In Silico Pipeline for the Development and Primer Design of Microsatellite Markers in Mangifera similis Blume

Mangifera similis Blume, a wild relative of the mango, is an important genetic resource for improving mango varieties. This chapter outlines an in silico pipeline for the development and primer design of microsatellite (SSR) markers for the chloroplast and the whole genome of M. similis, using bioinformatics and next-generation sequencing. The method enables efficient microsatellite identification, saving laboratory time and costs, and is particularly useful for tree species with limited genomic data. The workflow comprises steps such as DNA extraction, sequencing, library construction, in silico SSR mining, primer design, and marker validation. These SSR markers support analyses of genetic diversity and relationships among M. similis populations and are applicable across various Mangifera species. Ultimately, this protocol supports effective conservation genetics and sustainable management strategies for M. similis, while highlighting the species' significance as a reservoir of traits for mango improvement.