IC4R002-GWAS-2011-21915109

Project Title

Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa

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 of rice. Here we show the results of a genome-wide association study 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 cross-population-based mapping strategies, we identifi ed dozens of common variants infl uencing numerous complex traits. Signifi cant heterogeneity was observed in the genetic architecture associated with subpopulation structure and response to environment. This work establishes an open-source translational research platform for genome-wide association studies in rice that directly links molecular variation in genes and metabolic pathways with the germplasm resources needed to accelerate varietal development and crop improvement.

The Rice Diversity Panel consists of 413 Asian rice ( O. sativa ) cultivars, including many landraces, which originated from 82 countries, representing all the major rice-growing regions of the world. The panel contains 87 indica , 57 aus , 96 temperate japonica , 97 tropical japonica , 14 groupV/aromatic, and 62 highly admixed accessions. All accessions were purifi ed for two generations(single seed descent) before DNA extraction. In all, 20 of these 413 accessions were purifi ed as part of the Oryza SNP project. Six cultivars (Azucena, Moroberekan, Nipponbare, Dom-Sofi d, IR64, M-202) were purifi ed separately, once by Ali et al. and once as part of the Oryza SNP panel. Further information for each accession(accession name, accession number, country of origin and subpopulation ancestry based on PCA) is given in Supplementary Data 1 .

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
Department of Genetics, Stanford University, Stanford, California 94305, USA
Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14850, USA
USDA ARS,Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160, USA
Rice Research and Extension Center, University of Arkansas, Stuttgart, Arkansas 72160, USA
Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 3UU, UK
Department of Soil Science,Bangladesh Agricultural University, Mymensingh 2202, Bangladesh. Correspondence and requests for materials should be addressed to S.R.M.

(srm4@cornell.edu)