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<p>Seed-cotton yield (SCY) is one of the key yield traits and primary breeding targets in cotton. Numerous quantitative trait loci (QTLs) have been identified; however, there are few reports on interactions between QTLs. In this study, a genome-wide association study (GWAS) was performed on 312 upland cotton (<i>Gossypium hirsutum</i> L.) accessions by using the CottonSNP80K array. Four GWAS methods, GEMMA-LM, GEMMA-LMM, EMMAX, and FaST-LMM, were employed to identify quantitative trait nucleotides (QTNs) associated with SCY using the best linear unbiased predictors, while the 3VmrMLM method was used to detect QTN-by-QTN interactions (QQIs). The results of the phenotypic analysis showed that SCY exhibited a wide and continuous variation across five environments. The genotypic variance, environmental variance, and genotype-environment interaction variance all reached highly significant levels. Genotyping resulted in 47,894 polymorphic single nucleotide polymorphism markers, dividing the upland cotton accessions into two subpopulations. The four GWAS methods detected 15 significant QTNs, including nine stable QTNs identified by at least three methods. Single-marker/haplotype analysis confirmed that these nine QTNs collectively constituted three novel QTLs: <i>qSY-D03</i> (TM53448/TM53452/TM53454/TM53460), <i>qSY-D10</i> (TM74930), and <i>qSY-D12</i> (TM78919/TM78920/TM78921/TM78922). Gene Ontology enrichment analysis revealed 25 non-redundant candidate genes related to SCY. Further in-silico analysis of RNA-seq data from upland cotton TM-1 indicated that six genes exhibited high expression levels in ovules during specific developmental stages. Additionally, 21 QQIs were detected, including two significant and 19 suggestive interactions, leading to prediction of five pairs of protein–protein interactions involving four QQIs and five gene pairs. This study provides novel insights into the genetic architecture of SCY in upland cotton. The identified QTNs/QTLs and QQIs offer valuable genetic resources for future studies.</p>

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Detection of quantitative trait nucleotides (QTNs) and QTN-by-QTN interactions (QQIs) for seed-cotton yield in upland cotton (Gossypium hirsutum L.)

  • 期刊论文

  • 发表日期：

    2026年2月27日

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  • Haihong Zhao,
  • Jianan Li,
  • Jinjing Liu,
  • Mengyuan Li,
  • Nunu Sun,
  • Hui Sun,
  • Chengguang Dong,
  • Yuanyuan Wang,
  • Chengqi Li

摘要

Seed-cotton yield (SCY) is one of the key yield traits and primary breeding targets in cotton. Numerous quantitative trait loci (QTLs) have been identified; however, there are few reports on interactions between QTLs. In this study, a genome-wide association study (GWAS) was performed on 312 upland cotton (Gossypium hirsutum L.) accessions by using the CottonSNP80K array. Four GWAS methods, GEMMA-LM, GEMMA-LMM, EMMAX, and FaST-LMM, were employed to identify quantitative trait nucleotides (QTNs) associated with SCY using the best linear unbiased predictors, while the 3VmrMLM method was used to detect QTN-by-QTN interactions (QQIs). The results of the phenotypic analysis showed that SCY exhibited a wide and continuous variation across five environments. The genotypic variance, environmental variance, and genotype-environment interaction variance all reached highly significant levels. Genotyping resulted in 47,894 polymorphic single nucleotide polymorphism markers, dividing the upland cotton accessions into two subpopulations. The four GWAS methods detected 15 significant QTNs, including nine stable QTNs identified by at least three methods. Single-marker/haplotype analysis confirmed that these nine QTNs collectively constituted three novel QTLs: qSY-D03 (TM53448/TM53452/TM53454/TM53460), qSY-D10 (TM74930), and qSY-D12 (TM78919/TM78920/TM78921/TM78922). Gene Ontology enrichment analysis revealed 25 non-redundant candidate genes related to SCY. Further in-silico analysis of RNA-seq data from upland cotton TM-1 indicated that six genes exhibited high expression levels in ovules during specific developmental stages. Additionally, 21 QQIs were detected, including two significant and 19 suggestive interactions, leading to prediction of five pairs of protein–protein interactions involving four QQIs and five gene pairs. This study provides novel insights into the genetic architecture of SCY in upland cotton. The identified QTNs/QTLs and QQIs offer valuable genetic resources for future studies.