A research team led by academician Zhang Xianlong from Huazhong Agricultural University (HZAU) has published a paper titled Pangenome analysis reveals yield-and fiber-related diversity and interspecific gene flow in Gossypium barbadense L. in the journal Nature Communications.

The study sheds new light on the genetic foundations of fiber quality and yield, paving the way for high-end cotton breeding.

In collaboration with domestic and international institutions, the team assembled 12 representative Gossypium barbadense L. (Sea Island cotton) genomes using HiFi sequencing technology, covering the wild-to-domesticated continuum. They identified over 129,000 structural variants and revealed gene flow between G. barbadense and G. hirsutum (upland cotton), especially in the Caribbean region. This interspecific introgression may have introduced photoperiod-neutral traits into cultivated varieties.

Sea Island cotton is prized for its premium fiber but suffers from poor adaptability and low yield, leading to supply shortages and reliance on imports. To address this, HZAU researchers developed a graphical pangenome and conducted SV-GWAS analyses, identifying key genetic loci related to fiber length, strength, and lint percentage.

Notably, some favorable fiber-quality alleles such as FL3 remain underutilized and could be introgressed into elite cultivars through hybridization. However, a trade-off was found between lint yield and fiber quality, posing a challenge for simultaneous improvement.

Doctoral student Meng Qingying is the study's primary author, with Associate Professor Yuan Daojun as the corresponding author. Researchers from Xinjiang Agricultural University, Xinjiang Academy of Agricultural Sciences, Shihezi University, Iowa State University and United States Department of Agriculture also contributed.

SV-GWAS analysis identifies candidate genetic variants affecting Sea Island cotton fiber quality and yield. [Photo/news.hzau.edu.cn]