Genome-Wide Identification of the Cation/Proton Antiporter (CPA) Gene Family and Expression Pattern Analysis Under Salt Stress in Winter Rapeseed (Brassica rapa L.)

The <i>CPA</i> gene family regulates ionic balance and pH homeostasis in cells, significantly contributing to plant stress tolerance. In this study, a total of 63 <i>BrCPA</i> gene family members were identified in the whole genome of <i>Brassica rapa</i> L. (<i>B. rapa</i>), and the three subfamily members were <i>BrNHX</i> (9), <i>BrKEA</i> (15), and <i>BrCHX</i> (39), respectively. The members of the <i>BrCPA</i> gene family encoded 303-1259 amino acids, with molecular weights in the range of 32,860.39~139,884.73 kDa, distributed on 10 chromosomes, and contained 17 conserved motifs, <i>BrNHX</i> and <i>BraKEA</i>, and the <i>BrCPA</i> gene family members had the same molecular weights on 10 chromosomes and contain 17 conserved motifs. The <i>BrNHX</i> and <i>BraKEA</i> subfamilies have more exons than the <i>BrCHX</i> subfamily. An analysis of promoter cis-acting elements in the <i>BrCPA</i> gene showed that members of this gene family contain TC-rich, LTR, MBS, and ARE stress response elements. In addition, transcriptome analysis revealed the expression of <i>CPA</i> genes in <i>B. rapa</i> under salt stress. The selected genes were verified by RT-qPCR. By detecting the Na⁺ and K⁺ flow rates in the root and chloroplast cells of salt-tolerant and salt-sensitive varieties after salt treatment, it was found that the rate of Na⁺ and K⁺ efflux from the root and chloroplast cells of salt-sensitive varieties was significantly higher than that of salt-tolerant varieties. This investigation marks the first systematic identification of the <i>CPA</i> gene family in <i>B. rapa</i>. This study further explores its expression patterns and the efflux rates of Na⁺ and K⁺ across salt-tolerant varieties, providing a theoretical basis for understanding the role of the <i>CPA</i> gene family in the salt stress response of <i>B. rapa</i>.