Transcriptomic Insights into Salt Stress Response in Two Pepper Species: The Role of MAPK and Plant Hormone Signaling Pathways

Salt stress imposes significant plant limitations, altering their molecular, physiological, and biochemical functions. Pepper, a valuable herbaceous plant species of the <i>Solanaceae</i> family, is particularly susceptible to salt stress. This study aimed to elucidate the physiological and molecular mechanisms that contribute to the development of salt tolerance in two pepper species (<i>Capsicum baccatum</i> (moderate salt tolerant) and <i>Capsicum chinense</i> (salt sensitive)) through a transcriptome and weighted gene co-expression network analysis (WGCNA) approach to provide detailed insights. A continuous increase in malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) levels in <i>C. chinense</i> and higher activities of catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) in <i>C. baccatum</i> indicated more tissue damage in <i>C. chinense</i> than in <i>C. baccatum.</i> In transcriptome analysis, we identified 39 DEGs related to salt stress. Meanwhile, KEGG pathway analysis revealed enrichment of MAPK and hormone signaling pathways, with six DEGs each. Through WGCNA, the ME.red module was identified as positively correlated. Moreover, 10 genes, <i>A-ARR</i> (CQW23_24856), <i>CHIb</i> (CQW23_04881), <i>ERF1b</i> (CQW23_08898), <i>PP2C</i> (CQW23_15893), <i>ABI5</i> (CQW23_29948), <i>P450</i> (CQW23_16085), <i>Aldedh1</i> (CQW23_06433), <i>GDA</i> (CQW23_12764), <i>Aldedh2</i> (CQW23_14182), and <i>Aldedh3</i> (CQW23_11481), were validated by qRT-PCR. This study provides valuable insights into the genetic mechanisms underlying salt stress tolerance in pepper. It offers potential targets for future breeding efforts to enhance salt stress resilience in this crop.