Non-Sequencing-Based Microsatellite Development in Pomegranate (Punica granatum): Enrichment and Screening Protocol

The chapter reports an inexpensive, non-sequencing-based technique to develop microsatellite markers in pomegranate (Punica granatum). Microsatellites are also known as the polymorphic genetic markers that are usually used in genetic diversity, breeding, and population genetics. Even though next-generation sequencing (NGS) has quickly demonstrated speedy advancement in the development of markers, the given protocol provides a viable option in species with limited genomic information or in cases when sequencing is not a viable option. The strategy uses the enrichment strategy as a way of selectively isolating the DNA fragments having the microsatellite repeats, followed by a detailed screening procedure to identify the polymorphic loci. This is also geared towards providing an economical form of high-quality genetic markers production that can be utilized in genetic diversity, fingerprinting, and linkage mapping studies. The approach can be particularly applicable to the laboratories that do not have significant access to advanced sequencing technology.