Molecular Characterization of Opuntia spp

According to the different classification methods, the genus Opuntia belongs to the Cactaceae family native to the Americas, and encompasses several species ranging from 75 to 250. Many of these species are diffused, and some of them are cultivated in arid and semi-arid areas. The most economically important species is O. ficus-indica L. (Mill.), but the genus includes other important edible species (from diploid to octoploid), which are spread, wild, or cultivated in many regions worldwide. Opuntia species are gaining popularity in different areas, mainly arid and semi-arid, both for fruit production for human consumption and mainly for animal feeding using the tender and mature green part of the whole plant (cladodes). The taxonomic classification of the genus is hampered by several factors: the lack of reliable morphological descriptors, the recurrent intra-and intergeneric hybridization, the frequent polyploidy, and the phenotypic variation displayed by the genotypes under different ecological conditions. Due to the ambiguity of the different taxonomic hypotheses formulated based on morphological traits, in the last years, several DNA-based studies, relying on different categories of molecular markers, have been carried out in order to better assess variability level within the main cultivated species (O. ficus-indica) and to assess relationships and origin of the main species. The first set of studies aimed to characterize the genotypes cultivated for fruit production and the results achieved gave evidence of a narrow germplasm base involved in their origin compared to that of ornamental and wild species. Other studies evidenced a high similarity between O. ficus-indica and O. megacantha suggesting the latter could be a progenitor of the cultivated prickly pear varieties. Cytoplasmic markers were also employed on Opuntias; this approach evidenced a multiple maternal phylogeny for the fleshy fruit varieties classified as O. ficus-indica and revealed the most common varieties' narrow genetic base used for fruit production. In contrast, greater variability was revealed for genotypes used as forage. Several results converge on the hypothesis of a polyphyletic origin of O. ficus-indica; this is likely composed of several originary clones, selected and vegetatively propagated from different parental species for their favorable agronomic traits. However, many Opuntia species' different polyploidy levels hampers their clear phylogenetic assignment based on nuclear markers. Extranuclear molecular markers, located in the chloroplast and mitochondrial genomes, have also been employed to investigate the phylogenetic relationship among cultivated genotypes, wild accessions, and related species for the lack of recombination and maternal haploid inheritance and appear to be suitable for overcoming problems related to polyploidy. The main results from molecular studies will be reviewed in this chapter highlighting their potential for overcoming the faultiness of the taxonomy currently adopted. An integrated approach of molecular-based characterization and the adoption of accurate large-scale phenotyping of existing germplasm collections could lead to functional management of genetic resources for their sustainable conservation and plan future breeding strategies for improved genotypes to be cultivated in distinct areas for different purposes.