About BlackP2MSATdb

First black pepper SSR database PinigSSRdb of Kumari et al (2019) contains approximately 70 thousand putative SSR markers but all are anonymous loci as they are based on 916 Scaffold rather than 26 chromosomes. For population structure and diversity analysis, it is imperative to have SSR loci with known physical location (2-3 per chromosome) having Polymorphism Information Content (PIC) value >0.6 (4-12 alleles). Number of SSR loci can be drastically minimized, if markers are selected uniformly by taking the advantage of their known physical location over chromosome. Such selected markers can be a better diversity calculus for genomic as well as population variability with respect to random anonymous SSR loci (You et al 2005). Such chromosome and location specific SSR loci can be further used to trace the inheritance of particular chromosomal regions in molecular breeding programs from the foundation genotypes (Pestsova et al 2002). The latest de novo genome assembly of black pepper provided by Hu et al (2019) can be used prudently to cater these critical needs.
In this regard, BlackP2MSATdb is prepared. BlackP2MSATdb is a database of whole genome SSRs extracted from the reference genome provided by Hu et al., 2019; along with the polymorphic SSRs extracted after comparing whole genome black pepper SSRs with the SSRs extracted from genotype by sequencing (GBS) data of 29 genotypes of black pepper to study the variability among various black pepper genotypes.