Development of novel transcriptome-based SSR markers in Puccinia triticina and their potential application in genetic di
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ORIGINAL ARTICLE
Development of novel transcriptome-based SSR markers in Puccinia triticina and their potential application in genetic diversity studies Siddanna Savadi 1 & Pramod Prasad 2 & Kiran Sharma 2 & Ruchi Rathore 2 & Subhash C. Bhardwaj 2 & Om P. Gangwar 2 & Hanif Khan 2 & Subodh Kumar 2 & Neelu Jain 3 & Pushpendra K. Gupta 4 Received: 18 October 2019 / Accepted: 6 April 2020 # Sociedade Brasileira de Fitopatologia 2020
Abstract 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. Keywords Effector . Leaf rust . SSR . Transcriptome . Wheat
Introduction Puccinia triticina f. sp. tritici (syn. P. recondita) causing leaf rust is the most widespread pathogen in wheat growing areas Electronic supplementary material The online version of this article (https://doi.org/10.1007/s40858-020-00347-8) contains supplementary material, which is available to authorized users. * Subhash C. Bhardwaj [email protected] 1
ICAR-Directorate of Cashew Research, Puttur, D. K., Karnataka 574 202, India
2
ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh 171 002, India
3
ICAR- Indian Agricultural Research Institute, New Delhi 110 002, India
4
Chaudhary Charan Singh University, Meerut, Uttar Pradesh 200 005, India
of the world (Fetch and McCallum 2014; Junk et al. 2016). The spores of the pathogen can travel thousands of kilometers by wind and are capable of causing severe yield losses throughout the world (Kolmer 2005; Huerta-Espino et al. 2011). In the past, severe epidemics were caused by this fungus in several
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