Expressed Sequence Tags (EST): A Potential Source Of Genic Molecular Markers

An Expressed Sequence Tag or EST is a short sub-sequence of a cDNA. Expressed Sequence Tags (ESTs) provide a rapid and efficient approach for gene discovery and analysis of gene expression in eukaryotes. The availability of enormous amount of sequence data from complete or partial genes has made it possible to develop the molecular markers directly from the parts of genes. These markers are referred as "Genic Molecular Markers" (GMM). The development of GMMs, now permits a targeted approach for detection of nucleotide diversity in genes controlling agronomic traits in plant populations (Varshney et al. 2007)

The SSRs derived from EST is called EST-SSR. They normally contain trinucleotide repeat units primers to amplify EST-SSR and are designed based on the EST sequence flanking the SSR motif. A set of chickpea ESTs serves as a resource of high quality transcripts for gene discovery and development of functional markers associated with abiotic stress tolerance that will be helpful to facilitate chickpea breeding (Varshney et al. (2009).

Garcia et al. (2011) have successfully developed 315 EST-SSRs from 9,583 valid ESTs From sequences which were obtained from the Phaseolus vulgar is project site http://www.ccg.unam.mx/phaseolusest/ and these markers showed satisfactory rates of transferability, especially between species that have great economic and genomic values. The average PIC (Polymorphism Information Content) was 0.53 for genomic SSRs and 0.47 for EST-SSRs and successfully integrated 302 newly developed ESR-SSRs into a framework map composed of 123 genomic SSR markers producing 14 linkage groups.

References:

GARCIA, A. R., RANGEL, P. N., CLAUDIO, B., WELLINGTON, S. M., LEONARDO, C. M., MONALISA, S. C., TEREZA C. B. AND ROSANA, PV. B., 2011, The characterization of a new set of EST-derived simple sequence repeat (SSR) markers as a resource for the genetic analysis of Phaseolus vulgaris, BMC Genetics. 12:41
VARSHNEY, R. K., THUDI, M., AGGARWAL R. K. AND BORNER., 2007, Genomics-Assisted Crop Improvement:Genomics Approaches and Platforms.1st edition. Springer.
VARSHNEY, R. K., ANDREAS, G. AND MARK, E. S., 2005, Genic microsatellite markers in plants:
Features and applications. Trends in Biotech. 23:1.


About Author / Additional Info:
Presently I am working as a Scientific Officer at International Crop Research Institute For Semi-Arid Tropics (ICRISAT), Patancheru.