Location: Horticultural Crops ResearchTitle: Population genomics of fungal and oomycete pathogens Author
|Grunwald, Niklaus - Nik|
|Mcdonald, B - Eth Zurich|
|Milgroom, M - Cornell University - New York|
Submitted to: Annual Review of Phytopathology
Publication Type: Review Article
Publication Acceptance Date: 6/8/2016
Publication Date: 8/4/2016
Citation: Grunwald, N.J., McDonald, B.A., Milgroom, M.G. 2016. Population genomics of fungal and oomycete pathogens. Annual Review of Phytopathology. 54:323-346. doi:10.1146/annurev-phyto-080614-115913.
Technical Abstract: We are entering a new era in plant pathology where whole-genome sequences of many individuals of a pathogen species are becoming readily available. This era of pathogen population genomics will provide new opportunities and challenges, requiring new computational and analytical tools. Population genomics aims to discover genetic mechanisms underlying phenotypes associated with adaptive traits such as pathogenicity, virulence, fungicide resistance, and host specialization. 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 or segregating populations resulting from crosses. This review focuses on conceptual and methodological issues, and 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.