Cotton pan-genome retrieves the lost sequences and genes during domestication and selection

被引：106

作者：

Li, Jianying ^{[1
]}

Yuan, Daojun ^{[2
]}

Wang, Pengcheng ^{[1
]}

Wang, Qiongqiong ^{[1
]}

Sun, Mengling ^{[1
]}

Liu, Zhenping ^{[1
]}

Si, Huan ^{[1
]}

Xu, Zhongping ^{[1
]}

Ma, Yizan ^{[1
]}

Zhang, Boyang ^{[1
]}

Pei, Liuling ^{[1
]}

Tu, Lili ^{[1
]}

Zhu, Longfu ^{[1
]}

Chen, Ling-Ling ^{[3
]}

Lindsey, Keith ^{[4
]}

Zhang, Xianlong ^{[1
]}

Jin, Shuangxia ^{[1
]}

Wang, Maojun ^{[1
]}

机构：

[1] Huazhong Agr Univ, Natl Key Lab Crop Genet Improvement, Wuhan, Peoples R China

[2] Huazhong Agr Univ, Coll Plant Sci & Technol, Wuhan, Peoples R China

[3] Huazhong Agr Univ, Coll Informat, Hubei Key Lab Agr Bioinformat, Wuhan, Peoples R China

[4] Univ Durham, Dept Biosci, Durham, England

来源：

GENOME BIOLOGY | 2021年 / 22卷 / 01期

基金：

中国博士后科学基金; 中国国家自然科学基金;

关键词：

Cotton; Domestication; Improvement; Pan-genome; Copy number variation (CNV); Presence; absence variation (PAV); Gene loss; POPULATION-STRUCTURE; FIBER QUALITY; ASSOCIATION; DIVERSITY; INSIGHTS; REVEAL; RICE; WILD; DIFFERENTIATION; DIVERGENCE;

D O I：

10.1186/s13059-021-02351-w

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Background Millennia of directional human selection has reshaped the genomic architecture of cultivated cotton relative to wild counterparts, but we have limited understanding of the selective retention and fractionation of genomic components. Results We construct a comprehensive genomic variome based on 1961 cottons and identify 456 Mb and 357 Mb of sequence with domestication and improvement selection signals and 162 loci, 84 of which are novel, including 47 loci associated with 16 agronomic traits. Using pan-genome analyses, we identify 32,569 and 8851 non-reference genes lost from Gossypium hirsutum and Gossypium barbadense reference genomes respectively, of which 38.2% (39,278) and 14.2% (11,359) of genes exhibit presence/absence variation (PAV). We document the landscape of PAV selection accompanied by asymmetric gene gain and loss and identify 124 PAVs linked to favorable fiber quality and yield loci. Conclusions This variation repertoire points to genomic divergence during cotton domestication and improvement, which informs the characterization of favorable gene alleles for improved breeding practice using a pan-genome-based approach.

引用

页数：26

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