Table_2_Genetic Detection of Lint Percentage Applying Single-Locus and Multi-Locus Genome-Wide Association Studies in Chinese Early-Maturity Upland Cotton.docx

Upland cotton (Gossypium hirsutum L.) is the most important source of natural fiber in the world. Early-maturity upland cotton varieties are commonly planted in China. Nevertheless, lint yield of early-maturity upland cotton varieties is strikingly lower than that of middle- and late-maturity ones. How to effectively improve lint yield of early maturing cotton, becomes a focus of cotton research. Here, based on 72,792 high-quality single nucleotide polymorphisms of 160 early-maturing upland cotton accessions, we performed genome-wide association studies (GWASs) for lint percentage (LP), one of the most lint-yield component traits, applying one single-locus method and six multi-locus methods. A total of 4 and 45 significant quantitative trait nucleotides (QTNs) were respectively identified to be associated with LP. Interestingly, in two of four planting environments, two of these QTNs (A02_74713290 and A02_75551547) were simultaneously detected via both one single-locus and three or more multi-locus GWAS methods. Among the 42 genes within a genomic region (A02: 74.31–75.95 Mbp) containing the above two peak QTNs, Gh_A02G1269, Gh_A02G1280, and Gh_A02G1295 had the highest expression levels in ovules during seed development from 20 to 25 days post anthesis, whereas Gh_A02G1278 was preferentially expressed in the fibers rather than other organs. These results imply that the four potential candidate genes might be closely related to cotton LP by regulating the proportion of seed weight and fiber yield. The QTNs and potential candidate genes for LP, identified in this study, provide valuable resource for cultivating novel cotton varieties with earliness and high lint yield in the future.

陆地棉（Upland cotton，Gossypium hirsutum L.）是全球最重要的天然纤维来源。中国广泛种植早熟陆地棉品种，然而早熟陆地棉的皮棉产量显著低于中晚熟品种。如何有效提升早熟棉花的皮棉产量，已成为棉花研究的热点方向。本研究以160份早熟陆地棉种质资源的72792个高质量单核苷酸多态性（single nucleotide polymorphisms, SNP）为基础，采用1种单位点分析方法与6种多位点分析方法，针对皮棉产量构成核心性状之一的衣分（lint percentage, LP）开展全基因组关联分析（genome-wide association studies, GWAS）。研究共分别鉴定到4个和45个与LP显著关联的数量性状核苷酸（quantitative trait nucleotides, QTNs）。有趣的是，在4个种植环境中的2个环境里，其中2个QTN（A02_74713290和A02_75551547）可通过单位点方法及3种及以上多位点GWAS方法同时被检测到。在包含上述两个峰值QTN的基因组区域（A02: 74.31–75.95 Mbp）内的42个基因中，Gh_A02G1269、Gh_A02G1280及Gh_A02G1295在开花后20至25天的种子发育胚珠中表达量最高，而Gh_A02G1278则优先在纤维中表达，而非其他组织器官。上述结果表明，这4个潜在候选基因可能通过调控种子重量与纤维产量的比例，与棉花衣分性状密切相关。本研究鉴定到的LP相关QTN及潜在候选基因，可为未来培育早熟且高产皮棉的棉花新品种提供宝贵的遗传资源。