Leaf rust, caused by the fungus Puccinia triticina, is the most common rust disease of wheat in wheat‐producing areas worldwide. The Israeli population of P. triticina has been consistently monitored since 1993. A total of 784 single urediniospore isolates from Triticum aestivum were analysed during 2000–15. The structure of the pathogen population has changed to a large extent since 2000. The annual populations of P. triticina were separated into two distinct groups, 2000–11 and 2012–15, while populations of 2000–5 and 2006–12 were differentiated to a lesser extent. The change in the population originating from T. aestivum during the period 2000–15 is less significant compared to changes in the 1990s described previously. Diversity within the annual populations of P. triticina was rather stable during the period studied. Three new pathotypes, characterized by virulences on Lr3ka and Lr30 genes, became dominant between 2012 and 2015, while all but one prevailing pathotypes in 2000–11 were avirulent on these two genes. Significant changes in virulence frequencies on a number of Lr genes (Lr2c, Lr3ka, Lr15, Lr21, Lr23, Lr26, Lr30) and pairwise associations of virulences (mainly with Lr2c and Lr26) were registered in 2012–15 or earlier. It is postulated that the composition and pathotype structure of the P. triticina population in Israel is determined by wind‐disseminated urediniospores from neighbouring regions, where the migration of P. triticina from the eastern part of the Mediterranean Sea and from the Horn of Africa seem to have the greatest influence.
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