Development of novel markers, using computationally extracted classi type EST-SSRS, in wheat leaf rust fungus Puccinia triticina

Sipahi H., Yumurtaci A., Mert Z.

Genetika, vol.47, no.3, pp.917-926, 2015 (SCI-Expanded) identifier

  • Publication Type: Article / Article
  • Volume: 47 Issue: 3
  • Publication Date: 2015
  • Doi Number: 10.2298/gensr1503917s
  • Journal Name: Genetika
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus
  • Page Numbers: pp.917-926
  • Eskisehir Osmangazi University Affiliated: No

Abstract

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.