Assessment of genetic diversity of Brazilian and Mediterranean cactus cultivars by SSR markers and morphological traits

M. Nefzaoui, M.A. Lira, S.M. Udupa, M. Louhaichi, M. Boujghagh, D.C. Santos
The objective of this research was to compare phenotypic and molecular-based methods in assessing genetic diversity of cactus pear from two ex-situ collections, located in the Mediterranean Basin and the northeast of Brazil. Fifty randomly selected accessions (30 accessions from IPA, Pernambuco, Brazil, and 20 accessions from INRA Agadir, Morocco) were subjected to phenotypic and molecular characterization. Phenotypic characterization was achieved using FAO Cactusnet descriptors, while the molecular characterization used the simple sequence repeats (SSR) technique and eight recently recommended primers. The phenotypic data were subjected to principal component analysis (PCA) and agglomerative hierarchical clustering (AHC) using XLSTAT 2015 package. The unweighted pair-group method with arithmetic means (UPGMA) dendrogram based on Nei's genetic distance was used for molecular characterization, and the relationship between morphological and molecular traits was assessed by the Mantel test. SSR analysis revealed 72 alleles with an average allele number of nine per locus. All microsatellites used were found to be discriminative, with a mean polymorphic information content (PIC) estimated at 0.458. Genetic dissimilarities estimated between the accessions varied widely, suggesting that important genetic variability exists in the collection. All the markers used were either informative or highly informative and can be recommended to detect genetic diversity in Opuntia species; the most discriminant markers were Ops24 and Opuntia9, and the least discriminant was Opuntia5. The relationship between phenotypic traits and allele-based genetic distances from the SSR analysis was highly significant (r=0.4, p=0.01) and is here obtained for the first time while using SSR for molecular characterization. Consequently, the SSR technique is one of the best tools to assess the level of genetic diversity in Opuntia germplasm collections; it complements phenotypic characterization and is recommended for planning breeding programs and to revise the current taxonomic classification.
Nefzaoui, M., Lira, M.A., Udupa, S.M., Louhaichi, M., Boujghagh, M. and Santos, D.C. (2019). Assessment of genetic diversity of Brazilian and Mediterranean cactus cultivars by SSR markers and morphological traits. Acta Hortic. 1247, 171-182
DOI: 10.17660/ActaHortic.2019.1247.24
cactus pear, genetic variability, phenotypic characterization, microsatellite markers

Acta Horticulturae