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

Genome Biology

Daojun Yuan¹  Keith Lindsey²  Ling-Ling Chen³  Xianlong Zhang⁴  Longfu Zhu⁴  Shuangxia Jin⁴  Mengling Sun⁴  Huan Si⁴  Maojun Wang⁴  Qiongqiong Wang⁴  Zhenping Liu⁴  Zhongping Xu⁴  Pengcheng Wang⁴  Liuling Pei⁴  Jianying Li⁴  Yizan Ma⁴  Lili Tu⁴  Boyang Zhang⁴ 

[1] College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China;Department of Biosciences, Durham University, Durham, UK;Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China;National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China;

关键词: Cotton;    Domestication;    Improvement;    Pan-genome;    Copy number variation (CNV);    Presence/absence variation (PAV);    Gene loss;   

DOI  :  10.1186/s13059-021-02351-w

来源: Springer

【 摘 要 】

BackgroundMillennia 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.ResultsWe 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.ConclusionsThis 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.

【 授权许可】

CC BY