Genome-wide analysis of RVT_3 gene family in upland cotton

Soil salinization induces salt stress, which restricts plant growth and development, presenting significant obstacles to agricultural production and constraining productivity gains. To shift from managing saline-alkali lands to selecting salt-tolerant crops adapted to such conditions, identifying effective salt-tolerance genes in crops is essential.The RVT＿3 gene family, part of the retrotransposon group, features domains widely distributed across plant species.Prior salt-stress transcriptome analysis of upland cotton revealed that multiple genes within this family are associated with salt tolerance. In this study, bioinformatics analysis of the RVT＿3 family was performed using the PFam database,identifying 173 genes across the upland cotton genome. Analyses of phylogeny, gene structure, chromosome localization, and gene duplication were conducted, alongside an examination of cis-acting elements within these genes. Chromosome mapping revealed numerous fragment duplication events among RVT＿3 genes. Phylogenetic, gene structure,and conserved motif analyses indicated that genes within the same subfamily exhibit comparable structures and motifs.Cis-acting element analysis suggested potential involvement of this gene family in responses to diverse biotic and abiotic stresses. The RVT＿3 proteins were classified into three distinct subfamilies, with structural similarities among genes within each subgroup supporting subfamily differentiation. Of the 173 genes, 146 are distributed across the 26chromosomes of upland cotton. RT-qPCR data further confirmed the responsiveness of this gene family to salt stress in upland cotton. These findings offer insights into the evolutionary relationships and functional roles of the RVT＿3gene family, establishing a basis for deeper investigation into cotton′ s salt-tolerance mechanisms and supporting molecular breeding efforts for enhanced salt tolerance.