The landscape of gene-CDS-haplotype diversity in rice:Properties,population organization,footprints of domestication and breeding,and implications for genetic improvement
作者机构：nstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081.China College of AgronomyAnhui Agricultural UniversityHefeiAnhui230036China College of AgronomyHebei Agricultural UniversityBaodingHebei071001China Shenzhen BranchGuangdong 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 BiologyUniversity of CaliforniaBerkeleyCA94720USA
出 版 物：《Molecular Plant》 (分子植物（英文版）)
年 卷 期：2021年第14卷第5期
页 面：787-804页
核心收录：
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
主 题：gene-CDS-haplotype diversity functional alleles genome-wide selection signals evolution
摘 要：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 carry255179 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“favorablegcHaps 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.
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