Expression Landscape, Evolutionary Insights, and Duplication Patterns of Cinnamyl Alcohol Dehydrogenase Genes Under Macrophomina phaseolina Infection and Salt Stress in Sesame

Sesame ( Sesamum indicum ) has been cultivated for centuries, prized for its oil and medicinal properties. With the availability of its genome, the identification and characterization of key gene families have become a research priority. Cinnamyl Alcohol Dehydrogenase ( CAD ) gene plays a pivotal role in the phenylpropanoid pathway by catalysing the final step in lignin biosynthesis, specifically the production of monolignols. In this study, we identified CAD homologs and paralogs in the sesame genome using bioinformatic tools. Comparative synteny analysis with related species such as tomato and potato revealed evolutionary conservation and provided insights into the functional roles of sesame CAD genes ( SiCADs ). Phylogenetic and gene duplication analyses suggest that SiCADs genes have undergone purifying selection, indicating evolutionary pressure to maintain their functional integrity, particularly under environmental stress. To understand the role of these genes in stress responses, we performed RNA-seq analysis under two major stress conditions: infection with Macrophomina phaseolina , the causal agent of charcoal rot, and salt stress (NaCl). Expression profiling revealed that several SiCADs are differentially regulated in both wild ( S. mulayanum ) and cultivated ( S. indicum ) genotypes, with notable differences in expression patterns across stress types and time points. These findings underscore the potential role of SiCADs in defense and stress adaptation. This is the first comprehensive study of the CAD gene family in sesame, offering insights into their evolutionary dynamics and functional relevance. Subsequent, validation of obtained genic simple sequence repeats (gSSRs), will benefit the molecular breeding programs of sesame. The candidate genes identified in this study would provide a resource for gene cloning, functional validation, and molecular breeding, contributing to the development of stress-resilient sesame cultivars.