BACKGROUND Salinity is one of the most significant environmental factors limiting the productivity of cotton. However, the key genetic components responsible for the reduction in cotton yield in saline-alkali soils are still unclear. RESULTS Here, we evaluated three main components of lint yield, single boll weight (SBW), lint percentage (LP) and boll number per plant (BNPP), across 316 G. hirsutum accessions under four salt conditions over two years. Phenotypic analysis indicated that LP was unchanged under different salt conditions, however BNPP decreased significantly and SBW increased slightly under high salt conditions. Based on 57,413 high-quality single nucleotide polymorphisms (SNPs) and genome-wide association study (GWAS) analysis, a total of 42, 91 and 25 stable quantitative trait loci (QTLs) were identified for SBW, LP and BNPP, respectively. Phenotypic and QTL analysis suggested that there was little correlation among the three traits. For LP, 8 stable QTLs were detected simultaneously in four different salt conditions, while fewer repeated QTLs for SBW or BNPP were identified. Gene Ontology (GO) analysis indicated that their regulatory mechanisms were also quite different. Via transcriptome profile data, we detected that 10 genes from the 8 stable LP QTLs were predominantly expressed during fiber development. Further, haplotype analyses found that a MYB gene (GhMYB103), with the two SNP variations in cis-regulatory and coding regions, was significantly correlated with lint percentage, implying a crucial role in lint yield. We also identified that 40 candidate genes from BNPP QTLs were salt-inducible. Genes related to carbohydrate metabolism and cell structure maintenance were rich in plants grown in high salt conditions, while genes related to ion transport were active in plants grown in low salt conditions, implying different regulatory mechanisms for BNPP at high and low salt conditions. CONCLUSIONS This study provides a foundation for elucidating cotton salt tolerance mechanisms and contributes gene resources for developing upland cotton varieties with high yields and salt stress tolerance.

中文翻译：

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全基因组范围的关联揭示了棉花（棉陆地棉）在盐田条件下皮棉产量成分的遗传变异。

背景技术盐度是限制棉花生产率的最重要的环境因素之一。但是，仍不清楚导致盐碱土壤中棉花减产的关键遗传成分。结果在这里，我们在两年的四个盐分条件下，对316 G.hirsutum品种的皮棉产量，单铃重（SBW），皮棉百分比（LP）和单株铃数（BNPP）评估了三个主要成分。表型分析表明，在高盐条件下，LP保持不变，但BNPP显着降低，而SBW略有增加。根据57,413个高质量单核苷酸多态性（SNP）和全基因组关联研究（GWAS）分析，共确定了42个，91个和25个稳定的定量性状基因座（QTL），用于SBW，LP和BNPP，分别。表型和QTL分析表明这三个性状之间几乎没有相关性。对于LP，在四种不同的盐条件下同时检测到8个稳定的QTL，而针对SBW或BNPP的重复QTL较少。基因本体论（GO）分析表明，它们的调节机制也有很大不同。通过转录组谱数据，我们检测到来自8个稳定LP QTL的10个基因在纤维发育过程中主要表达。此外，单倍型分析发现，MYB基因（GhMYB103）在顺式调控区和编码区具有两个SNP变异，与皮棉百分比显着相关，这暗示了皮棉产量的关键作用。我们还确定BNPP QTL的40个候选基因是盐诱导的。在高盐条件下生长的植物中与碳水化合物代谢和细胞结构维持相关的基因丰富，而在低盐条件下生长的植物中与离子转运相关的基因活跃，这暗示了在高盐和低盐条件下BNPP的调控机制不同。结论本研究为阐明棉花耐盐机理提供了基础，并为开发高产和耐盐胁迫的陆地棉品种提供了基因资源。