Methods for Development of Microsatellite Markers: An Overview

Abstract

Microsatellite or Simple Sequence Repeat (SSR) markers have evolved to the status of a most versatile and popular genetic marker in a ubiquity of plant systems. Due to their co-dominant, hyper-variable and multiallelic nature, they are the prominent markers of choice for fingerprinting, conservation genetics, plant breeding and phylogenetic studies. Despite its development of a new set of SSR markers for a species remained time consuming and expensive for many years. However, with the recent advancement in genomics, new strategies/protocols are now available for the generation of SSR markers. This review presents an overview on microsatellite markers with a special emphasis on the various strategies used for the development of microsatellite markers

Natural hybridisation amongQuercus glabrescens,Q. rugosaandQ. obtusata(Fagaceae): Microsatellites and secondary metabolites markers

“…Simple sequence repeats (SSRs), also known as microsatellites, have been the most commonly used genetic markers to diagnose hybridisation and introgression due to its codominant inheritance and its high sensitivity in detecting variation (Senan et al . ). Another advantage of SSRs is their rapid mutation rate, which promotes differentiation between closely related taxa and, consequently, differences in allelic frequencies and the appearance of species‐specific variants, both of which are very useful traits for the identification of different genetic classes (pure and hybrid) and for the characterisation of the genetic structure of hybrid zones (Harrison & Larson ).…”

Genome-Wide Mining, Characterization and Development of miRNA-SSRs inArabidopsis thaliana

“…SSRs are co-dominant, and multi-allelic by nature and due to constant variation in the number of tandem repeats; they are known to be, robust, highly polymorphic (Brandstrom et al 2008, Heesacker et al 2008), locus-specific and co-dominant, thus becoming the markers of choice. (Gupta et al 1996; Ni et al 2002; Lightfoot and Iqbal, 2013; Senan et al 2014; Wang et al 2015). Previous reports show that SSRs are selectively neutral and are randomly distributed in the eukaryotic genome (Schlotterer, 2000; Schlotterer, 2004).…”

Transcriptome analysis of Phytophthora infestans and Colletotrichum coccodes in tomato to reveal resistance mechanisms

“…Microsatellites are multi-allelic and are considered to be one of the best markers for detection of polymorphism. However, development of SSR markers is expensive, laborious, time-consuming (Stępień et al, 2007), and in low frequency in plants (Senan et al, 2014). With the advantages of highly parallel and flexibility, microarray has become increasingly important in crop genetic studies, and it is well suited for applications such as QTL analysis and genotyping (Miller and Tang, 2009).…”