The Genomic Variation of 3,000 diverse Rice (Oryza sativa L.)Accessions:Discoveries And Applications In Rice Improvement

【作者】 黎志康； Fan Zhang； Whensheng Wang； Ramil Mauleon； Zhiqiang Hu； Dmytro Chebotarov； Shuaishuai Tai； Zhichao； Min Li； Tianqing Zheng； Roven Rommel Fuentes； Locedie Mansueto； Dario Copetti； Millicent Sanciangco； Kevin Christian Palis； Jianlong Xu； Chen Sun； Hongliang Zhang； Binying Fu； Yongming Gao； Xiuqin Zhao； Fei Shen； Xiao Cui； Hong Yu； Zichao Li； Miaolin Chen； Jeffery Detras； Yongli Zhou； Xinyuan Zhang； Yue Zhao； Dave Kudrna； Chunchao Wang； Rui Li； Ben Jia； Jinyuan Lu； Xianchang He； Zhaotong Dong； Jiabao Xu； Yanhong Li； Miao Wang； Jianxin Shi； Jing Li； Dabing Zhang； Seunhee Lee； Wushu Hu； Alexander Poliakov； Inna Dubchak； Victor Jun Ulat； Frances Nikki Borja； John Robert Mendoza； Jauhar Ali； Ming Yang； Yongchao Niu； Zhen Yue； Ma.Elizabeth B.Naredo； Jayson Talag； Xueqiang Wang； Jinjie Li； Xiaodong Fang； Ye Yin； Jean-Christophe Glaszmann； Jianwei Zhang； Jiayang Li； Ruaraidh Sackville Hamilton； Rod A.Wing； Chaochun Wei； Jue Ruan； Gengyun Zhang； Kenneth L.Mcnally； Nickolai Alexandrov； Hei Leung Hei；

【Author】 Zhikang Li;Fan Zhang;Whensheng Wang;Ramil Mauleon;Zhiqiang Hu;Dmytro Chebotarov;Shuaishuai Tai;Zhichao;Min Li;Tianqing Zheng;Roven Rommel Fuentes;Locedie Mansueto;Dario Copetti;Millicent Sanciangco;Kevin Christian Palis;Jianlong Xu;Chen Sun;Hongliang Zhang;Binying Fu;Yongming Gao;Xiuqin Zhao;Fei Shen;Xiao Cui;Hong Yu;Zichao Li;Miaolin Chen;Jeffery Detras;Yongli Zhou;Xinyuan Zhang;Yue Zhao;Dave Kudrna;Chunchao Wang;Rui Li;Ben Jia;Jinyuan Lu;Xianchang He;Zhaotong Dong;Jiabao Xu;Yanhong Li;Miao Wang;Jianxin Shi;Jing Li;Dabing Zhang;Seunhee Lee;Wushu Hu;Alexander Poliakov;Inna Dubchak;Victor Jun Ulat;Frances Nikki Borja;John Robert Mendoza;Jauhar Ali;Ming Yang;Yongchao Niu;Zhen Yue;Ma.Elizabeth B.Naredo;Jayson Talag;Xueqiang Wang;Jinjie Li;Xiaodong Fang;Ye Yin;Jean-Christophe Glaszmann;Jianwei Zhang;Jiayang Li;Ruaraidh Sackville Hamilton;Rod A.Wing;Chaochun Wei;Jue Ruan;Gengyun Zhang;Kenneth L.Mcnally;Nickolai Alexandrov;Hei Leung Hei;Institute of Crop Sciences,Chinese Academy of Agricultural Sciences;Shenzhen Institute for Innovative Breeding,Chinese Academy of Agricultural Sciences;International Rice Research Institute;School of Life Sciences and Biotechnology,Shanghai Jiao Tong University;Shanghai Center for Bioinformation Technology;BGI Genomics,BGI-Shenzhen;Agricultural Genomics Institute at Shenzhen,Chinese Academy of Agricultural Sciences;Anhui Agricultural University;Arizona Genomics Institute,School of Plant Sciences,University of Arizona;China Agricultural University;Institute of Genetics and Developmental Biology,Chinese Academy of Sciences;DOE Joint Genome Institute;Lawrence Berkeley National Laboratory;Advanced Science and Technology Institute,Department of Science and Technology,University of the Philippines-Diliman;Cirad,UMR Agap;

【机构】 Institute of Crop Sciences,Chinese Academy of Agricultural Sciences； Shenzhen Institute for Innovative Breeding,Chinese Academy of Agricultural Sciences； International Rice Research Institute； School of Life Sciences and Biotechnology,Shanghai Jiao Tong University； Shanghai Center for Bioinformation Technology； BGI Genomics,BGI-Shenzhen； Agricultural Genomics Institute at Shenzhen,Chinese Academy of Agricultural Sciences； Anhui Agricultural University； Arizona Genomics Institute,School of Plant Sciences,University of Arizona； China Agricultural University； Institute of Genetics and Developmental Biology,Chinese Academy of Sciences； DOE Joint Genome Institute； Lawrence Berkeley National Laboratory； Advanced Science and Technology Institute,Department of Science and Technology,University of the Philippines-Diliman； Cirad,UMR Agap；

【摘要】 Asian cultivated rice（Oryza sativa L.） is the staple food for the half world population with rich within species diversity.Comprehensive analyses of the genome resequencing data of a core collection of 3,010 rice accessions revealed four important aspects of the genomic diversity within O.sativa.First,over 42 million SNPs and >3 million small InDels were discovered against five reference genomes.Secondly,we discovered more than 90,000 structural（>100 bps） variations（SVs） when compared with the Geng reference genome,consisting primarily of small-sized deletions and translocations,plus many duplications and inversions.These SVs accounted for significant portion of the rice genome and involved most（～80%） rice genes.Thirdly,we discovered >12,000 full-length novel protein-coding genes plus 9000+ novel genes of partial sequences that are absent in the Nipponbare reference genome.The rice pan genome consists of ～62%core genes/gene families that are present in all rice lines,and ～38%distributed genes that are present only some of rice accessions.Fourthly,using large-effect SNPs and InDels of all loci in the PG,a rice functional haplotype database was constructed.The SNP,PG and SV variation clearly resolve the 3,010 rice accessions into two major subspecies,Xian（indica） and Geng（japonica）,plus Aus and Aro groups and multiple subpopulations within Xian and Geng.Significantly reduced diversity was found in genomic regions where over 1,000 agronomically important and domestication-related genes locate.Tremendous efforts have been taken to identify and mine genes/QTLs/alleles associated with a wide range of important traits in rice using the 3 k materials and SNP data.To demonstrate how the results of the 3 k RGP could be used in rice improvement,genomic constitutions of 476 BC₁ F₅ introgression lines（ILs） from our breeding program were constructed using high-quality reference genomes of their 9 parents and the 3 k RGP databases.When compared with their recurrent parent,Huang-hua-zhan（HHZ）,all these ILs had improved tolerances to more than 2 abiotic stresses（drought,salinity,submergence,low-input） in addition to high yield potential,more than 16 of these ILs were released as new varieties and grown in nearly 1 million ha in Asia and Africa.Many more of these ILs are in the pipeline to be released as new varieties in different rice ecologies in Asia.Deep analyses of the high quality genomic sequencing data of the 9 parents revealed allelic（haplotype） differenced at 9,334 loci plus gene presence/absence differences of ～10,000 genes differentiate HHZ and the 8 donors.Examination of genes responsive to 7 different selection schemes and GWAS analyses of the phenotypic data the 476 HHZ ILs across diverse environments led us to discover large numbers of loci and alleles associated with abiotic stress tolerances and yield traits.The generated genetic and genomic information of the HHZ ILs allowed us to propose novel breeding strategies how to use the genomic/genetic information of the ILs for developing superior rice varieties with significant improvement in multiple complex traits by genomebased breeding by design.更多还原

【Abstract】 Asian cultivated rice（Oryza sativa L.） is the staple food for the half world population with rich within species diversity.Comprehensive analyses of the genome resequencing data of a core collection of 3,010 rice accessions revealed four important aspects of the genomic diversity within O.sativa.First,over 42 million SNPs and >3 million small InDels were discovered against five reference genomes.Secondly,we discovered more than 90,000 structural（>100 bps） variations（SVs） when compared with the Geng reference genome,consisting primarily of small-sized deletions and translocations,plus many duplications and inversions.These SVs accounted for significant portion of the rice genome and involved most（～80%） rice genes.Thirdly,we discovered >12,000 full-length novel protein-coding genes plus 9000+ novel genes of partial sequences that are absent in the Nipponbare reference genome.The rice pan genome consists of ～62%core genes/gene families that are present in all rice lines,and ～38%distributed genes that are present only some of rice accessions.Fourthly,using large-effect SNPs and InDels of all loci in the PG,a rice functional haplotype database was constructed.The SNP,PG and SV variation clearly resolve the 3,010 rice accessions into two major subspecies,Xian（indica） and Geng（japonica）,plus Aus and Aro groups and multiple subpopulations within Xian and Geng.Significantly reduced diversity was found in genomic regions where over 1,000 agronomically important and domestication-related genes locate.Tremendous efforts have been taken to identify and mine genes/QTLs/alleles associated with a wide range of important traits in rice using the 3 k materials and SNP data.To demonstrate how the results of the 3 k RGP could be used in rice improvement,genomic constitutions of 476 BC₁ F₅ introgression lines（ILs） from our breeding program were constructed using high-quality reference genomes of their 9 parents and the 3 k RGP databases.When compared with their recurrent parent,Huang-hua-zhan（HHZ）,all these ILs had improved tolerances to more than 2 abiotic stresses（drought,salinity,submergence,low-input） in addition to high yield potential,more than 16 of these ILs were released as new varieties and grown in nearly 1 million ha in Asia and Africa.Many more of these ILs are in the pipeline to be released as new varieties in different rice ecologies in Asia.Deep analyses of the high quality genomic sequencing data of the 9 parents revealed allelic（haplotype） differenced at 9,334 loci plus gene presence/absence differences of ～10,000 genes differentiate HHZ and the 8 donors.Examination of genes responsive to 7 different selection schemes and GWAS analyses of the phenotypic data the 476 HHZ ILs across diverse environments led us to discover large numbers of loci and alleles associated with abiotic stress tolerances and yield traits.The generated genetic and genomic information of the HHZ ILs allowed us to propose novel breeding strategies how to use the genomic/genetic information of the ILs for developing superior rice varieties with significant improvement in multiple complex traits by genomebased breeding by design.更多还原