Population Genomics of Fungal and Oomycete Pathogens

Niklaus J. Grünwald, Bruce A. McDonald, Michael G. Milgroom
  • Annual Review of Phytopathology, August 2016, Annual Reviews
  • DOI: 10.1146/annurev-phyto-080614-115913

Population Genomics of Fungi

What is it about?

Population genomics aims to discover genetic mechanisms underlying phenotypes associated with adaptive traits such as pathogenicity, virulence, fungicide resistance, and host specialization, as genome sequences or large numbers of single nucleotide polymorphisms become readily available from multiple individuals of the same species. This emerging field encompasses detailed genetic analyses of natural populations, comparative genomic analyses of closely related species, identification of genes under selection, and linkage analyses involving association studies in natural populations or segregating populations resulting from crosses. The era of pathogen population genomics will provide new opportunities and challenges, requiring new computational and analytical tools. This review focuses on conceptual and methodological issues as well as the approaches to answering questions in population genomics. The major steps start with defining relevant biological and evolutionary questions, followed by sampling, genotyping, and phenotyping, and ending in analytical methods and interpretations. We provide examples of recent applications of population genomics to fungal and oomycete plant pathogens.

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The following have contributed to this page: Niklaus J Grunwald, Bruce A McDonald, and Niklaus J Grünwald