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 

作者单位：Institute of Crop SciencesChinese Academy of Agricultural Sciences Shenzhen Institute for Innovative BreedingChinese Academy of Agricultural Sciences International Rice Research Institute School of Life Sciences and BiotechnologyShanghai Jiao Tong University Shanghai Center for Bioinformation Technology BGI GenomicsBGI-Shenzhen Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural Sciences Anhui Agricultural University Arizona Genomics InstituteSchool of Plant SciencesUniversity of Arizona China Agricultural University Institute of Genetics and Developmental BiologyChinese Academy of Sciences Lawrence Berkeley National Laboratory 

会议名称：《2018中国作物学会学术年会》

会议日期：2018年

学科分类：09[农学] 0901[农学-作物学] 

关 键 词：Rice genome diversity population structure pan genomes genomics-based breeding by design 

摘      要：Asian cultivated rice(Oryza sativa L.) is the staple food for the half world population with rich within species *** analyses of the genome resequencing data of a core collection of 3,010 rice accessions revealed four important aspects of the genomic diversity within ***,over 42 million SNPs and 3 million small InDels were discovered against five reference ***,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 *** SVs accounted for significant portion of the rice genome and involved most(～80%) rice ***,we discovered 12,000 full-length novel protein-coding genes plus 9000+ novel genes of partial sequences that are absent in the Nipponbare reference *** 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 ***,using large-effect SNPs and InDels of all loci in the PG,a rice functional haplotype database was *** 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 *** reduced diversity was found in genomic regions where over 1,000 agronomically important and domestication-related genes *** 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 *** demonstrate how the results of the 3 k RGP could be used in rice improvement,genomic constitutions of 476 BC F introgression lines(ILs) from our breeding program were constructed using high-quality reference genomes of their 9 parents and the 3 k RGP *** compared with their recurrent parent,Huang-hua-