Development of novel SSR markers derived from genomic and transcriptomic data of Moringa oleifera L. var. PKM1 and their applicability

Limited genomic resources, especially on breeder-friendly simple sequence repeats (SSR), are available in Moringa, a multi-purpose miracle tree. This study predicted a total of 29913 genomic-SSRs and 1364 genic-SSRs from the omics data obtained from a Moringa cultivar, PKM1. Among the genomic SSR motifs, 1, 414, 2183, 25600, 1106 and 609 SSRs were Mono, Di, Tri, Tetra, Penta, and Hexa repeats, respectively. Higher frequency for AGAG (24.01%) followed by GAGA (16.68) and AAAA (13.18%) was observed in genic-SSRs sequences. Primer pairs for 22,336 genomic- and genic-SSR markers were developed and 117 SSR primer pairs were randomly selected and assayed in four representative Moringa cultivars and ecotypes. Consequently, 94.44% of them have showed high level of DNA polymorphism by generating 1 to 4 alleles per SSR marker (with an average of 1.75) among the investigated Moringa accessions with a maximum polymorphic information content (PIC) of 0.95. Besides using as simple and affordable indicator to differentiate morphologically similar Moringa ecotypes, the SSRs reported in this study will also have several other potential applications such as seed purity analysis, intellectual property protection, identification of introgressions in interspecific crosses, evolutionary studies, germplasm management, gene and/or QTL identification and marker-assisted selection.