Genome-wide identification and functional characterization of PP2C genes in the wild relative of sweet potato Ipomoea trifida.

BACKGROUND: Protein phosphatase 2 C (PP2C) proteins play crucial roles in plant growth, development, and stress responses. However, PP2C gene family members in Ipomoea trifida (wild relative of sweet potato) have not been comprehensively investigated, thereby limiting our understanding of their functions. RESULTS: We identified 91 PP2C genes (ItfPP2C1-91) that were unevenly distributed across all 15 I. trifida chromosomes. On the basis of a phylogenetic analysis, these genes were classified into 13 subfamilies, with subfamilies E, A, and D containing the most genes. Conserved motif and gene structure analyses revealed subfamily-specific patterns, with motif 2 identified as the most conserved motif. Numerous promoter cis-acting elements related to hormone responses and stress tolerance were identified. Tissue-specific ItfPP2C expression patterns were observed, with several genes expressed at high levels in all examined tissues, while other genes were expressed in specific tissues. Under drought conditions, most PP2C genes had upregulated expression levels, with significant increases in ItfPP2C15, 16, 30, and 77 (subfamily A) expression suggesting that they may be key drought-responsive candidate genes. In response to a stem nematode infection, ItfPP2C30, ItfPP2C77, and ItfPP2C89 were differentially expressed between resistant and susceptible varieties. Moreover, ItfPP2C90 expression was significantly induced in Z22 and L9 at 12 h. Hence, these genes may be involved in disease resistance. A protein interaction network analysis identified proteins that may interact with ItfPP2C30 and ItfPP2C77, most of which were ABA receptors (PYLs) and kinases (SnRK2s). CONCLUSIONS: Our comprehensive analysis of the PP2C gene family in I. trifida provides valuable insights into their evolutionary relationships, structural features, and potential functions related to growth and stress responses. ItfPP2C30 and ItfPP2C77 were identified as promising candidates for improving both drought and nematode resistance, with the encoded proteins potentially interacting with PYL and SnRK2 proteins in stress-related signaling pathways.