Genome-wide detection of SH3-associated molecular markers in Coffea cultivars using the Johara R-based bioinformatics pipeline

Coffee leaf rust (CLR), caused by Hemileia vastatrix, is a major constraint to global coffee production. This study screened for SH3-linked molecular markers associated with CLR resistance in the genomes of Coffea canephora DH200-94, C. eugenioides Bu-A, and C. arabica ET-39 using a custom R-based workflow (Johara pipeline). Ten molecular markers commonly linked to the SH3 resistance locus were analyzed via exact primer mapping, revealing varying patterns of marker presence across species. C. arabica ET-39 showed the highest number of matches, particularly in the Chromosome 3 regions, suggesting potential SH3-associated resistance, whereas C. eugenioides Bu-A had no detectable markers. This work highlights the utility of computational pipelines for rapid genome-scale detection of resistance-associated loci and provides insights for future breeding programs aimed at enhancing CLR resistance in coffee cultivars.