Genetic Divergence and Diversity in Himalayan Puccinia striiformis Populations from Bhutan, Nepal, and Pakistan

Muhammad Rameez Khan,Sidra Noreen Nazir,Suraj Baidya,David Hodson,Sangay Tshewang,Sajid Ali,Zia-Ur Rehman,Muhammad Imtiaz

doi:10.1094/phyto-01-19-0031-r

Abstract

The western Himalayan region in Pakistan has been shown to be the center of diversity of Puccinia striiformis; however, little is known about its genetic relations with the eastern part of the Himalayas. We studied the genetic structure of P. striiformis from Nepal (35 isolates) and Bhutan (31 isolates) in comparison with 81 Pakistani samples collected during 2015 and 2016, through microsatellite genotyping. Genetic analyses revealed a recombinant and highly diverse population structure in Pakistan, Bhutan, and Nepal. A high level of genotypic diversity (>0.90) was observed for the three countries of Pakistan (0.96), Bhutan (0.96), and Nepal (0.91) with the detection of 108 distinct multilocus genotypes (MLGs) in the overall population; 59 for Pakistan, 27 for Bhutan, and 26 for Nepal. Mean number of alleles per locus and gene diversity were higher in Nepal (3.19 and 0.458, respectively) than Bhutan (3.12 and 0.458, respectively). A nonsignificant difference between the observed and the expected heterozygosity in all populations further confirmed the recombinant structure. A clear population subdivision between the Himalayan region of Nepal, Bhutan, and Pakistan was evident, as revealed by FST values (ranging between 0.111 to 0.198), discriminant analysis of principal components, and resampling of MLGs. Limited gene flow could be present between Nepal and Bhutan, while the population from Pakistan was clearly distinct, and no divergence was present between two populations from Pakistan (Bajaur and Malakand). The overall high diversity and recombination signature suggested the potential role of recombination in the eastern Himalayan region (Nepal and Bhutan), which needs to be considered during host resistance deployment and in the context of aerial dispersal of the pathogen. Further surveillance should be made in the Himalayan region for disease management in the region and in the context of worldwide invasions.

Highlights

Food security in developing countries is always challenging, where many factors affect the continuous and sufficient supply of food including devastating epidemics of diseases of food crops
The western Himalayan region in Pakistan has been shown to be the center of diversity of Puccinia striiformis; little is known about its genetic relations with the eastern part of the Himalayas
This study describes the genetic structure of the P. striiformis population in the Himalayan region of Pakistan, Nepal, and Bhutan

Summary

Introduction

Food security in developing countries is always challenging, where many factors affect the continuous and sufficient supply of food including devastating epidemics of diseases of food crops. An important crop ensuring food security in many developing countries, is continuously facing environmental threats and disease risks. Rust diseases yellow rust (caused by Puccinia striiformis), pose severe threat to higher yield especially in the areas where the mild cold climate prevails during wheat cropping season (Chen 2005; Hovmøller et al 2011). The geographical range of P. striiformis is worldwide; it has occurred throughout recent history in Asia, Europe, and North Africa and in the early 1900s it was introduced into the Americas, and more recently into Australia and South Africa (Ali et al 2014a; Beddow et al 2015; Hodson 2011; Hovmøller et al 2010).

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