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Title:   Author  item
                                            Grunwald, Niklaus

                                                         - *Nik*item
                                            MCDONALD, B - Eth Zurichitem
                                            MILGROOM, M - Cornell University
  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.Interpretive Summary:
                                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.


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