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Genomic Variation in 3,010 Diverse Accessions of Asian Cultivated Rice


Asian cultivated rice (Oryza sativa L.) is grown worldwide as staple food of half of the world. By the year 2035, an additional 112 million metric tons of rice must be produced with less land and water under more fluctuating climates, requiring future rice cultivars with higher yielding and resilient to multiple abiotic and biotic stresses. The foundation to continuous improvement of rice is the rich genetic diversity within its population and wild relatives.

Recently, a research team led by Dr. Zhikang Li from Institute of Crop Sciences of Chinese Academy of Agricultural Sciences (CAAS), has analyzed genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project, which was participated by 16 universities and institutes from China and abroad as well.

Analyses of 3,010 rice genomes (3k RG) defined the population genomic organization of rice with respect to SNPs, large structural variations (SVs) and gene presence-absence variations (PAVs) of a rice core germplasm collection. Over 27 million SNPs and more than 2.4 million small indels were identified. Population structure analysis discovered unreported subpopulations with clear geographic origins with four subpopulations of Xian/Indica (East Asian, South Asian, South-East Asian, and one of diverse origins) and three subpopulations of Geng/Japonica (temperate from Eastern Asia, subtropical from continental South-Eastern Asia and tropical from archipelagic South-Eastern Asia). Genome-wide association studies for three highly-heritable traits revealed both novel and already known associations, demonstrating the utility of the 3k Rice panel for gene-trait association discovery. We observed a significant (p-value <10-12) reduction of nucleotide diversity near agronomically important genes. Many SVs (>100bp) are present in rice genomes, most of which are relatively translocations and small deletions. Sequence differences caused by SVs reach ~20Mbp within accessions of the same major group and ~60Mbp between accessions from different major group. With the discovery of over 10,000 novel full-length protein-coding genes, the rice pan-genome consists of ~59% core and ~41% distributed genes. On average, ~4,000 genes showed presence/absence variation between two accessions of the same major group while >6,000 differ between accessions from distinct major groups. Complex patterns of introgression in domestication genes are consistent with multiple modes of domestication. The public availability of all data generated from our deep analyses of the 3k RG is expected to contribute significantly to the current global efforts on rice functional genomic research and to future improvement of this important crop.

This study was supported by the 863 Program (Grant No.: 2014AA10A601) and National Key R&D Program (Grant No.: 2016YFD0100904) from the Chinese Ministry of Science & Technology, Bill & Melinda Gates Foundation Project (Grant No.: OPP1130530), the Agricultural Science and Technology Innovation Program Cooperation and Innovation Mission (Grant No.: CAAS-ZDXT201800), CAAS Innovative Team Award, International S&T Cooperation Program of China (Grant No.: 2012DFB32280), Shenzhen Peacock Plan, National Key Technology Support Program (Grant No.: 2015BAD01B02), Fundamental Research Funds for Central Non- Profit of CAAS (Grant No.: Y2017CG21) and National Natural Science Foundation of China (Grant No.: 31501291, 61472246 and 61272250).

By Wang Wensheng