Population Biology of Plant Pathogens Genetics, Ecology, and Evolution

About this book

Just like nature itself, the field of population biology in plant pathogens is constantly evolving, yet it has been more than 25 years since a comprehensive book on this important topic has been produced. Population Biology of Plant Pathogens fills this information gap by explaining how population genetics are applied in plant pathology today.

This interpretive guide is ideal for teachers and students of graduate-level plant pathology courses, as it provides a conceptual foundation of the genetics, ecology and evolution of plant pathogen populations while also introducing a wide array of examples that include plant pathogens of all major types: fungi, oomycetes, bacteria, viruses, and nematodes. Researchers and population biologists who wish to specifically study population biology in plant pathogens will also find this book an important tool, as it explains the basic tenets of population biology, population genetics, and the evolution of plant pathogens, and illustrates their applications in epidemiology and applied agriculture.

Population Biology of Plant Pathogens is structured to explain the wonders of evolutionary phenomena in plant pathogens in a logical and orderly fashion
- Chapters one through six address foundational concepts in population genetics, such as genetic markers, genetic diversity, mutation and random genetic drift, natural selection, and migration and population structure.
- Chapters seven and eight cover recombination and clonality
- Chapters nine and ten address gene-for-gene systems and disease resistance
- Chapter 11 focuses on emerging plant diseases
- Chapter 12 illustrates applications of population biology in epidemiology and applied agriculture

Population Biology of Plant Pathogens also contains other important features that further support learning. These include helpful sidebars that highlight topics to initiate discussion; concept summaries at the end of each chapter; a glossary of key terms, a list of commonly used abbreviations; recommended readings; and a comprehensive index.

Contents

1 Introduction to Population Biology and Evolution
Population Genetics
Introduction to Evolutionary Processes
Natural Selection
Mutation
Random Genetic Drift
Migration
Recombination
Interactions among Evolutionary Processes
Challenges in Studying the Population Biology of Plant Pathogens
Hypothesis Testing and Interpretations of Data in Population Biology
The Relevance of Population Biology in Plant Pathology
   Summary of Key Concepts
   Recommended Reading

2 Genetic Markers for Population Genetics
Characteristics of Ideal Genetic Markers
Selective Neutrality
Polymorphisms
Locus Specificity
Minimal Homoplasy
Independent, Unlinked Loci
Codominance
Repeatable, Unambiguous Scoring
Historical Perspectives on Genetic Markers in Plant Pathogens
Phenotypic Markers in Plant Pathogens
Molecular Markers Before the Advent of PCR
Advances in Genetic Markers Because of the Invention of PCR
PCR-Based Markers That Are Not Locus-Specific
Amplified Fragment Length Polymorphisms
Microsatellites
Discovery of Microsatellite Loci
Development and Scoring of Microsatellite Markers
Single Nucleotide Polymorphisms
Multilocus Sequencing and Small-Scale SNP Genotyping
High-Throughput SNP Genotyping with Hybridization Arrays
SNP Discovery and Genotyping Using Next-Generation Sequencing
Ascertainment Bias
Quantitative-Trait Loci and Genome-Wide Association Studies
A Simple Guide for Choosing Genetic Markers
   Summary of Key Concepts
   Recommended Reading

3 Sampling and the Estimation of Genetic Diversity
Defining Populations and Individuals
Random Sampling under Ideal Conditions
Defining a Target Population
Random Sampling from Populations of Plant Pathogens
Spatial Scale of Sampling
Temporal Considerations in Sampling
Sample Sizes and Replication
Sampling Plant Pathogen Populations in Practice
Sporadic Occurrence of Some Organisms
Independence of Sampling Units
Accounting for Underlying Genetic Structure
Genotyping
Allele Frequencies and Diversity at Single Loci
Allele Frequencies
Gene Diversity
Genotypic Diversity
Genotypic Richness
Commonly Used Diversity Indices
Genotypic Evenness
Comparing Genotypic Diversity Between Populations
Diversity Estimated from Relatedness of Multilocus Genotypes
Nucleotide Sequence Diversity
Evolutionary Processes That Increase or Decrease Genetic Diversity
Diversity in Populations of the Late Blight Pathogen, Phytophthora infestans
   Summary of Key Concepts
   Recommended Reading

4 Mutation and Random Genetic Drift
Mutation
Types of Mutation
Estimating Mutation Rates in Bacteria
Estimating Mutation Rates in Eukaryotes
Mutation Rates in RNA Viruses
Random Genetic Drift
Bottlenecks in Plant Virus Populations
Effective Population Size
Mutation and Drift: Muller’s Ratchet and Mutational Meltdown
Mutation and Drift: The Neutral Theory of Evolution
The Infinite-Alleles Model
The Infinite-Sites Model
Gene Genealogies and the Coalescent
Applications of the Coalescent Model
   Summary of Key Concepts
   Recommended Reading

5 Natural Selection
Fitness
Predicted Fitness: Single-Generation Components of Fitness
Realized Fitness: Population Growth Rates
Realized Fitness: Estimation of Relative Fitness in Serial-Passage Competition Experiments
Realized Fitness: Continuous Population Growth Models
Practical Considerations for Conducting Selection Experiments
Selection Acting on Single Genes: Experimental Approaches
Comparison of Isogenic Isolates
Randomizing Alleles to Genetic Backgrounds
Types of Selection
Selection Acting on Quantitative Phenotypes
Selection Acting on Single Genes: Negative, Positive, and Balancing Selection
Density-Dependent Selection
Hitchhiking Selection
Epistatic Selection
Detecting Selection Using Molecular Genetic Markers
Detecting Selection from Within-Population Polymorphisms: Tajima’s D Revisited
Detecting Selection from Divergence among Species: dN/dS Ratios
Trans-Species Polymorphisms and Balancing Selection
Selection for Fungicide Resistance
Genetics of Fungicide Resistance and the Strength of Selection
Estimating Baseline Frequencies of Resistance
Fitness Costs Associated with Fungicide Resistance
Epidemiology and Management of Fungicide Resistance
   Summary of Key Concepts
   Recommended Reading

6 Migration and Population Structure
Direct Estimates of Migration on an Ecological Timescale: Tracking Genotypes
Indirect Estimates of Migration on an Evolutionary Timescale: Population Structure
Fixation Index and Gene Diversity Analysis
Additional Methods for Estimating FST
Estimating the Number of Migrants from FST
Private Alleles and Nearest-Neighbor Methods
Caveats for Interpreting FST and Estimates of Migration Rates
Historical Versus Current Migration and Nonequilibrium Populations
Isolation by Distance
Clustering Methods to Assess Population Structure
Distance-Based Trees
Model-Based Bayesian Clustering Methods
Principal Components Analysis
Estimating Migration Using Coalescent Models
Populations Structured by Selection: Adaptation to Local Environments
Differentiation in Neutral Markers and Phenotypes under Selection
Differentiation of Pathogen Populations on Host Species: Evidence of Host Specialization
Metapopulation Structure
   Summary of Key Concepts
   Recommended Reading

7 Recombination and Randomly Mating Populations
Evolutionary and Ecological Significance of Sex and Recombination
Ecological Implications of Sexual Reproduction in Eukaryotic Plant Pathogens
Sexual Reproduction and Mating Systems in Eukaryotic Plant Pathogens
Mating Systems in Fungi and Oomycetes
Nematode Mating Systems
Mixed Modes of Reproduction
Nonmeiotic Mechanisms of Recombination in Eukaryotes
Gene Conversion
Mitotic Crossing Over
Parasexuality
Recombination in Bacteria
Mechanisms of Bacterial Recombination
Recombination and Reassortment in Plant Viruses
Viral Recombination
Reassortment of Segmented Viral Genomes
Effects of Sex and Recombination on Genotypic Diversity
Random Mating in Diploid Populations
What Is Random Mating?
Hardy–Weinberg Equilibrium
Inbreeding
Linkage Disequilibrium and Tests for Random Mating in Haploid Populations
Causes of Linkage Disequilibrium
   Selection
   Linkage
   Migration and Population Admixture
   Random Genetic Drift
Statistical Analysis of Linkage Disequilibrium
Multilocus Estimation of Linkage Disequilibrium: The Index of Association
Clone Corrections for Estimating Linkage Disequilibrium
Additional Tests of Random Mating
Parsimony Tree-Length Permutation Test
Mating-Type Ratios
Genotypic Diversity
Frequency of Sex When Populations Appear to Be Randomly Mating
Estimating the Frequency of Sex Experimentally
Changes in Linkage Disequilibrium to Estimate the Contribution of Sexual Inoculum
Mark-Release-Recapture Experiments to Estimate Recombination
The Biological Significance of Recombination in Plant Pathogen Populations
   Summary of Key Concepts
   Recommended Reading

8 Clonal Populations
Evolutionary Significance of Asexual Reproduction
Muller’s Ratchet Revisited
Evolutionary Advantages of Asexual Reproduction: The Disadvantages of Sex
Definitions of Clones and Clonal Lineages
Operational Definition of Clonal Lineages
Deviations from Random Mating Revisited
Overrepresentation of Multilocus Genotypes
Linkage Disequilibrium and Correlation among Different Sets of Markers
Excess Heterozygosity in Clonal Diploid Populations
Detecting Recombination
Phylogenetic Incompatibility Between Loci: The Four-Gamete Test
Phylogenetic Incompatibility Between Loci: Incongruence of Gene Trees
Network Analyses to Detect Recombination
Coalescent Methods to Estimate Recombination Rates
Detecting Signs of Sex
Organismal Signs of Sex
Molecular Signs of Sex
Examples of Clonal Plant Pathogens
A Clonal Rust Fungus: Puccinia triticina
A Mitosporic Fungus: Verticillium dahlia
A Mitosporic Fungus with Evidence of Sex and Recombination: Alternaria brassicicola
The Challenges of Inferring Clonality and Recombination
   Summary of Key Concepts
   Recommended Reading

9 Evolution in Gene-for-Gene Systems
Host Plant Immunity and Defenses
The Classic Gene-for-Gene Model
Races in Gene-for-Gene Systems
Selection for Virulent Races: The Breakdown of Resistance
Evolution of New Races
Coevolution in Gene-for-Gene Systems
The Arms Race and Trench Warfare Models of Coevolution
Fitness Costs in Gene-for-Gene Systems
Fitness Costs of Unnecessary High Virulence
   Bacterial Blight of Rice
   Bacterial Spot in Peppers
Fitness Costs of Disease Resistance
Metapopulation Dynamics in Gene-for-Gene Systems
Metapopulation Models of Gene-for-Gene Systems
Empirical Evidence for Metapopulation Structure in Gene-for-Gene Systems
Evolution of Gene-for-Gene Systems in Agriculture
   Summary of Key Concepts
   Recommended Reading

10 Durability and the Deployment of Disease Resistance
Quantitative and Qualitative Resistance
Durability of Quantitative Resistance
Differential Interactions to Detect Pathogen Specificity to Quantitative Resistance
Selection Experiments to Detect Pathogen Specificity to Quantitative Resistance
The Lack of Erosion of Quantitative Resistance
Factors Affecting Durability of Qualitative Resistance in Gene-for-Gene Systems
Epidemiological Factors Affecting Durability in Gene-for-Gene Systems
Fitness of Virulent Races
Predicting Durability Based on Pathogen Population Biology
Race Surveys
Sampling Pathogen Populations
Differential Cultivars for Determining Races
Estimating Effector Allele Frequencies
Breeding for Resistance and Gene Deployment
Screening for Resistance Against Diverse Pathogen Populations
Gene Pyramids
Exploiting Linkage Disequilibrium in Pathogen Populations for Breeding Gene Pyramids
Gene Deployment
Cultivar Mixtures
Integrated Disease Management and Durability
   Summary of Key Concepts
   Recommended Reading

11 Emerging and Reemerging Plant Diseases
Invasive Plant Pathogens: Introductions to New Geographic Areas
Biology of Invasive Plant Pathogens
Phylogeographic Methods to Infer the Sources of Introductions
Speciation and the Evolution of Host Specificity
What Is a Species?
Reproductive Isolation and Speciation
Host-Shift Speciation
Host Shifts and Cospeciation
Mechanisms for the Rapid Evolution of Novel Pathogen Genotypes
Plant Viruses Emerging by Recombination
Interspecific Hybrids in Eukaryotic Plant Pathogens
Horizontal Gene Transfer That Affects Pathogenicity and Virulence
   Horizontal Gene Transfer in Bacteria
   Horizontal Gene Transfer in Eukaryotes
Selection for Novel Pathogen Genotypes
Role of Agriculture and Other Extrinsic Factors in Disease Emergence
Host Populations in Modern Agriculture Promote Disease Emergence
Additional Effects of Agriculture on Pathogen Evolution
Environmental Factors That Promote Disease Emergence
   Climate Change
   Vector Populations
   Cultural Practices
Countermeasures to Reduce the Risk of Disease Emergence
   Summary of Key Concepts
   Recommended Reading

12 Contributions of Population Genetics in Plant Disease Epidemiology
Historical Links Between Population Genetics and Epidemiology
Descriptive Studies of Genetic Variation in Populations of Plant Pathogens
Identification of Cryptic Species
Epidemiological Inferences from Clonal Population Structure
Epidemiological Inferences from Population Subdivision
Epidemiological Inferences about Sexual Reproduction
Direct Tracking of Pathogen Genotypes for Epidemiological Inference
Identifying Sources of Primary Inoculum Using Genetic Markers
Inferences from Spatial Patterns of Pathogen Genotypes
Applications of Genetic Variation to Disease Management: Diagnosis and Quantification of Plant Pathogens
A Critical Assessment of the Relevance of Pathogen Genetic Variation to Plant Disease Management
Future Directions for Population Biology in Plant Pathology
Metagenomics and Plant Microbiomes
Landscape Genetics
Population Genomics and Association Mapping
   Summary of Key Points
   Recommended Reading

Appendix: Genetic Markers Historically Used for Genotyping Plant Pathogens
Glossary
Abbreviations
References
Index

Customer Reviews

Biography

Author Michael G. Milgroom has been a pioneer and leading researcher in the population genetics and population biology of plant pathogens for nearly 30 years. He has also taught this subject extensively at the graduate level for more than 20 years. His vast knowledge and experience are apparent through Population Biology of Plant Pathogens's many examples derived from original research, historical accounts, articles, and other sources from himself and his colleagues.