Identification and Expression Analysis of the CHX Gene Family in Capsicum annuum L.

The cation/H⁺ exchanger (<i>CHX</i>) gene family plays a vital role in maintaining K⁺/Na⁺ homeostasis in plants, yet its functional characterization in pepper (<i>Capsicum annuum</i> L.) remains largely unexplored. To elucidate the potential roles of <i>CHX</i> genes in stress adaptation and development in pepper, a genome-wide identification and systematic analysis of this gene family was performed. Using a combination of Hidden Markov Model (HMM) searches, phylogenetic reconstruction, conserved motif and promoter analysis, and expression profiling across tissues and under multiple stress conditions, a total of 23 <i>CaCHX</i> genes were identified, which are unevenly distributed across 10 chromosomes and classified into 6 phylogenetic subfamilies. Expression profiling revealed that most <i>CaCHX</i> genes were highly expressed in flowers, suggesting their potential involvement in reproductive development, while only <i>CaCHX12</i> and <i>CaCHX17</i> were detected in leaves. Under treatments such as abscisic acid (ABA), gibberellic acid (GA), NaCl, and jasmonic acid (JA), <i>CaCHX1</i>, <i>CaCHX20</i>, and <i>CaCHX23</i> exhibited distinct temporal expression patterns, suggesting their involvement in hormone-mediated stress responses. This study provides the first comprehensive genomic and transcriptomic overview of the <i>CHX</i> family in pepper, offering novel insights into its regulatory roles in flower development and stress tolerance and, thus supplying valuable genetic resources for molecular breeding aimed at enhancing pepper resilience.