Salt stress-induced alterations of photosynthesis and growth are associated with microRNA-mediated transcriptome regulatory networks in cotton

Despite advances in genetic engineering for cotton improvement, salt stress severely impacts cotton productivity. Photosynthesis is critical for cotton yield, but this decline is often exacerbated by the growth-defence trade-off under salt stress. Therefore, exploring semi-wild cotton relatives is a promising approach to understand such a trade-off. Here, we examined the growth-defence dilemma in semi-wild cotton genotypes by integrating multi-omics and machine learning (ML)-assisted phenotyping. The ML-assisted physiological screening distinguished 204 as a salt-sensitive genotype and TM-1 as a salt-tolerant genotype, based on leaf gas exchange, biomass production, and whole-plant responses to salt stress. The integrated microRNA-transcriptomics analysis indicated that TM-1 exhibited significant enriched miRNAs and differentially expressed genes (DEGs) in the transcriptional regulation of photosynthesis and carbon fixation, whereas 204 showed a more generalised response to salt stress. Weighted Gene Co-expression Network Analysis (WGCNA) identified three core modules associated with photosynthetic traits, with enriched hub genes in the Calvin cycle (RUBISCO, FBPase, PGK) and redox homeostasis (POD, CYP450). Notably, the downregulation of ghr-miR156b, ghr-miR160, ghr-miR164, and ghr-miR166b in TM-1 was consistent with the upregulation of their target genes. However, 204 showed less coordinated regulation with reduced expression of growth-related genes under salt stress. In agreement with these findings, both TM-1 and 204 showed higher antioxidant activities under salt stress, except for the activation of photosynthetic enzymes, which was higher in TM-1 only. Our study indicates a putative regulatory module of hub genes and miRNAs for biotechnological optimisation by potentially reducing growth-defence trade-offs in cotton.