Pangenome analysis reveals yield- and fiber-related diversity and interspecific gene flow in Gossypium barbadense L

Qingying Meng, Peihao Xie, Zhongping Xu, Jiwei Tang, Liuyang Hui, Jiaqi Gu, Xinxin Gu, Shihe Jiang, Yuxuan Rong, Jie Zhang, Joshua A. Udall, Corrinne E. Grover, Kai Zheng, Quanjia Chen, Jie Kong, Maojun Wang, Xinhui Nie, Zhongxu Lin, Shuangxia Jin, Jonathan F. Wendel, Xianlong Zhang and Daojun Yuan ()
Additional contact information
Qingying Meng: Huazhong Agricultural University
Peihao Xie: Huazhong Agricultural University
Zhongping Xu: Huazhong Agricultural University
Jiwei Tang: Huazhong Agricultural University
Liuyang Hui: Huazhong Agricultural University
Jiaqi Gu: Huazhong Agricultural University
Xinxin Gu: Huazhong Agricultural University
Shihe Jiang: Huazhong Agricultural University
Yuxuan Rong: Huazhong Agricultural University
Jie Zhang: Huazhong Agricultural University
Joshua A. Udall: Crop Germplasm Research Unit
Corrinne E. Grover: Iowa State University
Kai Zheng: Xinjiang Agricultural University
Quanjia Chen: Xinjiang Agricultural University
Jie Kong: Xinjiang Academy of Agricultural Sciences
Maojun Wang: Huazhong Agricultural University
Xinhui Nie: Shihezi University
Zhongxu Lin: Huazhong Agricultural University
Shuangxia Jin: Huazhong Agricultural University
Jonathan F. Wendel: Iowa State University
Xianlong Zhang: Huazhong Agricultural University
Daojun Yuan: Huazhong Agricultural University

Nature Communications, 2025, vol. 16, issue 1, 1-18

Abstract: Abstract Gossypium barbadense is renowned for its superior fiber quality, particularly its extra-long fibers, although its fiber yield is lower compared to G. hirsutum. Here, to further reveal fiber-related genomic variants of G. barbadense, we de novo assemble 12 genomes of G. barbadense that span the wild-to-domesticated continuum, and construct a graph-based pangenome by integrating these assemblies and 17 publicly available tetraploid cotton genome assemblies. We uncover the divergent evolutionary trajectories and subsequent exchanges between G. barbadense and G. hirsutum through investigation of structural variants (SVs). We perform the SV-based GWAS analysis in G. barbadense and identify four, three, and seven candidate SVs for fiber length, fiber strength, and lint percentage, respectively. Furthermore, we detect the underlying candidate genes and uncover the origin and distribution of favorable alleles, and reveal the tradeoff between lint percentage and fiber quality. These pangenome and trait-associated SVs provide insights into and resources for improving cotton fiber.

Date: 2025
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DOI: 10.1038/s41467-025-60254-x

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