ARS | Publication request: Genome-wide association mapping reveals rich genetic architecture of complex traits in Oryza sativa

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 2, 2011
Publication Date: September 13, 2011
Citation: Zhao, K., Tung, C., Eizenga, G.C., Wright, M.H., Ali, M., Price, A., Norton, G., Islam, R.M., Reynolds, A., Mezey, J., McClung, A.M., Bustamante, C.D., Mccouch, S.R. 2011. Genome-wide association mapping reveals rich genetic architecture of complex traits in Oryza sativa. Nature Communications. Available: DOI: 10.1038/ncomms1467.

Interpretive Summary: Domesticated Asian rice, Oryza sativa, is a cultivated grain crop that feeds over half of the world’s population. Understanding of the genetics behind the diverse agronomic, morphological, grain and stress resistance traits observed in rice cultivars can be the basis for improving yield, quality and sustainability. A set of 413 different rice cultivars, originating from 82 different countries, was phenotyped for 34 of these diverse phenotypic traits and genotyped with 44,100 DNA markers, called single nucleotide polymorphism markers. Using mathematical models, DNA markers were identified that were associated with the 34 agronomic, morphological, grain and stress resistance traits evaluated. Knowing where the genes controlling these traits of agronomic importance are located in the rice genome is the first step to identifying the biochemical pathways controlling these traits and subsequently accelerating rice varietal improvement.

Technical Abstract: Domesticated Asian rice, Oryza sativa, is a cultivated, inbreeding species that feeds over half of the world’s population. Understanding the genetic basis of diverse physiological, developmental, and morphological traits provides the basis for improving yield, quality and sustainability. Here, we present a genome-wide association study (GWAS) based on genotyping 44,100 SNP variants across 413 diverse accessions of O. sativa collected from 82 countries that were systematically phenotyped for 34 traits. Using novel cross-population-based mapping strategies, we identified dozens of common variants influencing numerous complex traits, revealing significant heterogeneity in the genetic architecture associated with subpopulation structure and response to environment. This work demonstrates the power of GWAS to dissect natural variation in rice and establishes an open-source translational research platform that directly links molecular variation in genes and metabolic pathways with the germplasm resources needed to accelerate varietal development and crop improvement.