Evaluation of the genetic diversity of mango (Mangifera indica L.) seedling germplasm resources and their potential parents with start codon targeted (SCoT) markers

Seedling germplasm resources are important for mango breeding. Genetic diversity analyses based on molecular data can provide useful information for germplasm management and varietal characterization. Start codon targeted (SCoT) markers are efficient and highly polymorphic markers for phylogenetic relationship analyses of multiple species and were used in the present study to determine genetic relatedness and variability among 168 mango (Mangifera indica L.) germplasm resources. Forty-five SCoT primers generated unambiguous and reproducible bands and a total of 337 fragments, with a mean of 7.49 fragments per primer. Of these, 244 (72.4%) were polymorphic. The number of polymorphic bands varied from 1 (SCoT55) to 10 (SCoT4 and 52), with an average of 5.42 amplicons per primer. The average polymorphism information content, Nei’s genetic diversity, Shannon’s information index and marker index were 0.823, 0.426, 0.603 and 4.460, respectively. A dendrogram generated using the unweighted pair-group method with arithmetic mean delineated the 168 germplasm resources into two major clusters. Analysis of molecular variance revealed higher genetic diversity (89%) within each population than among the populations (11%). Most mango seedling germplasm resources grouped with their potential parents, and genetic differences were also detected. Thirty-four seedling germplasm resources were identified as potential parents or sister lines. These results demonstrate that SCoT markers are useful for cultivar identification and genetic diversity analyses of mango cultivars. This genetic information will support germplasm management and cultivar improvement.