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Harnessing the genomic diversity of Asian cultivated rice(Oryza sativa L.):SNPs,pan genomes and structural variation

Wensheng WangZhiqiang HuZhichao WuMin LiShuaishuai TaiKenneth L.McNallyJianlong XuJ.AliHongliang ZhangBinying FuYongming GaoChen SunFan ZhangXinyuan ZhangFei ShenXiao CuiHong YuDmytro ChebotarovTianqing ZhengZichao LiMiaolin ChenYongli ZhouXiuqin ZhaoYue ZhaoRui LiBen JiaJingyuan LuXianchang HeZhaotong DongJianxin ShiJing LiDabing ZhangZhen YueJiayang LiXiaodong FangRamil MauleonMillicent SanciangcoJinjie LiYe YinChaochun WeiJue RuanGengyun ZhangNickolai AlexandrovZhikang Li

Institute of Crop Sciences,Chinese Academy of Agricultural SciencesSchool of Life Sciences and Biotechnology,Shanghai JiaoTong UniversityAgricultural Genomics Institute at Shenzhen,Chinese Academy of Agricultural SciencesShenzhen Institute for Innovative Breeding,Chinese Academy of Agricultural SciencesAnhui Agricultural UniversityBGI-ShenzhenInternational Rice Research InstituteChina Agricultural UniversityInstitute of Genetics and Developmental Biology,Chinese Academy of Sciences

摘要:Asian cultivated rice(Oryza sativa) is the staple food for the half world population with rich within species diversity.We present here results from comprehensive analyses of the genome resequencing data of a core collection of 3,000 rice accessions released by the 3,000 Rice Genomes Project.Three important aspects of the population genomic diversity within O.sativa were revealed.First,over 42 million SNPs and > 3 million small indels were discovered against five reference genomes.Population structure analysis discovered previously unreported subpopulations within O.sativa.Secondly,the pan genome(PG) analyses led us to discover more than 12,000 novel protein-coding genes that are absent in the reference Nipponbare genome.The rice PG consists of 56.7% core genes that are essential and present in all rice lines,and 43.3% distributed genes that are present only some of rice accessions and show a high level of diversity.Thirdly,we discovered more 90,000 structural variations(SVs) > 100 bp in the 3,000 rice genomes,most of which are small transpositions and deletions.The SNPs,PG and SV variation clearly differentiate the 3,000 accessions into four major varietal groups,and multiple subpopulations within them.Significantly reduced diversity was found in genomic regions where over 1,000 agronomically important and domesticationrelated genes locate.GWAS analysis for grain length,grain width and bacterial blight resistance revealed both novel and previously reported loci,demonstrating the utility and effects of population structure for gene/QTL discoveries.The tremendous genome diversity and population differentiation within O.sativa are inferred to be the consequences of the long process of diploidization and transition from its direct outcrossing ancestor to a predominant self-fertilization species during evolution.Our results provide additional evidence supporting the hypothesis that rice domestication and its subsequent cultivation took place repeatedly at different times and locations across South Asia,S.East Asia and China.Now,all the SNP,PG and SV data are publicly available for further analyses and confirmation.Tremendous efforts have also been taken to phenotype the 3,000 rice accessions to exploit genes and alleles for important traits of rice and to establish a comprehensive database for rice functional genomics and molecular breeding for future rice improvement.
会议名称:

第七届国际作物科学大会

会议时间:

2016-08-14

会议地点:

中国北京

  • 专辑:

    农业科技

  • 专题:

    农作物

  • 分类号:

    S511

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