the USDA Pisum core collection. The first sub-population is comprised of all cultivated pea varieties and landraces; the second of wild P. sativum ssp. elatius and abyssinicum and the accessions from the Asian highland (Afghanistan, India, Pakistan, China and Nepal); while the third is an admixture containing alleles from the first and second sub-populations. This structure was achieved using a stringent cutoff point of 15% admixture (q-value 85%) of the collection. Significant marker-trait associations were identified among certain markers with eight mineral nutrient concentrations in seed and other important phenotypic traits. Fifteen pairs of associations were at the significant levels of P= 0.01 when tested using the three statistical models. These markers will be useful in marker-assisted selection to breed pea cultivars with desirable agronomic traits and end-user qualities.

Last Modified: 7/25/2014
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