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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.

SUBMITTER: Wang W

PROVIDER: S-EPMC6784863 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

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

Wang Wensheng W Mauleon Ramil R Hu Zhiqiang Z Chebotarov Dmytro D Tai Shuaishuai S Wu Zhichao Z Li Min M Zheng Tianqing T Fuentes Roven Rommel RR Zhang Fan F Mansueto Locedie L Copetti Dario D Sanciangco Millicent M Palis Kevin Christian KC Xu Jianlong J Sun Chen C Fu Binying B Zhang Hongliang H Gao Yongming Y Zhao Xiuqin X Shen Fei F Cui Xiao X Yu Hong H Li Zichao Z Chen Miaolin M Detras Jeffrey J Zhou Yongli Y Zhang Xinyuan X Zhao Yue Y Kudrna Dave D Wang Chunchao C Li Rui R Jia Ben B Lu Jinyuan J He Xianchang X Dong Zhaotong Z Xu Jiabao J Li Yanhong Y Wang Miao M Shi Jianxin J Li Jing J Zhang Dabing D Lee Seunghee S Hu Wushu W Poliakov Alexander A Dubchak Inna I Ulat Victor Jun VJ Borja Frances Nikki FN Mendoza John Robert JR Ali Jauhar J Li Jing J Gao Qiang Q Niu Yongchao Y Yue Zhen Z Naredo Ma Elizabeth B MEB Talag Jayson J Wang Xueqiang X Li Jinjie J Fang Xiaodong X Yin Ye Y Glaszmann Jean-Christophe JC Zhang Jianwei J Li Jiayang J Hamilton Ruaraidh Sackville RS Wing Rod A RA Ruan Jue J Zhang Gengyun G Wei Chaochun C Alexandrov Nickolai N McNally Kenneth L KL Li Zhikang Z Leung Hei H

Nature 20180425 7703

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 betw ...[more]

PMID: 29695866

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Project description:BackgroundRice is one of the most important food crops in the world. With increasing world demand for food crops, there is an urgent need to develop new cultivars that have enhanced performance with regard to yield, disease resistance, and so on. Wild rice is expected to provide useful genetic resources that could improve the present cultivated species. However, the quantity and quality of these unexplored resources remain unclear. Recent accumulation of the genomic information of both cultivated and wild rice species allows for their comparison at the molecular level. Here, we compared the genome sequence of Oryza sativa ssp. japonica with sets of bacterial artificial chromosome end sequences (BESs) from two wild rice species, O. rufipogon and O. nivara, and an African rice species, O. glaberrima.ResultsWe found that about four to five percent of the BESs of the two wild rice species and about seven percent of the African rice could not be mapped to the japonica genome, suggesting that a substantial number of genes have been lost in the japonica rice lineage; however, their close relatives still possess their counterpart genes. We estimated that during evolution, O. sativa has lost at least one thousand genes that are still preserved in the genomes of the other species. In addition, our BLASTX searches against the non-redundant protein sequence database showed that disease resistance-related proteins were significantly overrepresented in the close relative-specific genomic portions. In total, 235 unmapped BESs of the three relatives matched 83 non-redundant proteins that contained a disease resistance protein domain, most of which corresponded to an NBS-LRR domain.ConclusionWe found that the O. sativa lineage appears to have recently experienced massive gene losses following divergence from its wild ancestor. Our results imply that the domestication process accelerated large-scale genomic deletions in the lineage of Asian cultivated rice and that the close relatives of cultivated rice have the potential to restore the lost traits.

Dataset Information

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

Publications

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

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