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<p>Genetic improvement of cottonseed oil content represents a crucial strategy for enhancing the comprehensive utilization of cotton. Here, genome-wide association study (GWAS) and weighted gene co-expression network analysis (WGCNA) were integrated to elucidate the genetic control underlying oil content. Phenotypic evaluation of 159 cotton accessions revealed extensive genetic variation, with kernel oil content ranging from 17.81% to 39.50%. Population structure analysis based on 20,213 single nucleotide polymorphisms (SNPs) classified the accessions into two major subpopulations. A total of 18 SNPs exhibited significant associations with oil content, two of which were stably detected across multiple environments using the FarmCPU model. Further haplotype analysis within linkage disequilibrium (LD) blocks confirmed a favorable haplotype on chromosome A05 that was strongly correlated with elevated oil content. Integration of publicly available transcriptome data from 11 ovule developmental stages with WGCNA identified modules significantly linked to oil content. Of the 74 candidate genes within LD intervals, 17 were assigned to WGCNA modules. Functional annotation and enrichment analyses highlighted four putative candidate genes (<i>GH_A05G1503</i>, <i>GH_A05G1506</i>, <i>GH_A05G1531</i>, and <i>GH_A10G2150</i>) involved in oil biosynthesis. These findings deepen our understanding of the genetic mechanisms governing cottonseed oil biosynthesis and lay a foundation for breeding high-oil cotton varieties.</p>

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Integration of GWAS and WGCNA reveals novel candidate genes for cottonseed oil content in Gossypium hirsutum L.

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年6月26日

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  • Beibei Lv,
  • Zhuanxia Pan,
  • Hangsong Gao,
  • Xueyu Zhang,
  • Liuliu Yang,
  • Gang Wang,
  • Gang Lan,
  • Zhanglong Huangfu,
  • Cairong Cao,
  • Baoguo Hou,
  • Zhi Xia,
  • Meng Zhang,
  • Xiuqin Qiao,
  • Chaozhu Xing,
  • Pengbo Li

摘要

Genetic improvement of cottonseed oil content represents a crucial strategy for enhancing the comprehensive utilization of cotton. Here, genome-wide association study (GWAS) and weighted gene co-expression network analysis (WGCNA) were integrated to elucidate the genetic control underlying oil content. Phenotypic evaluation of 159 cotton accessions revealed extensive genetic variation, with kernel oil content ranging from 17.81% to 39.50%. Population structure analysis based on 20,213 single nucleotide polymorphisms (SNPs) classified the accessions into two major subpopulations. A total of 18 SNPs exhibited significant associations with oil content, two of which were stably detected across multiple environments using the FarmCPU model. Further haplotype analysis within linkage disequilibrium (LD) blocks confirmed a favorable haplotype on chromosome A05 that was strongly correlated with elevated oil content. Integration of publicly available transcriptome data from 11 ovule developmental stages with WGCNA identified modules significantly linked to oil content. Of the 74 candidate genes within LD intervals, 17 were assigned to WGCNA modules. Functional annotation and enrichment analyses highlighted four putative candidate genes (GH_A05G1503, GH_A05G1506, GH_A05G1531, and GH_A10G2150) involved in oil biosynthesis. These findings deepen our understanding of the genetic mechanisms governing cottonseed oil biosynthesis and lay a foundation for breeding high-oil cotton varieties.