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. • ML based phenotyping classifies cotton genotypes with 91.67% accuracy. • Four key miRNAs regulate photosynthesis under salt stress in cotton. • WGCNA links carbon fixation and redox hub genes to salt tolerance. • Tolerant cotton overcomes growth-defense trade-off under salinity. • miRNA-mRNA networks provide targets for breeding salt-tolerant cotton.
Bilal et al. (Sat,) studied this question.