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Research articles

ScienceAsia 46 (2020): 6-10 |doi: 10.2306/scienceasia1513-1874.2020.001

In silico identification of expressed sequence tags based simple sequence repeats (EST-SSRs) markers in Trifolium species

Siddra Ijaza,*, Imran Ul Haqb, Bukhtawer Nasira

ABSTRACT:     The EST-SSRs (genic SSRs) are the microsatellites in expressed sequence tags (ESTs). Advancement in functional genomics has contributed mainly for the identification of ESTs in different species and made them available in databases. They are of transcribe regions, so are more conserved and considered with more cross transferability across the taxonomic borders. In Trifolium alexandrinum (Berseem), no expressed sequence tags (ESTs) are available in NCBI database yet. Therefore, in this study by considering the cross transferability potential of EST-SSRs, expressed sequence tags of Trifolium pratense and Trifolium repens were retrieved from NCBI database and their EST-SSRs were in silico identified. We retrieved 1014 ESTs for SSR identification from both Trifolium species and identified 198 EST-SSRs from them. In identified EST-SSRs, trinucleotide SSRs repeats were found to be more frequent. Of these 198 in silico identified EST-SSRs, 44 showed cross species amplification in T. alexandrinum and was proved for their transferability potential. The identified EST-SSRs could be a great source for genetic diversity and population genetics studies of Trifolium species. These EST-SSRs could be further screened to investigate their linkage to disease resistance in Trifolium species.

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a Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, University Road, Faisalabad, Pakistan
b Department of Plant Pathology, University of Agriculture, University Road, Faisalabad, Pakistan

* Corresponding author, E-mail: siddraijazkhan@yahoo.com

Received 5 May 2019, Accepted 6 Dec 2019