Development of novel transcriptome-based SSR markers in Puccinia triticina and their potential application in genetic diversity studies

In wheat, leaf rust caused by Puccinia triticina Eriks is a major disease that causes major losses in production. In the present study, microsatellite or SSR (simple sequence repeat) markers were developed for P. triticina using the transcriptome data obtained during wheat-P. triticina interactions. A total of 37,268 P. triticina differentially expressed transcripts were obtained in the comparative transcriptomics and of these, 6809 (1.8%) transcripts carried SSRs. Tri-nucleotide SSRs were the most abundant (52%) among the identified SSRs. Primer pairs were synthesized for 50 PtESSRs, of which 28 were found to be polymorphic in P. triticina pathotypes of the Indian subcontinent. The number of alleles per locus ranged from 2 to 12 with an average of 5.72. Polymorphic information content (PIC) ranged from 0.29 to 0.96 with an average of 0.69. The observed heterozygosity ranged from 0.10 to 0.48 with an average of 0.21. Interestingly, one SSR marker, namely PtESSR7, could distinguish between different virulence groups of pathotypes. BLAST analysis and in silico prediction of fungal effectors suggested that some of the PtESSR markers may have the potential to be functional markers in the leaf rust pathology. Dendrogram analyses detected two clusters in the 48 P. triticina pathotypes. Results of this study suggest that the newly developed PtESSR markers are useful for genetic studies in P. triticina pathogen. No relationship was found between the genetic diversity and geographic distributions of the P. triticina populations.