Super pan-genome-wide analysis of Hordeum WOX genes and identification of key members conferring salt stress tolerance

Abstract

The WUSCHEL-related homeobox (WOX) is a transcription factor family specific to plants, playing a key role in the initiation and maintenance of meristematic tissue, organ formation and response to abiotic stress. Here we identified 14–15 WOX genes in four Hordeum species, conducted their phylogenetic tree, determined their chromosome locations and gene structures, and analyzed their collinearity and cis-acting elements in promoters. Presence Absence Variation (PAV) analysis revealed that certain WOX genes in the four Hordeum species were lost and expanded. Duplication analysis discovered five types of duplications contributing to the formation of WOX genes, with dispersed duplication (DSD) being the main type in four Hordeum species. WOXs belonging to DSD exhibited a high number of long terminal repeat retrotransposons (LTR-RTs), indicating the potential role of LTR-RTs in the formation of WOX genes of the DSD type. Evaluation of Ka/Ks values showed that all WOX genes have undergone purification selection, with varying degrees among different clades of WOX genes. Furthermore, through pan-transcriptome analysis and quantitative experiments, we identified a common gene clade and the WOX13 co-expression networks responding to saline stress. Survival ratio statistics of Arabidopsis thaliana complementation lines under salt treatment suggested that HvWOX13 may play a crucial role in regulating salt tolerance. These findings provide new insights into evolutionary studies of WOX gene family and offer valuable gene resources for breeding crops with enhanced salt stress resistance.