Differentiation of Molecular Genotypes and Virulence Phenotypes of <italic>Puccinia triticina</italic> from Common Wheat in North America

Ordoñez, M. E., and Kolmer, J. A. 2009. Differentiation of molecular genotypes and virulence phenotypes of Puccinia triticina from common wheat in North America. Phytopathology 99:750-758. Wheat leaf rust caused by Puccinia triticina is widely distributed in the wheat growing regions of the United States and Canada, and is subject to selection for virulence phenotype by leaf rust resistance genes in wheat cultivars. The objective of this study was to determine the number of genetically differentiated groups of P. triticina that are currently present in North America. In total, 148 isolates of P. triticina from the 1980s to 2005 were collected from wheat-growing regions of the United States and Canada and tested for virulence on 20 lines of wheat with single genes for leaf rust resistance and for molecular genotype with 23 simple sequence repeat (SSR) markers. In total, 91 virulence phenotypes and 65 SSR genotypes were found. After removal of isolates with identical virulence and SSR genotypes, 125 isolates were included for further analysis. Bayesian cluster analysis indicated five different groups of isolates based on SSR genotypes that also differed for virulence to leaf rust resistance genes Lr2a, Lr2c, Lr3bg, Lr17, and Lr28. Isolates avirulent to Lr14a and Lr20 that have increased since 2003 had SSR genotypes identical or similar to older isolates in one of the five groups, indicating that these isolates were derived by mutation from the previously existing population of P. triticina. The representative collection of P. triticina isolates had characteristics consistent with an asexual dikaryotic population of genetically differentiated groups of SSR genotypes with high levels of heterozygosity and disequilibrium within which stepwise mutation at avirulence or virulence loci regularly occurs. Wheat leaf rust caused by Puccinia triticina Erikss. is the most common and widely distributed disease of wheat (Triticum aestivum L.) in North America and worldwide (33). The geographic range of Thalictrum speciossissimum L., the alternate host of P. triticina, and the origin of wheat overlap in southwest Asia (8), which is where P. triticina likely originated (39). Arthur (3) indicated that leaf rust of wheat was introduced to North America from Eurasia. Susceptible alternate hosts for P. triticina are not native in North America and P. triticina is not found on the native wild grasses, being restricted almost exclusively to wheat (4,28). In the absence of a suitable alternate host, P. triticina reproduces in North America by the asexual production of urediniospores on wheat. Leaf rust is found on soft red winter wheat cultivars that are grown in the southern and eastern states in the United States: soft white winter cultivars that are grown in New York, Michigan, and Ontario; hard red winter wheat cultivars that are grown in the southern-mid Great Plains states of the United States; and hard red spring wheat cultivars grown in the northern Great Plains states and the provinces of western Canada. Leaf rust is also found to a lesser extent on the soft white spring and winter wheat cultivars grown in the Pacific Northwest and the hard red spring cultivars in California. The wheat classes differ for leaf rust resistance genes (Lr); thus, different races or virulence phenotypes of P. triticina are found in the various regions of the United States and Canada. In recent years, many new phenotypes with virulence to Lr17, Lr24, and Lr41 have increased due to selection by hard red winter wheat cultivars in the southern Great Plains while phenotypes with virulence to Lr11and Lr26 are most common in the southeastern states where soft red winter wheat cultivars are grown (22). Virulence surveys of P. triticina have been conducted in the United States since 1926 (15) and Canada since 1931 (14); thus, changes in virulence phenotypes can be tracked over time and the selective effects of Lr genes in the wheat cultivars on the P. triticina population can be assessed. (21–23). Studies using various types of molecular markers combined with virulence have provided further insight into the population biology of P. triticina. Previous studies with random amplified polymorphic DNA (RAPD) (20) and amplified fragment length polymorphisim (AFLP) (19) markers determined that distinct groups of P. triticina related for molecular polymorphism and virulence phenotype were present in Canada in the early and mid1990s. The RAPD markers easily distinguished between isolates in different groups; however, there was very little polymorphism within the groups. The AFLP markers easily distinguished among isolates between and within groups of P. triticina virulence phenotypes; however, because AFLP and RAPD markers are dominantly expressed, it was not possible to distinguish between heterozygous and homozygous genotypes in either of these studies. Introductions of new P. triticina virulence phenotypes have occurred in recent years. In 1984, a leaf rust phenotype with virulence to Lr16, Lr27, and Lr31 and unique isozyme variation was first detected in Australia (30). In 2004, all of the leaf rust phenotypes identified in Australia were derived from this introduction. In 1996, phenotypes of P. triticina with virulence to resistance genes Lr17, Lr3bg, and LrB and avirulence to Lr28 were found in large numbers for the first time in the Great Plains of the United States and Canada. Based on AFLP markers and virulence, Kolmer (19) speculated that these virulence phenotypes were a recent introduction to North America. In 2001, phenotypes of P. triticina with virulence to previously resistant durum wheat cultivars were first found in Mexico (35). Isolates of P. triticina colCorresponding author: J. A. Kolmer; E-mail address: [email protected] doi:10.1094 / PHYTO-99-6-0750 This article is in the public domain and not copyrightable. It may be freely reprinted with customary crediting of the source. The American Phytopathological