USE OF TWO SIMILARITY COEFFICIENTS FOR GENOTYPING SOUTH AFRICAN CACTUS PEAR (OPUNTIA SPP.) VARIETIES USING AFLP MARKERS - Barbara K. Mashope, Liezel Herselman & Maryke T. Labuschagne

Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa

Currently molecular genotyping techniques are used independently, or in combination with descriptors, to measure genetic variation within breeding stocks.  Genotypic characterisation of cactus pear (Opuntia spp.) using biotechnology has, however, been hampered by the difficulty in extracting genomic DNA due to the presence of polysaccharide-rich mucilage and other secondary metabolites.  The objective of this study was to investigate the genetic diversity within the South African cactus pear germplasm using amplified fragment length polymorphisms (AFLPs).  Thirty-eight accessions of cactus pear were analysed using nine AFLP primer combinations.  Genomic DNA was extracted using the CTAB method, and the genotypes fingerprinted using AFLPs.  The nine primer combinations used generated 346 fragments, 168 of which were polymorphic.  The polymorphic information content (PIC) of the majority of the markers had a good discriminatory value, in the range of 0.3-0.5.  Genetic similarity estimates were computed using the Jaccard similarity and Simple Matching coefficients and the unweighted pair group method of arithmetic averages (UPGMA) used for cluster analysis.  Both similarity coefficients grouped most of the accessions into four clusters using.  Cultivated varieties were spread amongst different clusters, with the greatest percentage of them clustered in group III.  Cluster information of both dendrograms was evaluated using the cophenetic correlation coefficient (r).  The cophenetic correlation coefficient for the dendrogram constructed using the Jaccard’s similarity coefficient was r = 0.9528, and that using the Simple Matching coefficient was r = 0.9536.  Both statistics were close to one, indicating that the clustering based on each coefficient accurately reflected the data.  Either coefficient could be used for analysing genotypic variance within South African cactus pear varieties.