Xiang Ren

Background/Objectives: Soil salinization constitutes a critical threat to global agriculture, with cotton (Gossypium spp.) being highly susceptible. This abiotic stress most severely impacts cotton during the early sowing and seedling stages, compromising stand establishment and early growth. Manifestations of this stress include reduced germination rates, uneven emergence, stunted seedlings, and, ultimately, diminished boll set and fiber yield. Methods: To investigate the molecular basis of salt tolerance in cotton seed germination, we performed integrated transcriptomic and metabolomic profiling of Gossypium hirsutum cv. ST022-1056m5 under 150 mM NaCl stress at 24 h, 48 h, and 72 h, finding that salt stress significantly inhibited germination. Differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were identified, followed by functional enrichment and Weighted Gene Co-expression Network Analysis (WGCNA) to construct regulatory networks. Results: Transcriptomics revealed stage-specific differentially expressed genes, with predominant downregulation and enrichment in catalytic/transporter activities. Metabolomics showed distinct reprogramming, with 210 shared differentially accumulated metabolites enriched in lipids, organic acids, terpenoids, and phenolic acids. KEGG analysis highlighted time-dependent pathway shifts: sucrose metabolism and MAPK signaling at 24 h, photosynthesis at 48 h, and cuticular lipid biosynthesis at 72 h. Weighted Gene Co-expression Network Analysis (WGCNA) identified stage-associated modules and hub genes (GH_A02G0892, GH_A08G2853), and multi-omics integration indicated the strongest transcript–metabolite coordination at 24 h. Conclusion: Our study reveals dynamic molecular reprogramming underpinning stage-specific salt adaptation in germinating cotton seeds. These identified DEGs, DAMs, and hub genes represent promising candidate targets for molecular breeding and offer a crucial genetic basis for improving salt tolerance in cotton.

Salt stress is a major environmental constraint that severely limits cotton seed germination. However, the regulatory mechanisms governing salt stress responses during the post-germination stage remain largely unclear. Here, we employed an integrated transcriptomic and metabolomic approach to investigate salt-responsive mechanisms in the salt-tolerant cotton cultivar ST022-1056m5 (ST) following exposure to 150 mM NaCl. Our analysis identified 4368 differentially expressed genes (DEGs) and 441 differentially accumulated metabolites (DAMs) under salt stress conditions. Multi-omics integration revealed that alpha-linolenic acid and linoleic acid metabolic pathways were particularly responsive to salt stress. In the α-linolenic acid pathway, salt stress triggered substantial accumulation of jasmonic acid (JA) precursors and concurrent upregulation of key JA biosynthetic genes. Simultaneously, the linoleic acid metabolism pathway exhibited increased metabolite levels and enhanced the relative gene expression. These findings provide compelling evidence that alpha-linolenic acid and linoleic acid metabolism pathways collectively modulate post-germination salt stress responses in cotton, offering new insights into the molecular mechanisms underlying salt tolerance and presenting potential targets for breeding resilient cotton varieties.

The cytokinin response regulator (ARR) gene is essential for cytokinin signal transduction, which plays a crucial role in plant growth and development. However, the functional mechanism of ARR genes in cotton leaf abscission remains incompletely understood. In this study, a total of 86 ARR genes were identified within the genome of Gossypium hirsutum. These genes were categorized into four distinct groups based on their phylogenetic characteristics, supported by analyses of gene structures and conserved protein motifs. The GhARR genes exhibited an uneven distribution across 25 chromosomes, with three pairs of tandem duplication events observed. Both segmental and tandem duplication events significantly contributed to the expansion of the ARR gene family. Furthermore, numerous putative cis-elements were identified in the promoter regions, with hormone and stress-related elements being common among all 86 GhARRs. Transcriptome expression profiling screening results demonstrated that GhARRs may play a mediating role in cotton’s response to TDZ (thidiazuron). The functional validation of GhARR16, GhARR43, and GhARR85 using virus-induced gene silencing (VIGS) technology demonstrated that the silencing of these genes led to pronounced leaf wilting and chlorosis in plants, accompanied by a substantial decrease in petiole fracture force. Overall, our study represents a comprehensive analysis of the G. hirsutum ARR gene family, revealing their potential roles in leaf abscission regulation.

This study identified 13 GhTIR1/AFB members in G. hirsutum through bioinformatics methods and divided them into three subgroups by phylogenetic tree analysis. Motif and gene structure analysis showed that the genes in this family were highly conserved. Promoter cis-acting element analysis found that the promoters of GhTIR1/AFBs contained a large number of cis-acting elements in response to growth and development and abiotic stress. Further RT-qPCR results showed that GhTIR1/AFB genes responded to various abiotic stresses such as IAA, ABA, cold, and heat, and the expression levels of each gene changed obviously, especially Gh_D08G0763 (GhTIR1), which responded significantly to cold injury. Using VIGS (virus-induced gene silencing) technology to silence Gh_D08G0763 in the cold-tolerant cotton variety ZM36, it was found that the resistance of ZM36 to cold damage was significantly reduced. The physiological response mechanism of the Gh_D08G0763 in resisting cold damage was further analyzed through trypan blue staining of leaves and determination of enzyme activity levels. This study provided effective genetic resources for cotton cold-tolerance breeding.

Salinity is a major abiotic stress that restricts cotton growth and affects fiber yield and quality. Although studies on salt tolerance have achieved great progress in cotton since the completion of cotton genome sequencing, knowledge about how cotton copes with salt stress is still scant. S-adenosylmethionine (SAM) plays important roles in many organelles with the help of the SAM transporter, and it is also a synthetic precursor for substances such as ethylene (ET), polyamines (PAs), betaine, and lignin, which often accumulate in plants in response to stresses. This review focused on the biosynthesis and signal transduction pathways of ET and PAs. The current progress of ET and PAs in regulating plant growth and development under salt stress has been summarized. Moreover, we verified the function of a cotton SAM transporter and suggested that it can regulate salt stress response in cotton. At last, an improved regulatory pathway of ET and PAs under salt stress in cotton is proposed for the breeding of salt-tolerant varieties.