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.

Background: Cotton is a vital economic crop and reserve material and a pioneer crop planted on saline-alkaline soil. Improving the tolerance of cotton to saline alkaline environments is particularly important. Results: Salt-tolerant and salt-sensitive cotton plants at the three-leaf stage were subjected to 200 mM NaCl stress treatment, thereafter, microstructural observations beside physiological and biochemical analyses were performed on cotton leaves at 0 h (CK), 48 h (NaCl) and re-watering (RW) for 48 h. Salt stress altered microstructural observations and physiological and biochemical in ST and SS (p < 0.05). After re-watering, ST recovered fully, while SS sustained permanent oxidative and structural damage, indicating distinct salt tolerance. Transcriptome analysis was performed on cotton leaves under salt stress and re-watering conditions. KEGG analysis revealed that the response of cotton to salt stress and its adaptation to re-watering may be related to major protein families such as photosynthesis (ko 00195), photosynthesis-antenna protein (ko 00196), plant hormone signal transduction (ko 04075), starch and sucrose metabolism (ko 00500), and porphyrin and chlorophyll metabolism (ko 00860). A gray coexpression module associated with cotton restoration under salt stress was enriched according to WGCNA. Conclusions: Salt stress did not only affect the physiological and biochemical levels of cotton but also induced structural changes in cells and tissues. Re-watering was relatively effective in stabilizing the physiological and biochemical parameters, as well as the leaf microstructure, of cotton plants under salt stress. WGCNA revealed enriched gray coexpression modules related to the recovery of cotton plants under salt stress, and screening of the pivotal genes in the gray module revealed five critical hubs, namely, GH_A01G1528, GH_A08G2688, GH_D08G2683, GH_D01G1620 and GH_A10G0617. Overall, our findings can provide new insights into enhancing cotton salt tolerance and exploring salt tolerance genes in cotton,including screening cotton genetic resources using those potential responsive genes. This study provides a theoretical basis for further exploration of the molecular mechanism of cotton salt tolerance and genetic resources for breeding salt-tolerant cotton.

The VIM (belonged to E3 ubiquitin ligase) gene family is crucial for plant growth, development, and stress responses, yet their role in salt stress remains unclear. We analyzed phylogenetic relationships, chromosomal localization, conserved motifs, gene structure, cis-acting elements, and gene expression patterns of the VIM gene family in four cotton varieties. Our findings reveal 29, 29, 17, and 14 members in Gossypium hirsutum (G.hirsutum), Gossypium barbadense (G.barbadense), Gossypium arboreum (G.arboreum), and Gossypium raimondii (G. raimondii), respectively, indicating the maturity and evolution of this gene family. motifs among GhVIMs genes were observed, along with the presence of stress-responsive, hormone-responsive, and growth-related elements in their promoter regions. Gene expression analysis showed varying patterns and tissue specificity of GhVIMs genes under abiotic stress. Silencing GhVIM28 via virus-induced gene silencing revealed its role as a salt-tolerant negative regulator. This work reveals a mechanism by which the VIM gene family in response to salt stress in cotton, identifying a potential negative regulator, GhVIM28, which could be targeted for enhancing salt tolerance in cotton. The objective of this study was to explore the evolutionary relationship of the VIM gene family and its potential function in salt stress tolerance, and provide important genetic resources for salt tolerance breeding of cotton.