Genomic variation in 3,010 diverse accessions of Asian cultivated rice
Wensheng WangInstitute of Crop SciencesRamil MauleonInternational Rice Research Institute, Manila, PhilippinesZhiqiang HuInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaDmytro ChebotarovInternational Rice Research Institute, Manila, PhilippinesShuaishuai TaiBGI Genomics, BGI-Shenzhen, Shenzhen, ChinaZhichao WuAgricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, ChinaMin LiAnhui Agricultural University, Hefei, ChinaTianqing ZhengInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaRoven Rommel FuentesInternational Rice Research Institute, Manila, PhilippinesFan ZhangInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaLocedie MansuetoInternational Rice Research Institute, Manila, PhilippinesDario CopettiArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USAMillicent D. Alexandrov SanciangcoInternational Rice Research Institute, Manila, PhilippinesKevin PalisInternational Rice Research Institute, Manila, PhilippinesJianlong XuAgricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, ChinaChen SunSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, ChinaBinying FuInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaHongliang ZhangChina Agricultural University, Beijing, ChinaYongming GaoInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaXiuqin ZhaoInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaFei ShenChina Agricultural University, Beijing, ChinaXiao CuiSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, ChinaHong YuInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, ChinaZichao LiChina Agricultural University, Beijing, ChinaMiaolin ChenSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, ChinaJeffrey DetrasInternational Rice Research Institute, Manila, PhilippinesYongli ZhouInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaXinyuan ZhangAgricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, ChinaYue ZhaoSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, ChinaDave KudrnaArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USAChunchao WangInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaRui LiSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, ChinaBen JiaSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, ChinaJinyuan LuSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, ChinaHe Xian-ChangSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, ChinaZhaotong DongSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, ChinaJiabao XuAgricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, ChinaYanhong LiBGI Genomics, BGI-Shenzhen, Shenzhen, ChinaMiao WangBGI Genomics, BGI-Shenzhen, Shenzhen, ChinaJianxin ShiSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, ChinaJing LiChina Agricultural University, Beijing, ChinaDabing ZhangSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, ChinaSeunghee LeeArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USAWushu HuBGI Genomics, BGI-Shenzhen, Shenzhen, ChinaAlexander PoliakovDOE Joint Genome Institute, Walnut Creek, CA, USAInna DubchakDOE Joint Genome Institute, Walnut Creek, CA, USAVictor Jun UlatInternational Rice Research Institute, Manila, PhilippinesFrances Nikki BorjaInternational Rice Research Institute, Manila, PhilippinesJ. MendozaJauhar AliInternational Rice Research Institute, Manila, PhilippinesQiang GaoBGI Genomics, BGI-Shenzhen, Shenzhen, ChinaYongchao NiuBGI Genomics, BGI-Shenzhen, Shenzhen, ChinaZhen YueBGI Genomics, BGI-Shenzhen, Shenzhen, ChinaMa. Elizabeth B. NaredoInternational Rice Research Institute, Manila, PhilippinesJayson TalagArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USAXueqiang WangChina Agricultural University, Beijing, ChinaJinjie LiChina Agricultural University, Beijing, ChinaXiaodong FangBGI Genomics, BGI-Shenzhen, Shenzhen, ChinaYe YinBGI Genomics, BGI-Shenzhen, Shenzhen, ChinaJean-Christophe GlaszmannUMR AGAP, CIRAD, Montpellier, FranceJianwei ZhangArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USAJiayang LiChina Agricultural University, Beijing, ChinaRuaraidh Sackville HamiltonInternational Rice Research Institute, Manila, PhilippinesRod A. WingArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA. [email protected]Jue RuanAgricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China. [email protected]Gengyun ZhangBGI Genomics, BGI-Shenzhen, Shenzhen, China. [email protected]Chaochun WeiSchool of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China. [email protected]Nickolai AlexandrovInternational Rice Research Institute, Manila, Philippines. [email protected]Kenneth L. McNallyInternational Rice Research Institute, Manila, Philippines. [email protected]Zhikang LiChina Agricultural University, Beijing, ChinaHei LeungInternational Rice Research Institute, Manila, Philippines
2018en
ABI
Аннотация
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.
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