Introduction to Molecular Epidemiology of Plant Diseases (with a CD-ROM)

A brief introduction to molecular epidemiology of plant diseases has been provided in this book. It consists four parts. It first introduces basic concepts of molecular epidemiology and compares the differences between conventional epidemiology and molecular epidemiology and in Part I. Part II summarizes general molecular techniques useful in epidemiological studies. Additional readings for the details of some techniques will be needed and many relevant books and articles are available in different sources. Part III serves as a major part of the book in which we include seven chapters in aspects of molecular epidemiology of plant diseases. These aspects include pathogen’s identification, reproductive mode of fungal pathosens, quantification of initial inoculum, spatial and temporal developments, long-distance dispersal and migration, evolution and population genetics and disease management. Methodology of data analysis and applications of software are introduced in Part IV.

PART I INTRoDUCTION
　CHAPTER 1 INTRoDUCl’ION TO MoLECULAR EPIDEMIOLoGY
　　1—1 Basic concept of molecular epidemiology
　　1—2 Why molecular epidemiology
　　1—3 Comparisons between classical and molecular methods in epidemiology
　　1—4 Working approaches of molecular epidemiology
　　1—5 About the book
　　References and suggested readings
PARTⅡMoLECULAR TECHNIQUES USED IN EPIDEMIOLOGY
　CHAPTER 2 MOLECULAR MARKERS
　　2—1 Protein—based marker：Allozymes
　　2—2 DNA band—based markers
　　2—3 DNA sequence
　　References and suggested readings
　CltAPTER 3 PCR—BASED TECHNIQUES
　　3—1 Classical PCR
　　3—2 Allele—specific PCR
　　3—3 Nested PCR
　　3—4 Multiplex PCR
　　References and suggested readings
　CHAPTER 4 QUANTITATIVE REAL‘TIME PCR
　　4—1 Introduction
　　4—2 Basic real—time PCR methods
　　4—3 Primer and probe design for real—time PCR
　　4—4 Result analysis
　　4—5 Applications of real—time PCR
　　References and suggested readings
　CHAmR 5 PRIMER I)ESIGN
　　5—1 Some basic concepts for primer design
　　5—2 Computer programs used for primer design
　　5—3 An example of primer design using a computer program
　　5—4 Degenerated PCR primers
PARTⅢ MoLECULAR EPIDEMIOLOGY oF PLANT DISEASES
　CHAPTER 6 PATHoGEN IDENTIFICATIoN AND DISEASE DIAGNoSIS
　　6—1 Introduction
　　6—2 Use of species—specific genes or DNA regions for developing PCR primers
　　6—3 Use of anonymous unique DNA regions for developing PCR primers
　　6—4 PCR inhibitors
　　Summary
　　References and suggested readings
　CHAPTER 7 FUNGAL PATHoGEN REPRoDUCTIVE MoDES
　　7—1 Frequencies of genotypes
　　7—2 Deviation from Hardy—Weinberg expectations
　　7—3 Parsimony Tree Length Permutation(PTLPT)
　　7—4 Index of association(IA)
　　References and suggested readings
　CHAPTER 8 DETEMINATIoN AND QUANTIFICATION OF INITIAL INOCULUM OF EPIDEMICS
　　8—1 Introduction
　　8—2 Molecular methods for quantification of initial inoculum
　　8—3 Examples of quantification of initial inoculum using molecular methods
　　Remarkable conclusion
　　References and suggested readings
　CHPTER 9 TEMpORAL AND SPATIAL DEVELOPMENT oF PATHoGEN POPULATIoNS
　　9—1 Introduction
　　9—2 Molecular approaches
　　9—3 Monitoring pathogen population structures
　　9—4 Studying spatial—temporal dynamics of pathogen populations
　　9—5 Providing information needed for disease management
　　Summary
　　References and suggested readings
　CHAPTER 10 PATHoGEN LONG—DISTANCE DIsPERSAL AND MIGRATION
　　10—1 Introduction
　　10—2 Pathogen lon9—distance dispersal and disease epidemics
　　10—3 Traditional methods to determine or infer pathogen lon9—distance dispersal
　　10—4 Molecular methods to study pathogen lon9—distance dispersal
　　10一5 Examples
　　Summary
　　……
PART IV METHODOLOGY OF DATA ANLYSIS
INDEX