Genomic variation in 3,010 diverse accessions of Asian cultivated rice

Abstract

Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with the five major groups previously recognized, but also suggest several unreported subpopulations that correlate with geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 million small indels and over 90,000 structural variations that contribute to within- and between-population variation. Using pan-genome analyses, we identified more than 10,000 novel full-length protein-coding genes and a high number of presence–absence variations. The complex patterns of introgression observed in domestication genes are consistent with multiple independent rice domestication events. The public availability of data from the 3,000 Rice Genomes Project provides a resource for rice genomics research and breeding. Analyses of genetic variation and population structure based on over 3,000 cultivated rice (Oryza sativa) genomes reveal subpopulations that correlate with geographic location and patterns of introgression consistent with multiple rice domestication events.

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Affiliated Institutions

• Agricultural Genomics Institute at Shenzhen CN
• Chinese Academy of Sciences CN
• University of Arizona US
• China Agricultural University CN
• Institute of Crop Sciences CN
• BGI Genomics
• Institute of Genetics and Developmental Biology CN
• Joint Genome Institute US
• BGI Group (China) CN
• Centre de Coopération Internationale en Recherche Agronomique pour le Développement FR
• Genetic Improvement and Adaptation of Mediterranean and Tropical Plants FR
• Chinese Academy of Agricultural Sciences CN
• Shanghai Center For Bioinformation Technology CN
• International Rice Research Institute PH
• Shanghai Jiao Tong University CN

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