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<p>Verticillium wilt (VW), caused by the soil-borne fungus&#xa0;<i>Verticillium dahliae</i>, stands as one of the most destructive diseases affecting cotton production world-wide. Developing and deploying VW-resistant cotton varieties represents the most effective and sustainable strategy for mitigating the impact of VW. However, breeding VW-resistant upland cotton (<i>Gossypium hirsutum</i>, Gh) varieties is constrained by the limited VW resistance in Gh. One strategy for improving VW resistance of Gh varieties is to introgress resistance alleles from sea-island cotton (<i>Gossypium barbadense</i>, Gb). Interspecific chromosome segment substitution lines (CSSLs) developed based on Gh x Gb offer materials not only for breeding VW-resistant Gh varieties but also for mapping and cloning VW resistance genes. In this study, we used 318 CSSLs derived from Emian-22 (Gh) × 3–79 (Gb) for mapping of VW-resistant QTLs based on phenotypic data collected from 3&#xa0;years of field disease-nursery based experiments and 1.3 million single nucleotide polymorphisms identified among the CSSLs. A genome-wide association study revealed 77 VW resistance QTLs, with only 12 of them overlapping with known VW resistance loci, suggesting that the CSSL population is a valuable resource for mining novel VW-resistant alleles. In the two VW-resistant QTLs on chromosomes A01 and D12, nonsynonymous mutations were found in several annotated genes related to biotic stress responses. <i>Ghi_D12G018010</i> (<i>GhHIR1</i>) in the D12 locus was shown to positively contribute to VW resistance, as down-regulating the gene by virus-induced gene silencing led to reduction of VW resistance. The findings of this study provide candidate genes and markers for improving cotton VW resistance through molecular breeding.</p>

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CSSL-based GWAS identifies SNPs and candidate genes associated with Verticillium wilt resistance in cotton

  • 期刊论文

  • 发表日期：

    2026年2月8日

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  • Youzhong Li,
  • Xiaohui Jiang,
  • Hongyu Cao,
  • Xinyu Zhang,
  • Zhongxu Lin,
  • Qian-Hao Zhu,
  • Yanjun Li,
  • Fei Xue,
  • Shuaishuai Cheng,
  • Feng Liu,
  • Jie Sun

摘要

Verticillium wilt (VW), caused by the soil-borne fungus Verticillium dahliae, stands as one of the most destructive diseases affecting cotton production world-wide. Developing and deploying VW-resistant cotton varieties represents the most effective and sustainable strategy for mitigating the impact of VW. However, breeding VW-resistant upland cotton (Gossypium hirsutum, Gh) varieties is constrained by the limited VW resistance in Gh. One strategy for improving VW resistance of Gh varieties is to introgress resistance alleles from sea-island cotton (Gossypium barbadense, Gb). Interspecific chromosome segment substitution lines (CSSLs) developed based on Gh x Gb offer materials not only for breeding VW-resistant Gh varieties but also for mapping and cloning VW resistance genes. In this study, we used 318 CSSLs derived from Emian-22 (Gh) × 3–79 (Gb) for mapping of VW-resistant QTLs based on phenotypic data collected from 3 years of field disease-nursery based experiments and 1.3 million single nucleotide polymorphisms identified among the CSSLs. A genome-wide association study revealed 77 VW resistance QTLs, with only 12 of them overlapping with known VW resistance loci, suggesting that the CSSL population is a valuable resource for mining novel VW-resistant alleles. In the two VW-resistant QTLs on chromosomes A01 and D12, nonsynonymous mutations were found in several annotated genes related to biotic stress responses. Ghi_D12G018010 (GhHIR1) in the D12 locus was shown to positively contribute to VW resistance, as down-regulating the gene by virus-induced gene silencing led to reduction of VW resistance. The findings of this study provide candidate genes and markers for improving cotton VW resistance through molecular breeding.