DEVELOPMENT OF NOVEL MARKERS, USING COMPUTATIONALLY EXTRACTED CLASSI TYPE EST-SSRS, IN WHEAT LEAF RUST FUNGUS Puccinia triticina

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.