DNA Fingerprinting in Plants: Principles, Methods, and Applications, Second Edition, 2nd Edition (Paperback) book cover

DNA Fingerprinting in Plants

Principles, Methods, and Applications, Second Edition, 2nd Edition

By Kurt Weising, Hilde Nybom, Markus Pfenninger, Kirsten Wolff, Günter Kahl

CRC Press

472 pages | 31 B/W Illus.

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pub: 2005-02-28
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Description

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.

Reviews

"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

Table of Contents

PREFACE

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

Subject Categories

BISAC Subject Codes/Headings:
SCI011000
SCIENCE / Life Sciences / Botany
SCI049000
SCIENCE / Life Sciences / Biology / Molecular Biology