Source: https://pppmb.cals.cornell.edu/people/michael-milgroom/
Timestamp: 2019-04-22 22:17:35+00:00

Document:
My interests are primarily the population biology, genetics and evolution of plant pathogens, with applications to plant disease epidemiology and management. These interests integrate disciplines that are traditionally considered separately in the context of either biology or agriculture.
The overall goal of my research program is to understand the population biology and evolution of plant pathogens, and to bridge the gap between population biology and plant disease epidemiology.
For much of my career, my research has been aimed at the population genetics of fungi, particularly the chestnut blight fungus, Cryphonectria parasitica, the grape powdery mildew fungus, Erysiphe necator (formerly Uncinula necator), and more recently Verticillium dahliae, which causes Verticillium wilt on a large number of host plants. The first two of these fungal pathogens caused devastating epidemics when they were introduced from their native geographic ranges and host populations into new areas with naïve host species. Similarly, some clonal lineages of V. dahliae have been spread across the globe by agricultural activity. Recent research on these pathogens has been directed towards understanding the history and genetics of these biological invasions.
Currently the two main emphases of research in my program are: 1) the biology and ecology of Aspergillus flavus, one of the major species that produces aflatoxin, and 2) the population genetics of Verticillium dahliae.
One of the main research goals in my lab is to understand the ecological significance of aflatoxin production in the ecology and life history of A. flavus. Aflatoxin is a highly carcinogenic toxin produced by fungi in the genus Aspergillus and causes contamination of food supplies, especially in tropical countries. Strains of A. flavus that do not produce aflatoxin (nontoxigenic strains) are fairly common in nature, strongly suggesting that this polymorphism is maintained by balancing selection, i.e., that aflatoxin production may be favored in some environments but selected against in others. Our goal is to understand how and/or when aflatoxin production is favored. We are approaching this question by comparing the fitness of toxigenic and nontoxigenic strains under experimental conditions, in particular, in soil and maize-kernel microcosms.
In collaborations with colleagues in Spain, Israel and Penn State University, my lab is studying the population biology of Verticillium dahliae. We recently used genotyping by sequencing (GBS) to describe the population structure of V. dahliae in a geographically diverse collection. As in previous studies, we found that V. dahliae is composed of a handful of clonal lineages. However, because of the large numbers of single-nucleotide polymorphisms (SNPs) generated by GBS we determined that clonal lineages arose by recombination, probably by sexual reproduction even though V. dahliae is thought to be an asexual fungus. In the next phase of this research we are developing a diagnostic method based on SNPs that can uniquely determine which clonal lineage an isolate is in. This method will be applied to studies on adaptation of V. dahliae to different host plants, and the effects of crop rotation on the diversity of lineages in soil populations of V. dahliae.
In all of these courses, we use a “flipped classroom” approach with almost no lecturing. Instead, readings, videos, audios, tutorials and other out-of-class exercises prepare students for coming to class to discuss material they learn on their own. Class time is used for discussion and a variety of other student-centered interactive activities that reinforce their out-of-class learning. One of our goals is for students to learn how to read and understand primary research literature. Regular in-class discussion of research in the biology of infectious disease is done in small, structured-reading groups. Success with this teaching model has earned the two of us recognition in the form of the 2014 CALS Innovative Teaching Award, and the 2015 Excellence in Teaching from the American Phytopathology Society.
Rafiei, V., Banihashemi, Z., Jiménez-Díaz, R. M., Navas-Cortés, J. A., Landa, B. B., Jiménez-Gasco, M. M., Turgeon, B. G., & Milgroom, M. G. (2018). Comparison of genotyping by sequencing and microsatellite markers for unravelling population structure in the clonal fungus Verticillium dahliae. Plant Pathology. 67:76-86.
Drott, M. T., Lazzaro, B. P., Brown, D. L., Carbone, I., & Milgroom, M. G. (2017). Balancing selection for aflatoxin in Aspergillus flavus is maintained through interference competition with, and fungivory by insects. Proceedings of the Royal Society B: Biological Sciences. 284:20172408.
Milgroom, M. G., Jiménez-Gasco, M. M., Olivares-García, C., & Jiménez-Díaz, R. M. (2016). Clonal expansion and migration of a highly virulent, defoliating lineage of Verticillium dahliae. Phytopathology. 106:1038-1046.
Grünwald, N. J., McDonald, B. A., & Milgroom, M. G. (2016). Population genomics of fungal and oomycete pathogens. Annual Review of Phytopathology. 54:323-346.
Frenkel, O., Cadle-Davidson, L., Wilcox, W., & Milgroom, M. G. (2015). Mechanisms of resistance to an azole fungicide in the grapevine powdery mildew fungus, Erysiphe necator. Phytopathology. 105:370-377.
Mutiga, S., Were, V., Hoffman, V., Harvey, J., Milgroom, M. G., & Nelson, R. J. (2014). Extent and drivers of mycotoxin contamination: Inferences from a survey of Kenyan maize mills. Phytopathology. 104:1221-1231.
Milgroom, M. G., Jiménez-Gasco, M. d., García, C. O., Drott, M. T., & Jiménez-Díaz, R. M. (2014). Recombination between clonal lineages of the asexual fungus Verticillium dahliae detected by genotyping by sequencing. PLOS One. 9:e106740.
Pagán, I., Montes, N., Milgroom, M. G., & García-Arenal, F. (2014). Vertical transmission selects for reduced virulence in a plant virus and for increased resistance in the host. PLoS Pathogens. 10:e1004293.
Frenkel, O., Portillo, I., Brewer, M. T., Péros, J., Cadle-Davidson, L., & Milgroom, M. G. (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.
Brewer, M. T., Frenkel, O., & Milgroom, M. G. (2012). Linkage disequilibrium and spatial aggregation of genotypes in sexually reproducing populations of Erysiphe necator. Phytopathology. 102:997-1005.

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