Evolutionary expansion of the SnRK gene family in the halophyte Spartina alterniflora and functional characterization of salt-tolerant SaSnRK2.9

Abstract

The SnRK (Sucrose Non-fermenting 1-Related Protein Kinase) gene family plays critical roles in plant stress responses and growth regulation. In this study, we performed a genome-wide identification of SnRK genes across 49 plant species and and focused on functional characterization of key members in the halophyte Spartina alterniflora . A total of 1192 SnRK genes were identified across the 49 species, showing a progressive increase from algae to angiosperms. In S. alterniflora , 55 SaSnRK genes were identified and classified into SaSnRK1 (9), SaSnRK2 (21), and SaSnRK3 (25) subfamilies. These genes are unevenly distributed across 22 chromosomes and exhibit distinct gene structures and conserved motifs. Synteny analysis revealed that segmental duplication events have predominantly driven the expansion of the SaSnRK family. Codon usage analysis suggested that SaSnRK2 subfamily members are under stronger selective constraints and may represent highly expressed genes. Promoter cis -element analysis indicated an enrichment of stress- and hormone-related regulatory motifs. Expression profiling under increasing salt concentrations revealed divergent response patterns among SaSnRK2 subfamily genes, including both constitutively upregulated and high-salinity-specific isoforms. Functional characterization of a salt-inducible SaSnRK2 gene, SaSnRK2.9 , demonstrated that it physically interacts with two SaPP2C proteins and, when overexpressed in Arabidopsis , not only promotes earlier flowering by 4–6 days but also significantly enhances salt tolerance, with transgenic lines achieving a survival rate exceeding 50% following salt stress and recovery, compared to less than 20% in wild-type plants. These findings, obtained primarily through heterologous overexpression in Arabidopsis , provide mechanistic insights into how a halophytic SnRK2 kinase balances stress tolerance and developmental regulation. While direct in vivo evidence in S. alterniflora is still required, our results highlight SaSnRK2.9 as a promising candidate gene for improving salt tolerance and agronomic traits in crops.