Sea island cotton (Gossypium barbadense) has markedly superior high quality fibers, which plays an important role in the textile industry and acts as a donor for upland cotton (G. hirsutum) fiber quality improvement. The genetic characteristics analysis and the identification of key genes will be helpful to understand the mechanism of fiber development and breeding utilization in sea island cotton. In this study, 279 sea island cotton accessions were collected from different origins for genotyping and phenotyping fiber quality traits. A set of 6303 high quality single nucleotide polymorphisms (SNPs) were obtained by high-density CottonSNP80K array. The population characteristics showed that the sea island cotton accessions had wide genetic diversity and were clustered into three groups, with Group1 closely related to Menoufi, an original sea island cotton landrace, and Group2 and Group3 related to widely introduced accessions from Egypt, USA and Former Soviet Union. Further, we used 249 accessions and evaluated five fiber quality traits under normal and salt environments over 2 years. Except for fiber uniformity (FU), fiber length (FL) and fiber elongation (FE) were significantly decreased in salt conditions, while fiber strength (FS) and fiber micronaire (MIC) were increased. Based on 6303 SNPs and genome-wide association study (GWAS) analysis, a total of 34 stable quantitative trait loci (QTLs) were identified for the five fiber quality traits with 25 detected simultaneously under normal and salt environments. Gene Ontology (GO) analysis indicated that candidate genes in the 25 overlapped QTLs were enriched mostly in “cellular and biological process”. In addition, “xylem development” and “response to hormone” pathways were also found. Haplotype analyses found that GB_A03G0335 encoding an E3 ubiquitin-protein ligase in QTL TM6004 had SNP variation (A/C) in gene region, was significantly correlated with FL, FS, FU, and FE, implying a crucial role in fiber quality. The present study provides a foundation for genetic diversity of sea island cotton accessions and will contribute to fiber quality improvement in breeding practice.

中文翻译：

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全基因组关联分析揭示了海岛棉（Gossypium barbadense）纤维品质性状所涉及的基因座和候选基因。

海岛棉（Gossypium barbadense）具有显着优质的纤维，在纺织工业中起着重要的作用，并且是陆地棉（G. hirsutum）纤维质量改善的捐助者。遗传特征分析和关键基因的鉴定将有助于了解海岛棉纤维发育和育种利用的机理。在这项研究中，从不同来源收集了279种海岛棉的基因型和表型纤维品质性状。通过高密度CottonSNP80K阵列获得了6303个高质量的单核苷酸多态性（SNPs）。种群特征表明，海岛棉种质遗传多样性广，分为三类，第一类与梅努菲密切相关，原始的海岛棉本地品种，第2组和第3组与埃及，美国和前苏联广泛引进的种质有关。此外，我们使用了249个种质，并在2年中在正常和盐环境下评估了5种纤维质量特性。在盐分条件下，除了纤维均匀度（FU）外，纤维长度（FL）和纤维伸长率（FE）均显着降低，而纤维强度（FS）和纤维马克隆值（MIC）则增加。基于6303个SNP和全基因组关联研究（GWAS）分析，共确定了34个稳定的定量性状基因座（QTL），用于五个纤维质量性状，在正常和盐环境下同时检测到25个。基因本体论（GO）分析表明，在25个重叠的QTL中，候选基因主要在“细胞和生物学过程”中富集。此外，还发现了“木质部发育”和“对激素的反应”途径。单倍型分析发现，在QTL TM6004中编码E3泛素蛋白连接酶的GB_A03G0335在基因区域具有SNP变异（A / C），与FL，FS，FU和FE显着相关，这暗示着纤维质量的关键作用。本研究为海岛棉种质遗传多样性提供了基础，并将为提高育种实践中的纤维质量做出贡献。