Relationships among cultivated Opuntia ficus-indica genotypes and related species assessed by cytoplasmic markers

The taxonomic classification of the genus Opuntia, which includes several cultivated species, is complicated mainly because of inadequate morphological descriptors, the common intra- and inter-generic hybridization and the relationships between phenotypic variation and ecological conditions. The phylogenetic relationships among 72 cultivated genotypes, either selected for fruit or forage production, and wild accessions belonging to approximately 15 different species of Opuntia were inferred using cytoplasmic markers. Previous studies indicated as the most important cultivated accessions for fruit production have a polyphyletic origin but polyploidy hampered their clear phylogenetic assignment based on nuclear markers. Cytoplasmic markers are considered helpful for their maternal inheritance and for overcoming the multiple gene copy problem in polyploid phylogenetics already reported in the Opuntia genus. In particular, we combined in this work capillary electrophoresis for newly designed cpSSRs and high resolution melting for SNV analyses to identify chloroplast (ndhF-rpl32, psbJ-petA, atpB-rbcL, matK, ycf1) and mitochondrial (rpl5) DNA markers in a selected group of genotypes. The results revealed the presence of polymorphisms in the predicted cpSSRs and SNVs and clearly evidenced that most of the studied genotypes were closely related to Opuntia ficus-indica (L.) Miller. Plastid markers identified 11 chlorotypes and 8 unique genotypes. Interestingly the analysis evidenced a multiple maternal phylogeny for the fleshy fruit varieties classified as O. ficus-indica. These results allow questioning of the reliability of the current classification based on morphological parameters and reveal the narrow genetic base of the most common cultivated opuntias for fruit production, while forage genotypes evidenced greater variability.