SSRs are consisting of tandem repeats of one to six (bp). They are found in prokaryotes and eukaryotes (Thiel et al., 2003; Li et al., 2004). They are also known as simple sequence length polymorphisms (Tautz, 1989), microsatellite (Litt and Luty, 1989) short tandem repeats (Edwards et al., 1991). They are present in both coding and non-coding portions of the genome (Toth et al., 2000). SSRs are most important as compared to PCR based molecular markers such as RAPD, ISSR and AFLP due to their multi-allelic nature, co-dominant inheritance, sequence-specificity, high abundance in the genome, high reproducibility, easy detection by PCR, high rate of transferability and hyper-variability (Powell et al., 1996; Zane et al., 2002; Thiel et al., 2003; Kalia et al., 2011). The polymorphism generated by SSR due to variation in repeats number (Litt and Luty, 1989). SSRs are originated due to DNA strand slippage which leads to mispairing (Levinson and Gutman, 1987) and unequal recombination between sister chromatids during meiosis (Innan et al., 1997) or repetitive errors generated during DNA synthesis (Katti et al., 2001).
The principle of polymorphism detection is based on the primers designing from flanking sequences near SSR repeat motif. Amplification of genomic DNA performed using PCR with specific primers flanking the SSR repeat motifs. Running agarose or denaturing polyacrylamide gel to detect the variations of alleles. There are two types of SSRs based on their location: 1) genomic SSRs that are present throughout the genome, 2) genic-SSRs SSRs or EST-SSRs that are found in expressed region of the genome. Putative function can be determined by publically available databases through computational approaches therefore, EST-SSRs act as functional molecular markers.
Two traditional approaches are available for the development of genomic SSR markers, 1) SSR-enriched genomic library and 2) nonenriched genomic library construction. Both approaches involved the construction and hybridization of genomic DNA library with tandemly repeated oligonucleotides probes followed by cloning and sequencing of clones (Senan et al., 2014), These approaches of development of genomic SSR markers are very tedious, time consuming, costly and labor-intensive (Nakatsuji et al., 2011). On the other hand, the advancement of modern genomics makes the development of genic or EST-SSRs easy as enormous amount of ESTs of several organisms are available in various data banks (NCBI, DDBJ etc.).
Enormous amounts of freely accessible available data in data banks makes possible to develop EST-SSR markers via database mining approach. The development of EST-SSRs through in silico approach is rapid, efficient, cheaper, less labor involved and less time consuming as compared to genomic-SSRs development (Gupta et al., 2003; Bhattacharyya et al., 2014). ESTs are the short (200-800 bases), and single pass random sequence reads of cDNAs derived from cDNA libraries. EST-SSRs are more advantageous than the genomic SSRs due to less time consuming, easily available and cheapest to develop, detect variations in expressed portion of the genome and sequence-specificity.