Molecular characterization and genetic variability studies associated with fruit quality of indigenous mango (Mangifera indica L.) cultivars

Start codon-targeted (SCoT) markers were used for characterization and genetic comparison analysis among 20 mango cultivars (15 indigenous and 5 popular) with respect to fruit quality. Out of 80 SCoT markers used, 19 were able to amplify. These primers produced total 117 loci across 20 cultivars, of which 96 (79.57 %) were polymorphic with an average of 5.05 polymorphic fragments per primer. Out of 19, 17 SCoT primers produced 34 cultivar-specific DNA finger prints. These were 25 unique fragments for identification of 15 indigenous cultivars and 9 fragments for the identification of five popular cultivars. The three SCoT primers—40, 45, and 51 are most informative in identifying mango cultivars as they possess the higher primer index values. The 20 mango cultivars were clustered into two major groups based on the SCoT data analysis with UPGMA. Three indigenous cultivars—Khodi, Amrutiyo, and Kaju and one popular—Dasheri out grouped from other 16 cultivars and shared only minimum similarity (11 %). In clustering pattern, indigenous cultivars—Kaju and Amrutiyo grouped together and shared 37 % similarity with higher boot strapping values (63 %). Clustering pattern is corresponding well with their physical and/or biochemical properties of fruits. The results of principal coordinates analysis (PCoA) analysis were comparable to the cluster analysis. The first three most informative PC components explained 56.61 % of the total variation. In PCoA, three indigenous cultivars—Jamrukhiyo, Chappaniyo, and Sopari appears to be distinct from other 12 indigenous, which be different in fruit size, sugars, ascorbic acids, and carotenoids content. Similarly, popular cultivars—Jamadar and Kesar were also discrete from Alphonso, Dasheri, and Neelum in PCoA. The results demonstrate that the SCoT marker system is useful for cultivar identification and genetic diversity analysis of mango cultivars based on their biological traits.