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Characterization of EST-SSR markers in durum wheat EST library and functional analysis of SSR-containing EST fragments

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Abstract

The goal of this study is to identify characterization of expressed sequence tag (EST)-simple sequence repeats (SSR) markers from EST library of durum wheat and functional analysis of SSR-containing EST sequences for application in comparative genomics and breeding. 19,141 sequences were analyzed among which 18,937 ESTs were selected. Consistent with MISA results, 313 EST-SSRs were yielded. The final EST-SSRs were compared to the GenBank non-redundant database using BLASTX and classified based on these functions. Results indicated that the perfect EST-SSRs are the most frequent. The TTG/CTG imperfect EST-SSR had gamma-gliadin putative function that can be appropriate for durum wheat. Also, the mononucleotides and trinucleotides were the most frequent. Findings suggested that the identified EST-SSRs could be categorized into 83 types. Motifs TTG in trinucleotides and TC in dinucleotides had the highest frequency. TTG is the new motif in durum wheat identified in this study. We identified new EST-SSRs with more than trinucleotide and detected motifs that have potential to code amino acids. Arginine was the most frequent amino acid. Enzymes had the highest frequency among predicted functions. EST-SSRs have been identified in this study can be used for developing ESS-SSR-based detection tool for durum wheat in future studies and will be a useful resource for molecular breeding, genetics, genomics, and environmental stress studies. Motifs coding amino acids could be used as a new source of functional markers and biological study. In addition to, designed new PCR primer pairs are new resources for to identify useful alleles in transcription factors, storage proteins, and enzymes which incorporated them again into the cultivated material.

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Abbreviations

SSRs:

Simple sequence repeats

EST:

Expressed sequence tags

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  1. Plant Breeding and Biotechnology Department, Agriculture College, Tarbiat Modares University, Tehran, Iran

    Ali Akbar Asadi & Sajad Rashidi Monfared

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  1. Ali Akbar Asadi
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  2. Sajad Rashidi Monfared
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Correspondence to Sajad Rashidi Monfared.

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Communicated by S. Hohmann.

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Asadi, A.A., Rashidi Monfared, S. Characterization of EST-SSR markers in durum wheat EST library and functional analysis of SSR-containing EST fragments. Mol Genet Genomics 289, 625–640 (2014). https://doi.org/10.1007/s00438-014-0839-z

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  • DOI: https://doi.org/10.1007/s00438-014-0839-z

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