Table_1_Genome-Wide Association Analysis Reveals Loci and Candidate Genes Involved in Fiber Quality Traits Under Multiple Field Environments in Cotton (Gossypium hirsutum).XLSX

Fiber length, fiber strength, and fiber micronaire are the main fiber quality parameters in cotton. Thus, mining the elite and stable loci/alleles related to fiber quality traits and elucidating the relationship between the two may accelerate genetic improvement of fiber quality in cotton. Here, genome-wide association analysis (GWAS) was performed for fiber quality parameters based on phenotypic data, and 56,010 high-quality single nucleotide polymorphisms (SNPs) using 242 upland cotton accessions under 12 field environments were obtained. Phenotypic analysis exhibited that fiber length (FL) had a positive correlation with fiber strength (FS) and had a negative correlation with fiber micronaire (Mic). Genetic analysis also indicated that FL, FS, and Mic had high heritability of more than 80%. A total of 67 stable quantitative trait loci (QTLs) were identified through GWAS analysis, including 31 for FL, 21 for FS, and 22 for Mic. Of them, three pairs homologous QTLs were detected between A and D subgenomes, and seven co-located QTLs with two fiber quality parameters were found. Compared with the reported QTLs, 34 co-located with previous studies, and 33 were newly revealed. Integrated with transcriptome analysis, we selected 256, 244, and 149 candidate genes for FL, FS, and Mic, respectively. Gene Ontology (GO) analysis showed that most of the genes located in QTLs interval of the three fiber quality traits were involved in sugar biosynthesis, sugar metabolism, microtubule, and cytoskeleton organization, which played crucial roles in fiber development. Through correlation analysis between haplotypes and phenotypes, three genes (GH_A05G1494, GH_D11G3097, and GH_A05G1082) predominately expressed in fiber development stages were indicated to be potentially responsible for FL, FS, and Mic, respectively. The GH_A05G1494 encoded a protein containing SGS-domain, which is related to tubulin-binding and ubiquitin-protein ligase binding. The GH_D11G3097 encoded 20S proteasome beta subunit G1, and was involved in the ubiquitin-dependent protein catabolic process. The GH_A05G1082 encoded RAN binding protein 1 with a molecular function of GTPase activator activity. These results provide new insights and candidate loci/genes for the improvement of fiber quality in cotton.

纤维长度（FL）、纤维强度（FS）与纤维马克隆值（Mic）是棉花纤维品质的核心参数。因此，挖掘与纤维品质性状相关的优异稳定位点/等位基因，并阐明不同纤维品质性状间的关联机制，可加速棉花纤维品质的遗传改良进程。本研究基于242份陆地棉种质在12个田间环境下的表型数据，针对纤维品质参数开展全基因组关联分析（Genome-Wide Association Analysis, GWAS），共获得56010个高质量单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）。表型分析结果显示，FL与FS呈显著正相关，而与Mic呈显著负相关。遗传分析同样表明，FL、FS与Mic的遗传力均超过80%，表现出较高的遗传稳定性。通过GWAS分析，本研究共鉴定出67个稳定的数量性状位点（Quantitative Trait Loci, QTLs），其中调控FL的有31个、调控FS的有21个、调控Mic的有22个。其中，在A、D亚基因组间共检测到3对同源QTL，同时发现7个可同时调控两种纤维品质参数的共定位QTL。将本研究鉴定的QTL与已有报道的位点进行比对后发现，34个QTL与前人研究中的共定位位点重合，另有33个为全新鉴定的位点。结合转录组分析结果，本研究分别筛选出256个、244个和149个与FL、FS及Mic相关的候选基因。基因本体论（Gene Ontology, GO）富集分析显示，这三个纤维品质性状的QTL区间内的大部分基因，均参与糖生物合成、糖代谢、微管与细胞骨架组织等生物学过程，而这些过程在纤维发育中发挥关键调控作用。通过单倍型与表型的关联分析，最终筛选出3个在纤维发育阶段特异性高表达的基因：GH_A05G1494、GH_D11G3097与GH_A05G1082，分别被推测为调控FL、FS与Mic的关键候选基因。其中，GH_A05G1494编码一个包含SGS结构域的蛋白，该蛋白具有微管蛋白结合与泛素蛋白连接酶结合功能；GH_D11G3097编码20S蛋白酶体β亚基G1，参与泛素依赖的蛋白质分解代谢过程；GH_A05G1082编码RAN结合蛋白1，其分子功能为GTP酶激活蛋白活性。本研究结果为棉花纤维品质的遗传改良提供了全新的理论视角与候选位点/基因资源。