Development and characterization of microsatellite markers in mango (Mangifera indica) using next-generation sequencing technology and their transferability across species

Mango (Mangifera indica) is the most important horticultural fruit crop in India, but few genetic markers have been identified in it. In order to develop genomic marker resources for mango, we sequenced genomic DNA using next-generation sequencing technology on the IlluminaHiSeq 2000 platform and examined sequence data for microsatellite markers. High-quality raw data were assembled and 198,612 contigs were obtained after optimization. From these data, 159,228 scaffolds were generated covering a genome size of 253.6 Mbp. From the scaffolds, 106,049 microsatellite repeats were identified. Finally, we were able to design primers for 84,118 microsatellites. Ninety simple sequence repeat (SSR) markers were tested, employing 64 mango cultivars and four Mangifera species, for determination of polymorphism and cross-species amplification. We identified 2103 alleles, and the allele number per locus ranged from 15 to 36. The majority of these markers amplified DNA in related species with a transferability of 94.4–98.8 %. The present study increases the sequence coverage of the mango genome and the number of mango-specific SSR markers. This is also the first report of the development of genomic SSR markers in mango using next-generation sequence technology. The genomic SSR markers identified in this study will be useful in diversity, identification, mapping and breeding studies.