Genomic discrimination of the botanical groups conilon and robusta of Coffea canephora

The correct identification of Coffea canephora genotypes into the botanical groups Conilon, Robusta and their hybrids is fundamental for breeding strategies aimed at developing and selecting commercial clones; however, genotype discrimination is challenging when based only on morphological attributes. A total of 121 individuals were evaluated from the Incaper Active Germplasm Bank (BAG): 52 Conilon, 33 Robusta, and 36 hybrids (morphological intermediates showing traits of both groups). DArTseq™ SNPs were filtered, and 1,551 markers were used in the analyses. Cluster analyses revealed three genetic groups: one Robusta (G1) and two Conilon (G2 and G3). AMOVA indicated that 78.49% of the variation occurred among groups and 21.51% within groups. Differentiation was greatest between G1 and G3 (Fst = 0.77), followed by G1 and G2 (Fst = 0.46), whereas G2 and G3 showed lower differentiation (Fst = 0.31). G2 showed high genetic diversity and greater genotypic variability, with three SNP-defined genotypes, suggesting the presence of genetic hybrids. Ten SNPs, located on nine chromosomes and outside genic regions, were validated to discriminate the botanical groups, providing a molecular fingerprinting tool for the characterization of C. canephora germplasm in Brazil.