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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #348514

Research Project: Genomic Approaches and Genetic Resources for Improving Rice Yield and Grain Quality

Location: Dale Bumpers National Rice Research Center

Title: Association analysis using USDA diverse rice (Oryza sativa L.) germplasm collections to identify loci influencing grain quality traits

Author
item Edwards, Jeremy
item Huggins, Trevis
item Chen, Ming-hsuan
item Jackson, Aaron
item Mcclung, Anna
item Mcclung, Anna

Submitted to: Plant and Animal Genome
Publication Type: Abstract Only
Publication Acceptance Date: 10/27/2017
Publication Date: 1/18/2018
Citation: Edwards, J., Huggins, T.D., Chen, M., Jackson, A.K., McClung, A.M. 2018. Association analysis using USDA diverse rice (Oryza sativa L.) germplasm collections to identify loci influencing grain quality traits. Plant and Animal Genome Conference XXVI Proceedings. P0913.

Interpretive Summary:

Technical Abstract: he USDA rice (Oryza sativa L.) core subset (RCS) was assembled to represent the genetic diversity of the entire USDA-ARS National Small Grains Collection and consists of 1,794 accessions from 114 countries. The USDA rice mini-core (MC) is a subset of 217 accessions from the RCS and was selected to maximize genotypic, phenotypic and geographical diversity in a panel with a more manageable size for phenotyping and genotyping experiments. Recently, next generation resequencing data have become available for the MC accessions and high density fixed array SNP data have become available for 189 RCS accessions not included in the MC. In the current genome wide association study (GWAS), we use the new high density genotypic data along with previously reported and new phenotype data for grain traits, including grain dimensions, apparent amylose content (AAC), alkali spreading value (ASV, an indicator of gelatinization temperature), protein content, chalk percent, and agronomic traits that may influence grain quality, including plant height, and days to heading. The results identified several known starch genes, e.g., Waxy gene (granule bound starch synthase 1 (GBSS1)), along with 11 novel loci for grain starch traits and 7 for grain chalk. Many loci were significantly associated with multiple grain quality traits suggesting mediated pleiotropic effects. Based on these results, molecular markers will be designed and deployed for use in marker assisted selection to produce new rice varieties with high grain quality.