DNA Fingerprinting in Plants: Principles, Methods, and Applications, Second Edition

by Weising; Kurt

• ISBN13: 9780849314889
• ISBN10: 0849314887
• Edition: 2nd
• Format: Nonspecific Binding
• Copyright: 2005-02-28
• Publisher: CRC Press

Summary

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.

Table of Contents

Chapter 1 Repetitive DNA: An Important Source of Variation in Eukaryotic Genomes
1.1 Categories of DNA Sequence Mutations	2	(2)
1.2 Tandem-Repetitive DNA: The Biology of Mini- and Microsatellites	4	(10)
1.2.1 Minisatellites	5	(2)
1.2.1.1 Chromosomal Localization and Association with Other Repeats	6	(1)
1.2.1.2 Mutability and Evolution	6	(1)
1.2.1.3 Minisatellites in Organellar Genomes	7	(1)
1.2.1.4 Potential Functions of Minisatellites	7	(1)
1.2.1.5 Minisatellites as Molecular Markers	7	(1)
1.2.2 Microsatellites	7	(7)
1.2.2.1 Categories of Microsatellites	8	(2)
1.2.2.2 Chromosomal Localization and Association with Other Repeats	10	(1)
1.2.2.3 Mutability and Evolution	11	(2)
1.2.2.4 Microsatellites in Organellar Genomes	13	(1)
1.2.2.5 Potential Functions of Microsatellites	13	(1)
1.2.2.6 Microsatellites as Molecular Markers	14	(1)
1.3 Transposable Elements	14	(7)
1.3.1 Class I Transposons	14	(3)
1.3.2 Class II Transposons	17	(1)
1.3.3 Unclassified Transposons	18	(1)
1.3.4 Transposons and Genome Evolution	18	(1)
1.3.5 Transposons as Molecular Markers	19	(2)
Chapter 2 Detecting DNA Variation by Molecular Markers
2.1 Properties of Molecular Markers	21	(1)
2.2 Traditional Marker Systems	22	(6)
2.2.1 Protein Markers and Allozymes	22	(1)
2.2.2 DNA Sequencing	23	(1)
2.2.3 Restriction Fragment Length Polymorphism (RFLP) Analysis	24	(4)
2.2.3.1 Nuclear RFLPs and DNA Fingerprinting	25	(1)
2.2.3.2 RFLPs in Chloroplast and Mitochondrial DNA	26	(2)
2.3 The PCR Generation: Molecular Markers Based on In Vitro DNA Amplification	28	(47)
2.3.1 Principle of the PCR	29	(2)
2.3.2 Cleaved Amplified Polymorphic Sequences	31	(1)
2.3.3 PCR with Arbitrary Primers: RAPD and Its Variants	32	(9)
2.3.3.1 The Molecular Basis of RAPDs: Significance of Mispriming and Competition among Priming Sites	33	(4)
2.3.3.2 Properties of RAPD Markers	37	(1)
2.3.3.3 Advantages, Limitations, and Applications of RAPD Markers	38	(1)
2.3.3.4 Sequence-Characterized Amplified Regions	39	(1)
2.3.3.5 Expression Profiling with Arbitrary Primers	40	(1)
2.3.4 Microsatellites	41	(4)
2.3.4.1 Nuclear Microsatellite Markers	42	(2)
2.3.4.2 Chloroplast Microsatellite Markers	44	(1)
2.3.5 Inter-Repeat PCR	45	(9)
2.3.5.1 From A/u Repeats to Zinc Fingers: Repetitive DNA as a Primer Target 4.	.5
2.3.5.2 Primers Directed Toward Minisatellites	46	(1)
2.3.5.3 Primers Directed Toward Microsatellites	47	(5)
2.3.5.4 Primers Directed Toward Interspersed Repeats	52	(2)
2.3.6 DNA Profiling of Genic Regions: RGAP, SRAP, and TRAP	54	(2)
2.3.7 Hybridization of Microsatellites to RAPD and MP-PCR Products	56	(2)
2.3.8 AFLP Analysis and Its Variants	58	(12)
2.3.8.1 The AFLP Technique: Principle, Advantages, and Limitations	58	(4)
2.3.8.2 S-SAP Analysis	62	(2)
2.3.8.3 Selective Amplification of Microsatellite Polymorphic Loci	64	(2)
2.3.8.4 Microsatellite-AFLP	66	(1)
2.3.8.5 Methylation-Sensitive Amplified Polymorphisms	66	(2)
2.3.8.6 AFLP-Based Expression Profiling	68	(1)
2.3.8.7 Miscellaneous AFLP Variants	69	(1)
2.3.9 Single-Strand Conformation Polymorphism Analysis and Related Techniques	70	(2)
2.3.10 Miscellaneous Techniques	72	(10)
2.3.10.1 Minisatellite Variant Repeat Mapping	72	(1)
2.3.10.2 Two-Dimensional DNA Typing Methods	72	(1)
2.3.10.3 Single-Nucleotide Polymorphisms	73	(2)
Chapter 3 Laboratory Equipment
3.1 Incubators	75	(1)
3.2 Plant and Plant Cell Growth Equipment	76	(1)
3.3 Sterilization	76	(1)
3.4 Water Purification	76	(1)
3.5 Centrifuges	76	(1)
3.6 Refrigeration and Material Storage	77	(1)
3.7 Safety	77	(1)
3.8 Pipets	77	(1)
3.9 Supplies (Glassware and Plasticware)	78	(1)
3.10 DNA Detection and Quantitation	78	(1)
3.11 Electrophoresis Equipment	78	(1)
3.12 Documentation of Results	79	(1)
3.13 General Laboratory Equipment	79	(2)
Chapter 4 Methodology
4.1 Safety Precautions	81	(1)
4.2 Isolation, Purification, and Quantitation of Plant DNA	82	(25)
4.2.1 Collection and Preservation of Plant Tissue in the Field	82	(6)
4.2.1.1 Starting Material	83	(1)
4.2.1.2 Cooling, Freezing, and Lyophilization	84	(1)
4.2.1.3 Chemical Preservation	84	(1)
4.2.1.4 Drying	85	(2)
4.2.1.5 Preparing Herbarium Vouchers	87	(1)
4.2.1.6 Contamination	87	(1)
4.2.2 Plant DNA Extraction: General Considerations	88	(12)
4.2.2.1 Cell and Tissue Disruption	89	(1)
4.2.2.2 Lysis of Membranes and Organelles	90	(1)
4.2.2.3 Removal of Proteins and RNA	91	(1)
4.2.2.4 Removal of Polyphenols and Other Secondary Compounds	91	(1)
4.2.2.5 Removal of Polysaccharides	92	(1)
4.2.2.6 Removal of Organic Acids and Endogenous DNase Activities	92	(1)
4.2.2.7 General Strategies to Remove Cytoplasmic Contaminants	93	(2)
4.2.2.8 Herbarium Specimens and Other Difficult Substrates	95	(2)
4.2.2.9 High-Throughput Procedures	97	(1)
4.2.2.10 Commercial Kits	98	(1)
4.2.2.11 Megabase DNA Isolation Protocols	99	(1)
4.2.2.12 Choice of Procedure and Costs	99	(1)
4.2.2.13 Storage of DNA Solutions	100	(1)
4.2.3 CTAB Protocol I	100	(2)
4.2.4 CTAB Protocol II	102	(1)
4.2.5 SDS-Potassium Acetate Protocol	103	(1)
4.2.6 DNA Preparation via Nuclei	104	(1)
4.2.7 Quantitation of DNA	105	(2)
4.2.7.1 Ethidium Bromide Staining	106	(1)
4.2.7.2 Spectrophotometry	106	(1)
4.3 Basic Molecular Techniques	107	(31)
4.3.1 Restriction of DNA	107	(2)
4.3.2 Polymerase Chain Reaction	109	(5)
4.3.2.1 Primers	110	(1)
4.3.2.2 DNA Polymerase	110	(1)
4.3.2.3 Thermocycler and Temperature Regimen	110	(2)
4.3.2.4 Template Quality	112	(1)
4.3.2.5 Yield and Specificity	112	(1)
4.3.2.6 Contamination	113	(1)
4.3.3 DNA Sequencing	114	(1)
4.3.4 Agarose Gel Electrophoresis	115	(3)
4.3.5 PAA Gel Electrophoresis	118	(4)
4.3.5.1 Nondenaturing PAA Gels	118	(2)
4.3.5.2 Sequencing Gels	120	(2)
4.3.6 Detection of DNA in Gels	122	(2)
4.3.6.1 Ethidium Bromide Staining	123	(1)
4.3.6.2 Silver Staining	123	(1)
4.3.7 Gel Drying	124	(1)
4.3.8 Southern Blotting	125	(2)
4.3.9 Generation of Radiolabeled Probes, Primers, and PCR Products	127	(6)
4.3.9.1 End-Labeling of Oligonucleotides	128	(1)
4.3.9.2 Nick Translation	129	(1)
4.3.9.3 Random Priming	130	(1)
4.3.9.4 Removal of Unincorporated dNTPs	131	(2)
4.3.9.5 Nonradioactive Labeling Procedures	133	(1)
4.3.10 Blot Hybridization	133	(3)
4.3.10.1 Oligonucleotide Probes	134	(1)
4.3.10.2 Probes Generated by Nick Translation or Random Priming	135	(1)
4.3.11 Signal Detection	136	(2)
4.3.11.1 Autoradiography	136	(1)
4.3.11.2 Phosphorimaging	137	(1)
4.3.11.3 Automated DNA Sequencers	137	(1)
4.4 PCR with Arbitrary Primers	138	(9)
4.4.1 Standard RAPD Protocol	138	(1)
4.4.2 Influence of Reaction Conditions and Components	139	(7)
4.4.2.1 Primers	139	(3)
4.4.2.2 Polymerase	142	(1)
4.4.2.3 Thermocycler and Temperature Regimen	142	(1)
4.4.2.4 Template Concentration and Quality	143	(1)
4.4.2.5 Magnesium Concentration	144	(1)
4.4.2.6 PCR Additives	144	(1)
4.4.2.7 Reproducibility and Quality of Banding Patterns	145	(1)
4.4.3 Modifications	146	(1)
4.5 Microsatellite-Primed PCR	147	(5)
4.5.1 Standard Protocol of Microsatellite-Primed PCR	148	(1)
4.5.2 Influence of Reaction Conditions and Components	149	(1)
4.5.3 Modifications	150	(2)
4.5.3.1 Anchored vs. Unanchored Primers	150	(2)
4.5.3.2 Fragment Separation and Detection	152	(1)
4.6 PCR and Hybridization: Combinatory Techniques	152	(2)
4.6.1 Assessing the Genomic Copy Number of PCR Amplicons	153	(1)
4.6.2 Testing the Homology of Comigrating Bands	153	(1)
4.6.3 Random Amplified Microsatellite Polymorphism (RAMPO)	154	(1)
4.7 Amplified Fragment Length Polymorphism	154	(16)
4.7.1 Standard AFLP Protocol Using Radioisotopes	155	(4)
4.7.1.1 Step 1: Restriction of Template DNA and Ligation to Specific Adapters	155	(1)
4.7.1.2 Step 2: Preamplification	156	(2)
4.7.1.3 Step 3: Selective Amplification	158	(1)
4.7.1.4 Step 4: AFLP Fragment Separation and Autoradiography	159	(1)
4.7.2 AFLP Protocol Using Fluorescence-Labeled Primers	159	(3)
4.7.2.1 Steps 1 and 2	160	(1)
4.7.2.2 Step 3: Selective Amplification	160	(1)
4.7.2.3 Step 4: AFLP Fragment Separation and Fluorescence Detection	161	(1)
4.7.3 Selective Amplification of Microsatellite Polymorphic Loci and Microsatellite AFLP Protocols	162	(1)
4.7.4 Technical Aspects and Modifications	162	(7)
4.7.4.1 Restriction and Ligation of Template DNA	162	(3)
4.7.4.2 Preamplification and Selective Amplification	165	(2)
4.7.4.3 Fragment Separation and Detection	167	(2)
4.7.5 Robustness and Reproducibility	169	(1)
4.8 Generation and Analysis of Microsatellite Markers	170	(32)
4.8.1 Microsatellite Analysis Using Radioisotopes	171	(3)
4.8.2 Microsatellite Analysis Using Fluorochromes	174	(2)
4.8.3 Technical Aspects and Modifications	176	(2)
4.8.3.1 Fragment Separation and Visualization	176	(1)
4.8.3.2 Stutter Bands and Other PCR Artefacts	177	(1)
4.8.4 Generating Microsatellite Markers Without Cloning	178	(5)
4.8.4.1 Literature Screening	178	(1)
4.8.4.2 Database Mining	179	(1)
4.8.4.3 Marker Transferability between Species: Nuclear Microsatellites	180	(2)
4.8.4.4 Marker Transferability between Species: Chloroplast Microsatellites	182	(1)
4.8.5 Microsatellite Cloning	183	(19)
4.8.5.1 Conventional Libraries	183	(1)
4.8.5.2 Microsatellite Enrichment Based on Primer Extension	184	(1)
4.8.5.3 Microsatellite Enrichment Based on Selective Hybridization	185	(2)
4.8.5.4 Microsatellites from Cloned PCR Products	187	(1)
4.8.5.5 Miscellaneous Enrichment Procedures	188	(1)
4.8.5.6 Protocol: Microsatellite Enrichment Cloning Using Magnetic Beads	189	(10)
4.8.5.7 Primer Design	199	(1)
4.8.5.8 Factors Affecting the Efficiency of Microsatellite Cloning	200	(2)
4.8.5.9 Commercial Development of Microsatellite Libraries	202	(1)
4.9 CAPS Analysis of cpDNA and mtDNA	202	(5)
4.9.1 Standard CAPS Protocol	203	(2)
4.9.2 Choice of CAPS Primers	205	(2)
Chapter 5 Evaluation of Molecular Marker Data
5.1 Robustness and Reproducibility	207	(3)
5.1.1 Reliability	208	(1)
5.1.2 Band Homology	208	(1)
5.1.3 Band Linkage and Neutrality	209	(1)
5.2 Fragment Sizing and Matching	210	(3)
5.2.1 General Precautions	211	(1)
5.2.2 Equipment	212	(1)
5.3 Multilocus vs. Single-Locus Approaches	213	(1)
5.3.1 Multilocus Markers	213	(1)
5.3.2 Single-Locus Markers and Polyploids	213	(1)
5.4 Band Sharing and Genetic Distances	214	(5)
5.4.1 Coefficients of Similarity	214	(1)
5.4.2 Dissimilarity Coefficients and Genetic Distances	215	(1)
5.4.3 Identity and Uniqueness	215	(2)
5.4.4 Clonal Structure	217	(2)
5.5 Ordination, Clustering, and Dendrograms	219	(4)
5.5.1 Ordination Techniques	219	(2)
5.5.2 Construction of Dendrograms	221	(2)
5.6 Population Genetic Analysis	223	(9)
5.6.1 Measures of Variation	223	(3)
5.6.2 Genetic Differentiation between Populations	226	(3)
5.6.2.1 F Statistics and Related Measures	226	(2)
5.6.2.2 Analysis of Variance	228	(1)
5.6.2.3 Shannon's Index	228	(1)
5.6.3 Genetic Distances between Populations	229	(1)
5.6.4 Inbreeding Coefficient and Mating Systems	229	(1)
5.6.5 Estimation of Relatedness and Paternity Testing	230	(1)
5.6.6 Migration and Hybridization	231	(1)
5.6.7 Gene Flow, Isolation-by-Distance, and Spatial Structure	232	(1)
5.7 Phylogeography and Nested Clade Analysis	232	(1)
5.8 Statistical Testing of Hypotheses: Analytical and Computational Methods	233	(2)
Chapter 6 Applications of DNA Fingerprinting in Plant Sciences
6.1 A Brief History of DNA Fingerprinting	235	(2)
6.1.1 Minisatellite and Oligonucleotide DNA Probes Detect Genetic Variation	235	(1)
6.1.2 PCR-Based Methods Enter the Stage	236	(1)
6.1.3 Microsatellite DNA Analyses Yield Codominant Markers	237	(1)
6.1.4 Universal Organellar DNA Primers Produce Uniparental Markers	237	(1)
6.2 Genotype Identification	237	(9)
6.2.1 Individual-Specific DNA Fingerprints	238	(2)
6.2.2 Cultivar Identification	240	(3)
6.2.2.1 Patenting and Protecting Plant Varieties	240	(1)
6.2.2.2 Choice of DNA Marker Method for Cultivar Identification	241	(1)
6.2.2.3 Propagation and Reproduction of Crop Species	242	(1)
6.2.3 In Vitro-Propagated Plant Material and Somaclonal Variation	243	(2)
6.2.4 Sports and Other Mutants	245	(1)
6.3 Genetic Diversity	246	(18)
6.3.1 Variation and Relatedness among Cultivars	247	(1)
6.3.2 Analysis of Population Genetic Diversity and Its Distribution	248	(9)
6.3.2.1 Choice of Molecular Marker Method for Population Genetics	249	(1)
6.3.2.2 Influence of the Breeding System on Genetic Diversity	250	(1)
6.3.2.3 Clones and Ramets	251	(1)
6.3.2.4 Estimating Gene Flow via Pollen and Seeds	252	(3)
6.3.2.5 Effects of Habitat Fragmentation	255	(2)
6.3.3 Hybridization and Introgression	257	(4)
6.3.3.1 Hybridization in Wild Populations	257	(2)
6.3.3.2 Hybrid Distances and Diagnostic Markers	259	(1)
6.3.3.3 Hybridization between Wild and Cultivated Plants	259	(1)
6.3.3.4 Hybridization in Gymnosperms	260	(1)
6.3.3.5 Polyploidy	260	(1)
6.3.4 Plant Conservation	261	(1)
6.3.5 Germplasm Characterization and Preservation	262	(2)
6.3.5.1 Gene Banks	263	(1)
6.3.5.2 Core Collections	264	(1)
6.4 Plant Taxonomy and Systematics	264	(6)
6.4.1 Taxonomic Relationships Revealed by Multilocus DNA Methods	264	(4)
6.4.2 Microsatellite Markers in Taxonomic Studies	268	(1)
6.4.3 Taxonomic Consequences from DNA Profiling Data	269	(1)
6.5 Phylogeography	270	(7)
6.5.1 Phylogeography Based on cpDNA	270	(4)
6.5.1.1 Postglacial Recolonization of Central and Northern Europe	271	(1)
6.5.1.2 Phylogeographic Case Studies in Tropical Trees	271	(1)
6.5.1.3 Phylogeographic Case Studies in Gymnosperms	272	(2)
6.5.2 Phylogeography Based on Nuclear Genes	274	(3)
Chapter 7 Linkage Analysis and Genetic Maps
7.1 Generating High-Density Genetic Maps	277	(10)
7.1.1 Selection of Parent Plants	277	(1)
7.1.2 Mapping Population	278	(1)
7.1.3 Linkage Analysis	279	(1)
7.1.4 The Genetic Map	279	(6)
7.1.5 Cytogenetic Maps	285	(1)
7.1.6 Genetic vs. Physical Maps	285	(2)
7.2 Synteny: The Comparative Analysis of Genomes	287	(1)
7.3 Marker-Assisted Selection	288	(1)
7.4 Molecular Markers and Positional Cloning	289	(4)
Chapter 8 Which Marker for What Purpose: A Comparison
8.1 Morphological Characters and Allozymes vs. DNA Markers	293	(2)
8.2 Different Kinds of DNA Markers	295	(3)
8.2.1 Discriminatory Power	295	(1)
8.2.2 Genetic Distances	296	(1)
8.2.3 Within- and Among-Population Variation	297	(1)
8.2.4 Gene Tagging and Genetic Linkage Mapping	297	(1)
8.2.5 Costs	298	(1)
8.3 Conclusions	298	(3)
Chapter 9 Future Prospects: SNiPs and Chips for DNA and RNA Profiling
9.1 Single-Nucleotide Polymorphisms	301	(4)
9.1.1 What Is a SNIP?	301	(1)
9.1.2 SNP Discovery	302	(1)
9.1.3 SNP Genotyping	303	(1)
9.1.4 SNPs in Plant Genomes	304	(1)
9.1.5 Perspective	305	(1)
9.2 DNA Microarrays	305	(3)
9.3 Expression Profiling and Expression Markers	308	(3)
Appendix 1 Plant DNA Isolation Protocols	311	(12)
Appendix 2 Commercial Companies	323	(6)
Appendix 3 Computer Programs Dealing with the Evaluation of DNA Sequence Variation and Molecular Marker Data	329	(8)
Appendix 4 Web-Pages of Interest	337	(2)
References	339	(88)
Index	427