Comprehensive Genomic Analysis of the CDPK Gene Family in Pecan (Carya illinoinensis) and Their Potential Roles in Salt Stress Response

Calcium-dependent protein kinases (CDPKs) are crucial for plant development and stress responses. In this study, we performed a comprehensive genomic analysis of the <i>CDPK</i> gene family in pecan (<i>Carya illinoinensis</i>) and evaluated their potential roles in salt stress responses. A total of 31 <i>CiCDPK</i> genes were identified and classified into four subgroups through phylogenetic analysis. Structural and promoter analyses revealed conserved motifs and regulatory elements linked to stress responses. Gene duplication analysis showed that WGD and DSD events were primary drivers of <i>CiCDPK</i> expansion, shaped by purifying selection. GO and KEGG annotations highlighted roles in kinase activity, calcium binding, and signal transduction, while interaction networks suggested involvement in ROS regulation and ATP-dependent phosphorylation. Tissue-specific expression patterns indicated distinct roles of <i>CiCDPKs</i>, with <i>CiCDPK20</i> and <i>CiCDPK31</i> predominantly expressed in male flowers and seeds, respectively. Transcriptome data showed that <i>CiCDPKs</i> exhibited distinct responses to abiotic and biotic stress, highlighting their functional specialization under various conditions. qRT-PCR analysis further confirmed the involvement of 16 <i>CiCDPKs</i> in salt stress adaptation, supporting their critical roles in signal transduction pathways during salinity stress. This study provides insights into <i>CiCDPK</i> functions, offering potential applications in breeding pecan varieties with enhanced salt tolerance.