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Genetic Variation and Association Mapping of Protein Concentration in Brown Rice Using a Diverse Rice Germplasm Collection

Rolfe J. Bryant, Aaron K. Jackson, Kathleen M. Yeater, Wengui G. Yan, Anna M. McClung, Robert G. Fjellstrom
Cereal Chemistry 2013 v.90 no.5 pp. 445-452
USDA, ancestry, brown rice, chromosomes, cultivars, endosperm, genes, genetic markers, genetic variation, germplasm, germplasm conservation, proteins, provenance, quantitative trait loci, Eastern European region, United States
Protein is the second most abundant constituent in the rice grain next to starch. Association analysis for protein concentration in brown rice was performed using a “mini-core” collection, which represents the germplasm diversity found in the USDA rice world collection. Protein concentration was determined in replicated trials conducted in two southern U.S. locations, and association mapping was performed by using 157 genomewide DNA markers. Protein concentration ranged from 5.4 to 11.9% among the 202 accessions. Protein variation owing to accession and accession × location interaction were highly significant. Ample variation was seen within each subpopulation by ancestry, as well as within the 14 geographic regions where the accessions originated. Accessions from Eastern Europe had the highest level of protein. Ten markers on eight chromosomes were significantly associated with protein concentration. Five of these markers occurred near known protein precursor genes or quantitative trait loci, and the other five markers were novel for the association with protein concentration in rice. The germplasm and genetic markers identified in this study will assist breeders in developing cultivars tailored for applications requiring specific protein concentration in the rice grain. The research results contribute to the potential discovery of novel rice storage protein pathways in the endosperm.