Worldwide population structure of the wheat rust fungus Puccinia striiformis in the past

• Existence of subdivision in the past worldwide Puccinia striiformis population.
• Recombination and diversity in the past Himalayan and near-Himalayan population.
• Confirmation of the center of diversity in the Himalayas.
• Clear indications of long-distance migration over geographical regions.
• Temporal dynamics of worldwide P. striiformis population.

Puccinia striiformis is a basidiomycete causing yellow rust on wheat. The availability of historic samples of this pathogen from the ‘Stubbs collection’ enabled us to investigate past population structure and temporal dynamics on a global scale. A set of 212 single genotype urediniospore isolates, representing samples collected from five continents between 1958 and 1991, were genotyped using 19 polymorphic microsatellite markers. The population genetic analyses revealed the existence of seven genetic groups in the past worldwide P. striiformis population. This genetic grouping generally corresponded with geographical sample origin except for the Middle East, where six of the seven genetic groups were represented. The presence of many genetic groups in the Middle Eastern population reflected a low differentiation from the populations in East Africa (FST = 0.052) and in South Asia (FST = 0.064). A high diversity and recombinant population structure was observed in China and South Asia, while a clonal population structure was observed in NW Europe, East Africa and the Mediterranean region. The high genetic diversity in the Himalayan region supported recent studies suggesting a putative center of diversity for P. striiformis in this area. Four of the 89 multilocus genotypes detected were resampled in different geographical regions suggesting long-distance migration in the past. Comparison of the past populations with more recent ones, represented by 309 isolates mainly collected between 2001 and 2009, revealed temporal divergence for all populations except for Northwest Europe. Overall, we observed a clear subdivision within the worldwide population structure of P. striiformis and migration in the past.