Genetic Diversity and Disease Resistance Genes Profiling in Cultivated Coffea canephora Genotypes via Molecular Markers

Knowledge of the genetic diversity and resistance genes of <i>Coffea canephora</i> genotypes is essential to identify genetic resources that are better adapted to current climate conditions. This study aimed to molecularly characterize and evaluate the genetic diversity of coffee plants cultivated in Rondônia (Amazonia), Brazil, using SNP molecular markers, and to identify plants carrying resistance genes to two major coffee diseases: rust (<i>Hemileia vastatrix</i>) and coffee berry disease (CBD; <i>Colletotrichum kahawae</i>). Genetic diversity analysis revealed five main groups: Group II included 33 genotypes, primarily of the Robusta botanical variety; Group III contained 18 genotypes of the Conilon variety; Group V, the largest, comprised 85 genotypes, mostly hybrids between Robusta and Conilon. Groups I and IV showed fewer, more divergent genotypes. Molecular markers linked to resistance genes enabled the identification of clones with pyramided resistance alleles for both diseases. Three genotypes exhibited a complete pyramided configuration, while others showed different combinations of resistance loci. Marker patterns also allowed classification of genotypes based on origin, variety, and genealogy. These findings provide a valuable foundation for guiding crosses in breeding programs aiming to develop disease-resistant and climate-resilient clones and hybrids, while also supporting cultivar and clone traceability.