Saline-alkali stress is one of the major abiotic stresses threatening crop growth. Cotton, as a “pioneer crop” that can grow in saline and alkali lands, is of great significance for understanding the regulatory mechanisms of plant response to stresses. Upland cotton has thus become a model plant for researchers to explore plant responses to saline-alkali stresses. In this study, RNA sequencing was employed to analyze tissue-specific expression of root tissues of TM-1 seedlings 20 min after exposure to compound saline-alkali stress. The RNA-Seq results revealed significant molecular differences in the responses of different root regions to the stress treatment. A total of 3939 differentially expressed genes (DEGs) were identified from pairwise comparisons between the non-root tip and root tip samples, which were primarily enriched in pathways including plant hormone signal transduction, MAPK signaling, and cysteine and methionine metabolism. Combined with the expression pattern investigation by quantitative real-time PCR (qRT-PCR) experiments, a key gene, GhERF2 (GH_A08G1918, ethylene-responsive transcription factor 2-like), was identified to be associated with saline-alkali tolerance. Through virus-induced gene silencing (VIGS), the GhERF2-silenced plants exhibited a more severe wilting phenotype under combined salt-alkali stress, along with a significant reduction in leaf chlorophyll content and fresh weights of plants and roots. Additionally, these plants showed greater cellular damage and a lower ability to scavenge reactive oxygen species (ROS) when exposed to the stress. These findings suggest that the GhERF2 gene may play a positive regulatory role in cotton responses to salt-alkali stress. These findings not only enhance our understanding of the molecular mechanisms underlying cotton response to compound saline-alkali stress, but also provide a foundation for future molecular breeding efforts aimed at improving cotton saline-alkali tolerance.

Verticillium wilt (VW) caused by Verticillium dahliae (Vd) is a devastating fungal cotton disease characterized by high pathogenicity, widespread distribution, and frequent variation. It leads to significant losses in both the yield and quality of cotton. Identifying key non-synonymous single nucleotide polymorphism (SNP) markers and crucial genes associated with VW resistance in Gossypium hirsutum and Gossypium barbadense, and subsequently breeding new disease-resistant varieties, are essential for VW management. Here, we sequenced the transcriptome and metabolome of roots of TM-1 (G. hirsutum) and Hai7124 (G. barbadense) after 0, 1, and 2 days of V991 inoculation. Transcriptome analysis identified a total of 72,752 genes, with 5814 differentially expressed genes (DEGs) determined through multiple group comparisons. KEGG enrichment analysis revealed that the key pathways enriched by DEGs obtained from both longitudinal and transverse comparisons contained the glutathione metabolism pathway. Metabolome analysis identified 995 metabolites, and 22 differentially accumulated metabolites (DAMs), which were correlated to pathways including glutathione metabolism, degradation of valine, leucine, and isoleucine, and biosynthesis of terpenoids, alkaloids, pyridine, and piperidine. The conjoint analysis of transcriptomic and metabolomic sequencing revealed DAMs and DEGs associated with the glutathione metabolism pathway, and the key candidate gene GH_D11G2329 (glutathione S-transferase, GSTF8) potentially associated with cotton response to VW infection was selected. These findings establish a basis for investigating the mechanisms underlying the cotton plant’s resistance to VW.

The BSL gene family, comprised of phosphatase genes with kelch domains, plays vital roles in plant responses to brassinosteroid (BR) signaling and immune reactions to abiotic stress. However, there is no BSL-related reports in cotton, which has been regarded as an ideal crop for investigating genome ploidy and tolerance pioneer. In this study, a key drought response gene GHBSL7 was identified via genome-wide analysis of evolutionary trajectories and responses to abiotic stresses of cotton BSL genes. Functional identification using VIGS silence and RNA-seq revealed that GHBSL7 may participate cotton responses to drought through regulating the homeostasis of ROS and glycolytic pathway by regulating TcTPI and GAPDH genes in the central metabolic network. This study provides fundamental insights into the interplay of phytohormone signaling and molecular targets for future development of drought-tolerant cotton cultivars.