Genomic exploration and functional insights into the diversification of the Snf2 gene family in subgenomes of Triticum aestivum

Abstract

Sucrose nonfermenting 2 (Snf2) family proteins function as the ATP-dependent catalytic engines of chromatin remodeling complexes, which harness ATP hydrolysis energy to alter chromatin structure and nucleosome positioning, enabling regulatory factor access to DNA. Plant genomes contain numerous Snf2 family proteins, several of which have been demonstrated to act as key developmental regulators at different stages in model plants like Arabidopsis and rice. Despite their vital roles, the Snf2 genes in Triticum aestivum remain largely uncharacterized. Here, we report the identification of 112 wheat Snf2 genes that were unevenly distributed across the 21 chromosomes, with 40 genes on the A subgenome, 33 on the B subgenome, and 39 on the D subgenome, and phylogenetically classified these Snf2 genes into 18 subfamilies related to the 6 Snf2 groups in Arabidopsis. Evolutionary analysis revealed that purifying selection has largely driven the evolution of Snf2 genes, acting as the primary selective force shaping the Snf2 gene family in wheat, while segmental duplications have served as the main mechanism for expanding the gene family. All identified Snf2 proteins contained at least one Helicase_C and SNF2_N domain among 10 conserved domains, and their gene structures consisted of 3–38 exons. Tissue-specific expression analysis uncovered distinct expression patterns among Snf2 gene family members, including some with enhanced reproductive tissue expression, while analysis under various abiotic and biotic stresses revealed differential regulation of specific family members in response to these conditions. Overall, these systematic analyses including identification, evolutionary relationships, and expression profiling provide valuable insights into the wheat Snf2 family while establishing a genomic framework to elucidate Snf2 functional roles in wheat growth, development, and stress responses.