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

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 esistance 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 associated with defense-related functions, including NBS-LRR domains, kinases and pathogenesis-related proteins. Analysis of coding regions revealed 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 previously associated with resistance to Phytophthora spp., and that encode proteins such as class I chitinase, protease, ACD11, NADH oxidoreductase (NADH-OxR) and aquaporin NIP6-1, which are directly involved in defense responses. These results broaden understanding of defense mechanisms in T. cacao genotypes, identify potential candidates for future functional validation, and can be applied in marker-assisted breeding programs focused on disease resistance.