Microsatellite markers: an overview of the recent progress in plants

Abstract

In recent years, molecular markers have been utilized for a variety of applications including examination of genetic relationships between individuals, mapping of useful genes, construction of linkage maps, marker assisted selections and backcrosses, population genetics and phylogenetic studies. Among the available molecular markers, microsatellites or simple sequence repeats (SSRs) which are tandem repeats of one to six nucleotide long DNA motifs, have gained considerable importance in plant genetics and breeding owing to many desirable genetic attributes including hypervariability, multiallelic nature, codominant inheritance, reproducibility, relative abundance, extensive genome coverage including organellar genomes, chromosome specific location and amenability to automation and high throughput genotyping. High degree of allelic variation revealed by microsatellite markers results from variation in number of repeat-motifs at a locus caused by replication slippage and/or unequal crossing-over during meiosis. In spite of limited understanding of the functions of the SSR motifs within the plant genes, SSRs are being widely utilized in plant genome analysis. Microsatellites can be developed directly from genomic DNA libraries or from libraries enriched for specific microsatellites. Alternatively, microsatellites can also be found by searching public databases such as GenBank and EMBL or through cross-species transferability. At present, EST databases are an important source of candidate genes, as these can generate markers directly associated with a trait of interest and may be transferable in close relative genera. A large number of SSR based techniques have been developed and a quantum of literature has accumulated regarding the applicability of SSRs in plant genetics and genomics. In this review we discuss the recent developments (last 4-5 years) made in plant genetics using SSR markers.

Rootstock breeding in Prunus species: Ongoing efforts and new challenges

“…A molecular marker may be a short DNA sequence, such as a single base-pair change (single nucleotide polymorphism, SNP), or a long one, like minisatellites, which are usually defined as the repetition in tandem of a short (6 to 100 bp) motif spanning 0.5 kb to several kilobases (Vergnaud and Denoeud, 2000). Other important kind of molecular markers are microsatellites or Simple Sequence Repeats (SSRs), which are sequences of 1 to 6 bp repeated in tandem that are frequently found in the genomes of prokaryotes and eukaryotes (Zane et al, 2002;Kalia et al, 2011). The increased genomic resources available from the last years, such as whole genome sequences and high-density genotyping platforms, are revealing important structural and regulatory genes, as well as molecular polymorphisms associated with important agronomic traits (Verde et al, 2012;Dirlewanger et al, 2012).…”

Breeding rootstocks for Prunus species: Advances in genetic and genomics of peach and cherry as a model

“…Microsatellites (Litt and Luty, 1989) or simple sequence repeat (SSR; Tautz et al, 1986) are among the most used markers; they are sequences of 2 to 6 bp (Chambers and MacAvoy, 2000) repeated in tandem that are frequently detected in prokaryote and eukaryote genomes (Kalia et al, 2011;Zane et al, 2002). They are found in both coding and non-coding regions and distributed throughout the genome.…”

“…The characteristics of microsatellite sequences have made them the molecular marker of choice for many types of studies because of their high polymorphism and ability to identify both alleles in diploid organisms and given that they are co-dominant. They are very useful in identifying individuals propagated sexually or vegetatively since it is very improbable that two randomly selected individuals will have exactly the same alleles if several markers are used (Parida et al, 2009;Kalia et al, 2011). These markers have been widely used for the molecular characterization of scion cultivars of Prunus species (Cantini et al, 2001;Dirlewanger et al, 2002;Aranzana et al, 2003a;Struss et al, 2003;Pedersen, 2006;Rojas et al, 2008;Akpinar et al, 2010;Maghuly and Laimer, 2011) and rootstock cultivars (Serrano et al, 2002;Struss et al, 2002;Liu et al, 2007;Turkoglu et al, 2010;Arismendi et al, 2012).…”

Methods for Development of Microsatellite Markers: An Overview

“…Moreover, it is relatively simple, reproducible and cost effective approach for isolating microsatellites from diverse plant species with higher efficiency (Kalia et al, 2011).…”