Diversity in Puccinia striiformis populations causing the 2013 yellow rust epidemics on major wheat cultivars of Pakistan

ABSTRACT

Wheat yellow/stripe rust pathogen Puccinia striiformis is highly diverse and recombinant in the north of Pakistan in the Himalayan region. However, little is known about the role of this diversity in disease epidemics in areas where wheat yellow rust is an important disease in both irrigated and rain-fed wheat (i.e., in the plains of Pakistan). We explored the population diversity in P. striiformis during the rust epidemics of 2013 in the major wheat-growing regions of Pakistan (the Himalayan region, central Khyber Pakhtunkhwa [KP], southern KP, central and northern Punjab). Disease severities among commonly grown cultivars ranged from 5% to 100%. Microsatellite genotyping with 16 simple sequence repeat (SSR) markers revealed a high diversity among 266 isolates collected during the season, with the Simpson diversity index (Simpson 1949) ranging from 0.870 (Himalayan) to 0.955 (southern KP). The recombination signature was stronger in the Himalayan population and central KP compared with wheat-growing regions of Punjab and southern KP. The overall diversity was higher in Pakistan relative to the clonal populations present in Europe, Australia, and the Americas. Analyses of population subdivision revealed no clear evidence of spatial structure for samples from Pakistan, with a maximum fixation index (F_ST) value of only 0.10. The lack of clear population subdivision could be attributed to migration of pathogen. In turn, the high diversity of P. striiformis in Pakistan represents a potential threat to wheat production in the region and worldwide, as a possible source to found clonal populations in diverse wheat-growing areas.

KEYWORDS:

• Stripe rust
• Khyber Pakhtunkhwa
• microsatellite genotyping
• population genetics
• Himalayan region

ACKNOWLEDGMENTS

We acknowledge the support of Dr. Fazle Subhan, Mr. Muhammad Irfan, Dr. Khilwat Afridi, and Dr. Efat Nawaz during the 2013 sampling. We thank Dr. Gurcharn Singh Brar and Prof. Randy Kutcher for allowing us to use SSR data of isolates representing PstS1_related and PstPr. We also thank Dr. Annemarie F. Justesen, Dr. Tine Thach, Prof. Dr. Mogens S. Hovmøller, and Prof. Dr. Gene Milus for providing inputs on various versions of the manuscript as well providing technical help for sequencing.

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Funding

This work was supported by the US Department of Agriculture Agricultural Research Service under agreement no. 58-0206-0-171 F (Wheat Productivity Enhancement Program [WPEP]) and Start-up Research Grant, Higher Education Commission, Pakistan.