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

引用

Molecular Plant 2021年第5期14卷 787-804页

作者： Fan Zhang Chunchao Wang Min Li Yanru Cui Yingyao Shi Zhichao Wu Zhiqiang Hu Wensheng Wang Jianlong Xu Zhikang Li nstitute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing100081.China College of Agronomy Anhui Agricultural UniversityHefeiAnhui230036China College of Agronomy Hebei Agricultural UniversityBaodingHebei071001China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong518120China Department of Plant and Microbial Biology University of CaliforniaBerkeleyCA94720USA

Polymorphisms within gene coding regions represent the most important part of the overall genetic diversity of *** characterized the gene-coding sequence-haplotype(gcHap)diversity of 45963 rice genes in 3010 rice *** 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 *** found that 39218 rice genes carry>255179 major gcHaps of potential functional ***(87.5%)of the detected gcHaps were specific to subspecies or *** 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 *** 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 *** 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 *** gcHap data were demonstrated to have greater power than SNPs for the detection of causal genes that affect complex *** 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

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