The landscape of gene-CDS-haplotype diversity in rice:Properties,population organization,footprints of domestication and breeding,and implications for genetic improvement  

作　　者：Fan Zhang Chunchao Wang Min Li Yanru Cui Yingyao Shi Zhichao Wu Zhiqiang Hu Wensheng Wang Jianlong Xu Zhikang Li 

机构地区：[1]nstitute of Crop Sciences,Chinese Academy of Agricultural Sciences,Beijing,100081.China [2]College of Agronomy,Anhui Agricultural University,Hefei,Anhui,230036,China [3]College of Agronomy,Hebei Agricultural University,Baoding,Hebei,071001,China [4]Shenzhen Branch,Guangdong Laboratory for Lingnan Modern Agriculture,Genome Analysis Laboratory of the Ministry of Agriculture,Agricultural Genomics Institute at Shenzhen,Chinese Academy of Agricultural Sciences,Shenzhen,Guangdong,518120,China [5]Department of Plant and Microbial Biology,University of California,Berkeley,CA,94720,USA

出　　处：《Molecular Plant》2021年第5期787-804,共18页分子植物（英文版）

基　　金：funded by the National Key Research and Development Program of China(2016YFD0100301);the National Natural Science Foundation of China(31771762);the Agricultural Science,and Technology Innovation Program and the Cooperation and Innovation Mission(CAAS-ZD>CT202001);the Talent Introduction Program(RC311901)of Anhui Agricultural University.

摘　　要：Polymorphisms within gene coding regions represent the most important part of the overall genetic diversity of rice.We characterized the gene-coding sequence-haplotype(gcHap)diversity of 45963 rice genes in 3010 rice accessions.With an average of 226±390 gcHaps per gene in rice populations,rice genes could be classified into three main categories:12865 conserved genes,10254 subspecific differentiating genes,and 22844 remaining genes.We found that 39218 rice genes carry>255179 major gcHaps of potential functional importance.Most(87.5%)of the detected gcHaps were specific to subspecies or populations.The inferred proto-ancestors of local landrace populations reconstructed from conserved predominant(ancient)gcHaps correlated strongly with wild rice accessions from the same geographic regions,supporting a multiorigin(domestication)model of Oryza sativa.Past breeding efforts generally increased the gcHap diversity of modern varieties and'caused significant frequency shifts in predominant gcHaps of 14266 genes due to independent selection in the two subspecies.Low frequencies of“favorable”gcHaps at most known genes related to rice yield in modern varieties suggest huge potential for rice improvement by mining and pyramiding of favorable gcHaps.The gcHap data were demonstrated to have greater power than SNPs for the detection of causal genes that affect complex traits.The rice gcHap diversity dataset generated in this study would facilitate rice basic research and improvement in the future.

关 键 词：gene-CDS-haplotype diversity functional alleles genome-wide selection signals evolution 

分 类 号：S511[农业科学—作物学]