SNP-based genomic variation in candidate disease resistance genes of Theobroma cacao

Abstract Theobroma cacao is a species with high economic value whose production is impaired by multiple factors, including yield losses caused by pathogens such as Moniliophthora perniciosa , Phytophthora spp., Ceratocystis cacaofunesta , and Moniliophthora roreri . In this context, knowledge of the genetic variability underpinning resistance is crucial to elucidate plant–pathogen interactions and develop resistant cultivars. In this study, we employed bioinformatics tools to predict candidate resistance genes and analyze their genomic variability based on SNPs in the T. cacao genome. A total of 4,523 candidate genes encoding 6,193 proteins were identified, among which 196 genes remain uncharacterized but contain domains typically associated with plant defense functions, including NBS-LRR domains, kinases and pathogenesis-related proteins. Functional annotation of coding regions variants identified 17,576 SNPs, of which 9,014 were classified as missense variants, 8,418 were synonymous variants, and 156 were high-impact variants, including start-loss, stop-loss, and stop-gain mutations. Enrichment analysis of these coding-region genes identified biological pathways and processes involved in plant defense, including oxidative phosphorylation, plant–pathogen interaction, MAPK signaling pathways in plants and phenylpropanoid biosynthesis. Furthermore, five genes were located within quantitative trait loci, intervals previously reported in studies of resistance to Phytophthora spp., encoding proteins including class I chitinase, protease, ACD11, NADH oxidoreductase (NADH-OxR) and aquaporin NIP6-1, all of which have been associated with biological functions relevant to plant defense responses. These findings contribute to the understanding of potential defense-related mechanisms in T. cacao and identify promising candidate genes and variants for future functional validation. Following experimental validation, these candidates may contribute to the development of molecular markers for disease-resistance breeding programs.