Integrated transcriptomics and metabolomics analyses reveal jasmonic acid metabolic pathways for improving the chilling tolerance in cotton seedlings

Cotton (Gossypium spp.) originated in tropical and subtropical regions, spreading to higher latitudes through domestication while retaining thermophilic characteristics. Xinjiang, a major cotton-producing area in China, frequently experiences ‘late spring cold snaps’ due to its location, causing chilling injury during critical sowing periods. Current research on cotton chilling stress primarily focuses on physiological studies such as evaluations of chilling stress and biochemical indices but lacks systematic investigation into the difference among varieties. Phenotypic screening across seed germination, cotyledon, and seedling stages identified upland cotton (Gossypium hirsutum) cultivar, Junmian1 exhibits superior cold tolerance relative to the sensitive genotype C1470. Under chilling stress, Junmian1 protects chloroplasts and other cellular structures in its first true leaf to survive the chilling stress. Weighted gene co-expression network analysis (WGCNA) analysis pinpointed Module Brown as a chilling-tolerance responsive hub, with subsequent validation via virus-induced gene silencing (VIGS) confirming the regulatory roles of GhRBL (Ribulose-bisphosphate carboxylase), GhGI (GIGANTEA), and lncRNA MSTR.1631 in cold tolerance. Additionally, integrated metabolomic and transcriptomic analyses demonstrated that jasmonic acid plays a crucial role in enhancing cotton's chilling tolerance at seedling stage. The primary difference in chilling tolerance between Junmian1 and C1470 is attributed to the signaling efficiency of the jasmonic acid synthesis and metabolism pathways. These findings establish JA metabolic engineering as a viable approach for enhancing cold resilience in early-stage cotton seedlings.