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Detection of QTNs and QTN-by-environment interactions for plant height in upland cotton (G. hirsutum L.) using the 3VmrMLM method

ZHAO Hai-Hong1,LI Meng-Yuan2,LIU Jin-Jing2,WANG Yuan-Yuan3,DU Lei2,WANG Juan4,DONG Cheng-Guang4,*,LI Cheng-Qi2,*   

  1. 1 Science Experiment Center, Yuncheng University, Yuncheng 044000, Shanxi, China; 2 Life Science College, Yuncheng University, Yuncheng 044000, Shanxi, China; 3 College of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, Henan, China; 4 Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi 832000, Xinjiang, China
  • Received:2025-02-10 Revised:2025-07-09 Accepted:2025-07-09 Published:2025-07-24
  • Contact: 李成奇, E-mail: lichq2010@126.com; 董承光, E-mail: dcg318@163.com E-mail:haihong1974@126.com
  • Supported by:
    本研究由国家自然科学基金项目(32201763), 农业农村部农业生物育种重大项目(2023ZD04040-5-2)和山西省基础研究计划项目(20210302123081)资助。

Abstract: Plant height is a key architectural trait in cotton, closely associated with yield and suitability for mechanized harvesting. In this study, 340 upland cotton (G. hirsutum L.) varieties (lines) were used as experimental materials. The CottonSNP80K chip and the 3VmrMLM method were applied to perform a genome-wide association study (GWAS) of plant height across six environments (five individual environments and one combined multi-environment). The goal was to identify quantitative trait nucleotides (QTNs) and QTN-by-environment interactions (QEIs). Genotyping yielded 47,959 polymorphic SNP markers, which were used to divide the varieties into two sub-populations. Phenotypic analysis revealed that plant height exhibited broad and continuous variation in all environments, with genotypic variance, environmental variance, and genotype-by-environment interaction variance all reaching highly significant levels. A total of 111 QTNs associated with plant height were identified across the six environments. Among them, two stable QTNs, TM66913 (D08) and TM79201 (D12), were consistently detected in at least three environments. Five QTNs overlapped with previously reported QTLs or marker loci. Notably, three genes—GH_D08G0118, GH_D08G0131, and GH_D12G1786—were significantly enriched in both Gene Ontology (GO) and KEGG pathway analyses. Of these, GH_D08G0118 showed higher expression levels in the stem of the upland cotton cultivar TM-1. Eight QEIs were detected, three of which represented significant interactions. Functional enrichment analysis of genes near the significant loci revealed significant enrichment of 15 genes in GO terms and 2 genes in KEGG pathways; GH_D08G1507 also showed elevated expression in the stem of TM-1. Moreover, the 3VmrMLM method detected numerous small-effect loci, helping to partially address the “missing heritability” problem commonly associated with complex traits. The QTNs, QEIs, and their corresponding effects identified in this study provide novel insights into the genetic architecture of plant height in upland cotton and offer valuable resources for the molecular breeding of cotton varieties with optimized plant height. 

Key words: 3VmrMLM, upland cotton, plant height, QTN, QTN-by-environment interaction (QEI), effect

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