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Title: Development of microsatellite markers from the transcriptome of Erysiphe necator for analyzing population structure in North America and Europe

item FRENKEL, OMER - Cornell University
item PORTILLO, IVAN - University Of Bologna
item BREWER, MARIN - Cornell University
item PEROS, JEAN-PIERRE - Institut National De La Recherche Agronomique (INRA)
item Cadle-Davidson, Lance
item MILGROOM, MICHAEL - Cornell University

Submitted to: Plant Pathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/30/2011
Publication Date: 1/15/2012
Citation: Frenkel, O., Portillo, I., Brewer, M., Peros, J., Cadle Davidson, L.E., Milgroom, M. 2012. Development of microsatellite markers from the transcriptome of Erysiphe necator for analyzing population structure in North America and Europe. Plant Pathology. 61:106-119.

Interpretive Summary: We sequenced the expressed genes of the grape powdery mildew fungus and identified a type of DNA marker called microsatellites. We used these DNA markers to examine the genetic diversity in grape powdery mildew in North America and Europe. We found that the greatest genetic diversity for the fungus is in the Eastern U.S., which is the pathogen’s center of origin. The pathogen populations in the Northeastern and Southeastern U.S. are slightly different from one another. There are two genetic groups of the pathogen in Europe, and we were able to find close relatives for one of the two in the U.S. Isolates that infect muscadine grapes are genetically different from those that infect bunch grapes. Our improved understanding of grape powdery mildew genetic diversity will help us improve grape disease management strategies.

Technical Abstract: We used transcriptome sequences of the grape powdery mildew fungus, Erysiphe necator, to develop microsatellite markers (EST-SSRs) to study its relatively unexplored population structure in its center of diversity in eastern North America. Screening the transcriptome sequences revealed 116 contigs with candidate microsatellites, from which we developed eleven polymorphic microsatellite markers from 31 markers tested. Two of the eleven markers did not produce consistent results in the US but were useful in differentiating European isolates into the well-documented genetic groups A and B. Using the remaining nine markers, we genotyped 129 isolates from different regions and hosts in eastern US and compared them to samples from southern France and Italy. One marker was hypervariable, with 19 alleles detected in the US, and was excluded from analyses. Genetic diversity in the eastern US was much greater than in Europe. Bayesian cluster analyses showed that nine isolates from North America had high affinities with, but differed from, European group A; no isolates with affinity to group B were found in the eastern US. Genetic differentiation was also detected between regions within the eastern US (southeast vs. northeast) and between isolates from V. rotundifolia and isolates from the other Vitis hosts. This research suggests that transcriptome sequencing of fungal pathogens is useful for developing genetic markers in protein-coding regions and highlights the potential role of these markers in future population biology studies of E. necator.