Comprehensive analysis of the GmCPA gene family and natural variation in GmCHX20b in soybean reveals the role of the PlsC domain in salt tolerance

Soil salinization, aggravated by climate change, is a major constraint on global agricultural productivity. The ionic imbalance induced by excessive soil salinity disrupts cellular ion homeostasis, impairing various metabolic pathways in soybean and consequently reducing plant growth and agronomic traits. While the regulatory roles of Na +/ H + and K +/ H + antiporters are pivotal for maintaining cellular ion homeostasis, the underlying mechanisms governing salt tolerance in soybean remain unclear. The study aimed to comprehensively identify GmCPA genes, encoding cation/proton antiporters, and elucidate their physiological functions under salt stress through comparative analyses of natural variation in soybean cultivars, with emphasis on the functional significance of the PlsC (Phospholipid/glycerol acyltransferase) domain in GmCHX20b . A total of 75 GmCPA genes were identified and unevenly distributed on 20 soybean chromosomes. Phylogenetic and collinearity analyses provided valuable insights into the evolutionary divergence and gene duplication patterns of GmCPA genes. Promoter analysis of GmCPA genes revealed numerous cis -acting regulatory elements associated with stress, hormones, light signaling, and developmental regulation. Transcriptomic analysis showed that GmCPA genes are expressed in specific tissues and transcriptionally induced under salt stress. Notably, GmCHX20b has functionally diverged, exhibiting natural variation in the presence or absence of the PlsC domain across soybean cultivars. Phenotypic and ion homeostasis analyses under salt stress in soybean cultivars with natural variants of GmCHX20b highlight the PlsC domain contributes to salt tolerance independently of the sodium/hydrogen exchanger domain. These insights into the functional diversification of GmCHX20b underscore the contribution of the PlsC domain to salt stress tolerance. ● Natural variation in GmCHX20b haplotypes correlates with soybean salt tolerance ● Both Na + /H + exchanger and PlsC domains of GmCHX20b are essential under salt stress ● The PlsC domain is implicated in PA signaling associated with membrane stability ● GmCHX20b links ion transport and lipid signaling during salt stress