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.

Microsatellite markers: what they mean and why they are so useful

“…To construct and sequence genomic libraries, the DNA is fragmented, ligated to adaptors and inserted into vectors for transforming Escherichia coli . Most protocols involve a stage of enrichment for repetitive sequences that can be achieved using selective hybridization, PCR or both techniques ( Senan et al ., 2014 ). In enrichment by hybridization, positive clones are detected using radioactively or chemically labeled SSR probes.…”

“…However, non-enriched libraries and alternative methods derived from other molecular markers (e.g. RAPD and AFLP) have also been used to find SSRs (see Senan et al ., 2014 ).…”

Microsatellite markers in common bean (Phaseolus vulgaris L.)

“…They are characterized by their codominant transmission (the heterozygotes can be distinguished from homozygotes), wide genomic distribution, high polymorphism, hypervariable, and informative nature, providing considerable pattern, relative abundance with uniform genome coverage, higher mutation rate than standard, and easy sample preparation (Abdul-Muneer, 2014;Senan et al, 2014). Di-, tri-and tetranucleotide repeats are the most frequently used in molecular genetic studies (Selkoe and Toonen, 2006).…”

“…With the advancement in genomics, availability of new molecular tools and sequencing platforms for exploring genomic information, several alternative strategies were devised to reduce the time invested in microsatellite isolation and to significantly increase the yield of microsatellite loci. Microsatellites can be developed through enriched/non-enriched small insert genomic library construction, by utilizing the products generated by other molecular markers or by the application of next-generation sequencing systems (gSSRs), from EST sequences (expressed sequence tag) (genic or EST-SSRs), through interspecific or intergeneric transferability (Kalia et al, 2011;Senan et al, 2014).…”

Analysis of Simple Sequence Repeats Information from Floral Expressed Sequence Tags Resources of Papaya (<i>Carica papaya</i> L.)

“…Both the methods involve construction of genomic DNA library, following the hybridization with tandemly repeated oligonucleotides probes, cloning and sequencing of candidate clones [24], which makes these methods of development very tedious, time consuming, expensive and labor-intensive [25]. On the other hand, with the advancement of modern genomics, genic or EST-SSRs are comparatively easier to develop as large numbers of ESTs of various organisms are available in various data banks.…”