Yang Tao, Wang Honggang, Song Jikun, Zhao Kang, Pang Bo, Wang Yongpan, Luo Ping, Liang Weiwei, Shi Shunyu, Wang Jie, Lin Yifeng, Li Jing, Wang Zhenrui, Guo Yongqin, Gao Wenwei
Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China.
State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000, China.
Theor Appl Genet. 2025 Jun 9;138(7):138. doi: 10.1007/s00122-025-04911-1.
Genetic variation in a Gossypium barbadense population was revealed using resquencing. GWAS and RNA-seq on Gossypium barbadense population identified several candidate genes associated with fiber length, micronaire, and elongation. Sea Island cotton (Gossypium barbadense), a premier tetraploid cotton species, is globally renowned for its fibers, which exhibit thermal expansion and contraction properties similar to those of animal fibers such as cashmere. Despite its significance, there remains a limited understanding of how genes influence primary traits across germplasms and the relationship between predictive factors identified through genomic selection (GS) technology and heritability. This study aimed to address this academic gap. A total of 203 Sea Island cotton accessions were incorporated for resequencing. Population evolution analysis revealed three distinct groups, which were largely shaped by geographical distribution and breeding objectives. Then, genome-wide association study (GWAS) was performed on 15 traits related to yield, fiber quality, and plant morphological, identifying a greater number of loci associated with fiber quality traits that exhibited higher broad sense heritability. Transcriptomic and gene expression analysis identified six key genes involved in regulating fiber length (GB_A05G1764 and GB_A05G1761), fiber micronaire (GB_A05G1895 and GB_A05G1771), and fiber elongation (GB_A05G1702 and GB_A05G1707). Furthermore, geographical and temporal analyses indicated that these traits underwent directional selection in Sea Island cotton. In addition, this study explored the effects of marker density, significant marker quantities, and population size on prediction accuracy using GS technology, finding that traits with higher broad sense heritability, such as fiber quality, achieved higher prediction accuracy, while those with lower broad sense heritability, such as plant morphological, showed reduced accuracy. This study provides an important reference for future GS breeding, in addition to deepening the scientific understanding of the genetic evolution of Sea Island cotton.
通过重测序揭示了海岛棉群体的遗传变异。对海岛棉群体进行全基因组关联研究（GWAS）和RNA测序，鉴定出了几个与纤维长度、马克隆值和伸长率相关的候选基因。海岛棉是一种优质的四倍体棉花品种，以其纤维而闻名于世，其纤维具有与羊绒等动物纤维相似的热膨胀和收缩特性。尽管其具有重要意义，但对于基因如何影响种质中的主要性状以及通过基因组选择（GS）技术确定的预测因子与遗传力之间的关系，人们的了解仍然有限。本研究旨在填补这一学术空白。共纳入203份海岛棉种质进行重测序。群体进化分析揭示了三个不同的群体，它们在很大程度上受地理分布和育种目标的影响。然后，对与产量、纤维品质和植株形态相关的15个性状进行了全基因组关联研究，鉴定出了更多与纤维品质性状相关的位点，这些性状表现出较高的广义遗传力。转录组和基因表达分析确定了六个参与调节纤维长度（GB_A05G1764和GB_A05G1761）、纤维马克隆值（GB_A05G1895和GB_A05G1771）和纤维伸长率（GB_A05G1702和GB_A05G1707）的关键基因。此外，地理和时间分析表明，这些性状在海岛棉中经历了定向选择。此外，本研究利用GS技术探讨了标记密度、显著标记数量和群体大小对预测准确性的影响，发现广义遗传力较高的性状，如纤维品质，预测准确性较高，而广义遗传力较低的性状，如植株形态，预测准确性较低。本研究除了加深对海岛棉遗传进化的科学理解外，还为未来的GS育种提供了重要参考。
