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The Length Polymorphism Of SSR

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SSRs are consisting of 1 to 6 bp tandem repeats (mono-, di-, tri-, tetra and penta-, hexanucleotides). They are found throughout all genomes including prokaryotes and eukaryotes (Li et al., 2004; Thiel et al., 2003). They are also known as simple sequence length polymorphisms (SSLPs; Tautz, 1989), microsatellite (Litt and Luty, 1989), short tandem repeats (STRs; Edwards et al., 1991). They are present in both coding and non-coding portions of the genome (Toth et al., 2000). They are more important molecular marker as compared to PCR-based markers like RAPD, ISSR and AFLP due to their sequence-specific, multiallelic nature, co-dominant inheritance, abundance in the genome, high transferability rate, high reproducibility, does not required high quality of DNA and gives good result with low quantity of template DNA (10-100ng/reaction) (Powell et al., 1996; Zane et al., 2002; Theil et al., 2003). The polymorphic nature of SSR was detected by Litt and Luty (1989).

The length polymorphism of SSR arises due to variation in repeats number (Ellegren, 2004). These variations occur due to slippage of strand which creates mispairing (Levinson and Gutman, 1987) and repetitive errors generated during replication of DNA (Schlotterer and Tautz, 1992; Katti et al., 2001), or unequal crossing-over between sister chromatids during meiosis (Innan et al., 1997). The principle of length polymorphism of SSR is based on the primers designing from SSR repeat motif flanking sequences. Amplification is performed using PCR and running agarose or denaturing polyacrylamide gel for visualization of variations in alleles. There are two types of SSRs on the basis of their location: (1) SSRs that are distributed throughout the genome are called genomic-SSRs, (2) SSRs that are found only within genes are called as genic-SSRs or Expressed Sequence Tags-SSRs (EST-SSRs). With the advancement of functional genomics a large numbers of ESTs and other DNA sequences of various organisms are available in various data banks.

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Availability of these large amounts of freely accessible data led to the development of EST-based SSR markers through data mining. Development of EST-SSRs or genic-SSRs in silico has become a fast, efficient, and relatively inexpensive method compared with the development of genomic-SSRs (Gupta et al., 2003; Senan et al., 2014). Genic-SSRs act as functional markers owing to their origin from expressed portion of genome. They possess several advantages such as ease of use, less time consuming, cheapest to develop, occurrence in expressed portion, sequence-specificity and high rate of transferability i.e. the ability to effectively transfer SSR markers across species and genera so they provide the better estimate of polymorphism (Gupta et al., 2003).

Genic-SSRs can also be used for comparative genomics study. EST-SSRs developed for one species can be utilized for the related plant species for which small amount of data on ESTs and SSRs is available in public databases by identifying rate of transferability in these species. It is believed that EST-SSRs in the genetic maps revealed about the distribution of genes along the genetic map. They can also be used for comparative mapping study (comparing the gene order of identical genes) in related plant species owing to their origin from conserved region of the genome (Varshney et al., 2005).

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