Ma Qi, Zhang Xueli, Li Jilian, Ning Xinzhu, Xu Shouzhen, Liu Ping, Guo Xuefeng, Yuan Wenmin, Xie Bin, Wang Fuxiang, Wang Caixiang, Su Junji, Lin Hai
College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
Institute of Cotton Research, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China.
Int J Mol Sci. 2025 Mar 17;26(6):2697. doi: 10.3390/ijms26062697.
The boll opening rate (BOR) is an early maturity trait that plays a crucial role in cotton production in China, as BOR has a significant effect on defoliant spraying and picking time of unginned cotton, ultimately determining yield and fiber quality. Therefore, elucidating the genetic basis of BOR and identifying stably associated loci, elite alleles, and potential candidate genes can effectively accelerate the molecular breeding process. In this study, we utilized the mixed linear model (MLM) algorithm to perform a genome-wide association study (GWAS) based on 4,452,629 single-nucleotide polymorphisms (SNPs) obtained through whole-genome resequencing of a natural population of 418 upland cotton accessions and phenotypic BOR data acquired from five environments. A total of 18 SNP loci were identified on chromosome D11 that are stable and significantly associated with BOR in multiple environments. Moreover, a significant SNP peak (23.703-23.826 Mb) was identified, and a gene and favorable allelic variation (GG) related to BOR were found in this genomic region, significantly increasing cotton BOR. Evolutionary studies have shown that may have been subjected to artificial selection throughout the variety selection process. This study provides valuable insights and suggests that the gene and its favorable allelic variation (GG) could be potential targets for molecular breeding to improve BOR in upland cotton. However, further research is needed to validate the function of this gene and explore its potential applications in cotton breeding programs. Overall, this study contributes to the advancement of genetic improvement in early maturity and has important implications for the sustainable development of the cotton industry.
棉铃开放率（BOR）是一个早熟性状，在中国棉花生产中起着至关重要的作用，因为BOR对脱叶剂喷洒和籽棉采摘时间有显著影响，最终决定产量和纤维品质。因此，阐明BOR的遗传基础并鉴定稳定相关的位点、优异等位基因和潜在候选基因，可以有效加速分子育种进程。在本研究中，我们利用混合线性模型（MLM）算法，基于对418份陆地棉自然群体进行全基因组重测序获得的4,452,629个单核苷酸多态性（SNP）以及从五个环境中获取的表型BOR数据，进行全基因组关联研究（GWAS）。在D11染色体上共鉴定出18个SNP位点，这些位点在多个环境中与BOR稳定且显著相关。此外，还鉴定出一个显著的SNP峰值（23.703 - 23.826 Mb），并在该基因组区域发现了一个与BOR相关的基因和有利等位变异（GG），显著提高了棉花的BOR。进化研究表明， 在整个品种选育过程中可能受到了人工选择。本研究提供了有价值的见解，并表明该基因及其有利等位变异（GG）可能是改良陆地棉BOR的分子育种潜在靶点。然而，需要进一步研究来验证该基因的功能，并探索其在棉花育种计划中的潜在应用。总体而言，本研究有助于早熟遗传改良的进展，对棉花产业的可持续发展具有重要意义。
