Development of novel markers, using computationally extracted classi type EST-SSRs, in wheat leaf rust fungus Puccinia triticina
2015
Sipahi, Hülya (University of Sinop, Sinop (Turkey). Faculty of the Arts and Sciences, Department of Biology) | Yumurtaci, Ayşen (Marmara University, Istanbul (Turkey). Faculty of Science and Letters, Department of Biology) | Mert, Zafer (Central Research Institute for Field Crops, Ankara (Turkey). Department of Plant Pathology)
This study focused on the development of EST-simple sequence repeats markers and the detection of their transferability and their utility for evaluating wheat leaf rust pathogen diversity. A total of 44,407 publicly available EST sequences derived from Puccinia triticina were computationally mined. Di-nucleotide repeat density covered the vast majority of assembled ESTs (45%). The tri-repeat motif (TCT) and penta- repeat motif (TTCTT) were the most repeated motif. A set of 103 Class I type sequences containing simple sequence repeats were further analyzed by BLASTX similarity. Nineteen primer pairs flanking regions of EST-SSRs were designed. Of the 19 primer pairs tested, 10 successfully amplified fragments. Their polymorphism was evaluated with 8 Puccinia triticina (Pt) single-uredinal isolates collected from the different regions of Turkey. These newly developed EST-SSR primer pairs can be implicated as stable markers for pathogen diversity analysis. It was also shown that some leaf rust EST-SSR markers were capable of cross-amplification in P. graminis f. sp. tritici.
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