2nd Edition
DNA Fingerprinting in Plants Principles, Methods, and Applications, Second Edition
Given the explosive development of new molecular marker techniques over the last decade, newcomers and experts alike in the field of DNA fingerprinting will find an easy-to-follow guide to the multitude of techniques available in DNA Fingerprinting in Plants: Principles, Methods, and Applications, Second Edition. Along with step-by-step annotated protocols, the authors fully discuss the technical aspects and modifications of existing techniques, the influence of reaction components and conditions, and the analysis of the results.
This second edition has been completely revised to address the exponential changes in the field since the first edition, focusing on PCR-based techniques but also including more sophisticated ones. The authors include numerous case studies to illustrate applications of the methods, more than 1600 references to the literature, and descriptions of reagent formulation, equipment, and computer programs used for evaluating molecular marker data. They compare the various methods, including the costs and benefits of each, helping readers determine which is best suited to a particular application.
The well-rounded, cross-referenced, and unified nature of this book makes it intrinsically easier to follow than the edited, multi-authored books currently available. It is an absolute necessity on the lab bench of anyone involved in plant research, DNA profiling, and molecular markers.
REPETITIVE DNA: AN IMPORTANT SOURCE OF VARIATION IN EUKARYOTIC GENOMES
Categories of DNA Sequence Mutations
Tandem-Repetitive DNA: The Biology of Mini- and Microsatellites
Minisatellites
Microsatellites
Transposable Elements
Class I Transposons
Class II Transposons
Unclassified Transposons
Transposons and Genome Evolution
Transposons as Molecular Markers
DETECTING DNA VARIATION BY MOLECULAR MARKERS
Properties of Molecular Markers
Traditional Marker Systems
Protein Markers and Allozymes
DNA Sequencing
Restriction Fragment Length Polymorphism (RFLP) Analysis
The PCR Generation: Molecular Markers Based on In Vitro DNA Amplification
Principle of the PCR
Cleaved Amplified Polymorphic Sequences
PCR with Arbitrary Primers: RAPD and Its Variants
Microsatellites
Inter-Repeat PCR
DNA Profiling of Genic Regions: Resistance Gene Analog Polymorphism, Sequence-Related Amplified Polymorphism, and Target Region Amplification Polymorphism
Hybridization of Microsatellites to RAPD and MP-PCR Products
AFLP Analysis and Its Variants
Single-Strand Conformation Polymorphism Analysis and Related Techniques
Miscellaneous Techniques
LABORATORY EQUIPMENT
METHODOLOGY
Safety Precautions
Isolation, Purification, and Quantitation of Plant DNA
Collection and Preservation of Plant Tissue in the Field
Plant DNA Extraction: General Considerations
CTAB Protocol I
CTAB Protocol II
SDS-Potassium Acetate Protocol
DNA Preparation via Nuclei
Quantitation of DNA
Basic Molecular Techniques
Restriction of DNA
Polymerase Chain Reaction
DNA Sequencing
Agarose Gel Electrophoresis
PAA Gel Electrophoresis
Detection of DNA in Gels
Gel Drying
Southern Blotting
Generation of Radiolabeled Probes, Primers, and PCR Products
Blot Hybridization
Signal Detection
PCR with Arbitrary Primers
Standard RAPD Protocol
Influence of Reaction Conditions and Components
Modifications
Microsatellite-Primed PCR
Standard Protocol of Microsatellite-Primed PCR
Influence of Reaction Conditions and Components
Modifications
PCR and Hybridization: Combinatory Techniques
Assessing the Genomic Copy Number of PCR Amplicons
Testing the Homology of Comigrating Bands
Random Amplified Polymorphic Microsatellites
Amplified Fragment Length Polymorphism
Standard AFLP Protocol Using Radioisotopes
AFLP Protocol Using Fluorescence-Labeled Primers
Selective Amplification of Microsatellite Polymorphic Loci and Microsatellite AFLP Protocols
Technical Aspects and Modifications
Robustness and Reproducibility
Generation and Analysis of Microsatellite Markers
Microsatellite Analysis Using Radioisotopes
Microsatellite Analysis Using Fluorochromes
Technical Aspects and Modifications
Generating Microsatellite Markers Without Cloning
Microsatellite Cloning
CAPS Analysis of cpDNA and mtDNA
Standard CAPS Protocol
Choice of CAPS Primers
EVALUATION OF MOLECULAR MARKER DATA
Robustness and Reproducibility
Reliability
Band Homology
Band Linkage and Neutrality
Fragment Sizing and Matching
General Precautions
Equipment
Multilocus vs. Single-Locus Approaches
Multilocus Markers
Single-Locus Markers and Polyploids
Band Sharing and Genetic Distances
Coefficients of Similarity
Dissimilarity Coefficients and Genetic Distances
Identity and Uniqueness
Clonal Structure
Ordination, Clustering, and Dendrograms
Ordination Techniques
Construction of Dendrograms
Population Genetic Analysis
Measures of Variation
Genetic Differentiation between Populations
Genetic Distances between Populations
Inbreeding Coefficient and Mating Systems
Estimation of Relatedness and Paternity Testing
Migration and Hybridization
Gene Flow, Isolation-by-Distance, and Spatial Structure
Phylogeography and Nested Clade Analysis
Statistical Testing of Hypotheses: Analytical and Computational Methods
APPLICATIONS OF DNA FINGERPRINTING IN PLANT SCIENCES
A Brief History of DNA Fingerprinting
Minisatellite and Oligonucleotide DNA Probes Detect Genetic Variation
PCR-Based Methods Enter the Stage
Microsatellite DNA Analyses Yield Codominant Markers
Universal Organellar DNA Primers Produce Uniparental Markers
Genotype Identification
Individual-Specific DNA Fingerprints
Cultivar Identification
In Vitro-Propagated Plant Material and Somaclonal Variation
Sports and Other Mutants
Genetic Diversity
Variation and Relatedness among Cultivars
Analysis of Population Genetic Diversity and Its Distribution
Hybridization and Introgression
Plant Conservation
Germplasm Characterization and Preservation
Plant Taxonomy and Systematics
Taxonomic Relationships Revealed by Multilocus DNA Methods
Microsatellite Markers in Taxonomic Studies
Taxonomic Consequences from DNA Profiling Data
Phylogeography
Phylogeography Based on cpDNA
Phylogeography Based on Nuclear Genes
LINKAGE ANALYSIS AND GENETIC MAPS
Generating High-Density Genetic Maps
Selection of Parent Plants
Mapping Population
Linkage Analysis
The Genetic Map
Cytogenetic Maps
Genetic vs. Physical Maps
Synteny: The Comparative Analysis of Genomes
Marker-Assisted Selection
Molecular Markers and Positional Cloning
WHICH MARKER FOR WHAT PURPOSE: A COMPARISON
Morphological Characters and Allozymes vs. DNA Markers
Different Kinds of DNA Markers
Discriminatory Power
Genetic Distances
Within- and Among-Population Variation
Gene Tagging and Genetic Linkage Mapping
Costs
Conclusions
FUTURE PROSPECTS: SNIPS AND CHIPS FOR DNA AND RNA PROFILING
Single-Nucleotide Polymorphisms
What Is a SNiP
SNP Discovery
DNA Microarrays
Expression Profiling and Expression Markers
APPENDIX 1: PLANT DNA ISOLATION PROTOCOLS
APPENDIX 2: SUPPLIERS AND SELLERS OF REAGENTS AND EQUIPMENT
APPENDIX 3: COMPUTER PROGRAMS DEALING WITH THE EVALUATION OF DNA SEQUENCE VARIATION AND MOLECULAR MARKER DATA
APPENDIX 4: WEB PAGES OF INTEREST
REFERENCES
INDEX
Biography
Kurt Weising, Hilde Nybom, Markus Pfenninger, Kirsten Wolff, Günter Kahl
"this is a good book and a useful addition to the shelf. It should be in the library (or preferably the lab) of all institutes carrying out DNA fingerprinting in plants. Its reference list is extensive, and it is a source of a wide range of interesting pieces of information. The different expertise of the authors has resulted in a wide-ranging and detailed assessment of the subject. The authors should be congratulated on the production of a good successor to the first edition of the book."
--Michelle Hollingsworth in the Annals of Botany"… many readers will find this book interesting. … It is analytically written and contains much valuable information. It involves perhaps all published plant DNA isolation protocols, a brief description of them, and notes on their uses. … the book contains a plethora of information on plant DNA fingerprinting."
— Elias Anastassopoulos, Tei Larissas, School of Agriculture, Dep. Of Plant Production, Larissa, Greece in Economic Botany 61(1) 2007
