Population Genomics of Fungal and Oomycete Pathogens.
We are entering a new era in plant pathology in which whole-genome sequences of many individuals of a pathogen species are becoming readily available. 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.
Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon 97330; email: nik.grunwald@ars.usda.gov.|Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331.|Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853; email: mgm5@cornell.edu.
Niklaus J
NJ
Grünwald
Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland; email: bruce.mcdonald@usys.ethz.ch.
Bruce A
BA
McDonald
Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853; email: mgm5@cornell.edu.
Michael G
MG
Milgroom
D005658:Fungi / Q000235:genetics* / Q000502:physiology; D016681:Genome, Fungal; D023281:Genomics; D009868:Oomycetes / Q000235:genetics* / Q000502:physiology; D010935:Plant Diseases / Q000382:microbiology; D010944:Plants / Q000382:microbiology*
QTL mapping; adaptation; comparative genomics; evolution; genome-wide association; population genetics