Research articles
ScienceAsia 46 (2020):ID 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
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