Comprehensive genomic analysis of CiPawPYL-PP2C-SnRK family genes in pecan (Carya illinoinensis) and functional characterization of CiPawSnRK2.1 under salt stress responses

Abscisic acid (ABA) is a pivotal regulator of plant growth, development, and responses to environmental stresses. The ABA signaling pathway involves three key components: ABA receptors known as PYLs, PP2Cs, and SnRK2s, which are conserved across higher plants. This study comprehensively investigated the PYL-PP2C-SnRK gene family in pecan, identifying 14 PYL genes, 97 PP2C genes, and 44 SnRK genes, which were categorized into subgroups through phylogenetic and sequence structure analysis. Whole-genome duplication (WGD) and dispersed duplication (DSD) were identified as major drivers of family expansion, and purifying selection was the primary evolutionary force. Tissue-specific expression analysis suggested diverse functions in different pecan tissues. qRT-PCR validation confirmed the involvement of CiPawPYLs, CiPawPP2CAs, and CiPawSnRK2s in salt stress response. Subcellular localization analysis revealed CiPawPP2C1 in the nucleus and CiPawPYL1 and CiPawSnRK2.1 in both the nucleus and the plasma membrane. In addition, VIGS indicated that CiPawSnRK2.1-silenced pecan seedling leaves display significantly reduced salt tolerance. Y2H and LCI assays verified that CiPawPP2C3 can interact with CiPawPYL5, CiPawPYL8, and CiPawSnRK2.1. This study characterizes the role of CiPawSnRK2.1 in salt stress and lays the groundwork for exploring the CiPawPYL-PP2C-SnRK module, highlighting the need to investigate the roles of other components in the pecan ABA signaling pathway.