Metabolomic and transcriptomic analyses reveal positive roles of root border cells in salinity resistance in cotton (Gossypium hirsutum L.)

Root border cells (RBCs) play important roles in plant stress tolerance. However, their roles and underlying mechanisms in salinity stress responses remain largely unknown. To elucidate the salinity-induced metabolic adaptations and transcriptional responses of RBCs in cotton ( Gossypium hirsutum L.), we performed a comparative analysis of the metabolomes and transcriptomes of RBCs and adjacent naked root tips (NRTs, RBCs removed) under salinity stress. A total of 150 and 195 differentially accumulated metabolites, along with 10,593 and 7270 differentially expressed genes (DEGs) were identified in RBCs and NRTs, respectively. RBCs exhibited elevated accumulation of glycerophospholipids, sterols, unsaturated fatty acids and betaine relative to NRTs, which are crucial for maintaining membrane stability and osmoregulation. Enrichment analysis revealed that the α-linolenic acid metabolism pathway, participating in both lipid metabolism and jasmonic acid (JA) biosynthesis, was specially enriched in RBCs. DEGs associated with JA and salicylic acid signaling pathways showed markedly higher upregulation in RBCs than in NRTs, indicating stronger stress-responsive signaling in RBCs under salinity stress. Notably, azelaic acid (AZA), a lipid signaling molecule, was accumulated at higher levels in RBCs. Exogenous AZA application increased the production of RBCs and improved cotton seedling salinity tolerance. Taken together, higher accumulation of membrane-stabilizing and signaling lipids, as well as stronger JA/SA signal transduction promote salinity tolerance in RBCs. These findings expand our understanding of plant metabolic alterations in response to salinity stress and offer potential targets for improving cotton salinity tolerance. • Root border cells accumulate higher levels of glycerophospholipids and unsaturated fatty acids to maintain membrane stability in response to salinity stress. • The enhanced jasmonic acid and salicylic acid signaling pathways, as well as α-linolenic acid metabolism pathway promote salinity tolerance in RBCs. • The exogenous application of azelaic acid can significantly improve cotton salinity tolerance.