作物学报2025，Vol.51Issue(10)：2619-2631,中插1-中插47,60.DOI:10.3724/SP.J.1006.2025.54020
利用3VmrMLM方法检测陆地棉株高QTN及QTN-环境互作(QEI)
Detection of QTNs and QTN-by-environment interactions for plant height in upland cotton(G.hirsutum L.)using the 3VmrMLM method
摘要
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 envi-ronments(five individual environments and one combined multi-environment).The goal was to identify quantitative trait nucleo-tides(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 continu-ous 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 sig-nificant 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"miss-ing 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.关键词
3VmrMLM/陆地棉/株高/QTN/QTN-环境互作(QEI)/效应Key words
3VmrMLM/upland cotton/plant height/QTN/QTN-by-environment interaction(QEI)/effect引用本文复制引用
赵海红,李梦媛,刘锦婧,王园园,杜磊,王娟,董承光,李成奇..利用3VmrMLM方法检测陆地棉株高QTN及QTN-环境互作(QEI)[J].作物学报,2025,51(10):2619-2631,中插1-中插47,60.基金项目
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. This study was supported by the National Natural Science Foundation of China(32201763),the Major Project in Agricultural Biological Breeding of the Ministry of Agriculture and Rural Affairs(2023ZD04040-5-2),and the Fundamental Research Project of Shanxi Province(20210302123081). （32201763）
