Methods of Genome Analysis in Plants

This extensively illustrated book describes in detail the classical and molecular techniques of elucidating genomic and phylogenetic relationships in plants. The advent of novel techniques like genomic painting, chromosome microdissection, and microcloning has added a new level of sophistication to plant genome analysis and gene mapping. Each of the 20 chapters covers the nature, advantages, and limitations of a genome analysis technique. Each chapter has been written by one or more specialists, who have given an authoritative account of the subject. This invaluable sourcebook will be useful to professionals and graduate students interested in genome analysis, gene mapping, and organic evolution. The book will particularly benefit cytogeneticists, plant breeders, taxonomists, biosytematists, molecular biologists, and biotechnologists.

Genome Analysis: A Prologue, P.P. Jauhar
MEIOTIC AND KARYOTYPIC DATA IN GENOME ANALYSIS
Chromosome Pairing as a Tool in Genome Analysis: Merits and Limitations, P.P. Jauhar and L.R. Joppa
Historical Perspective
The Rationale of Genome Analysis
Chromosome Pairing in Diploid Hybrids: Its Limitations
Triploid Hybrids: Preferential Pairing and a Realistic Test for Intergenomic Affinity
Amphidiploids: Complete Opportunity for Preferential Pairing
Quantification of the Pairing Data
Discrimination of Pairing Between Parental Chromosomes
Numerical Meiotic Models and the Inference of Genome Affinities
Chromosome Pairing in Presence of Phl
Other Limitations of Chromosome Pairing
The Dilemma of Genomic Designation
Conclusions and Perspectives
References
Chromosome Banding and Genome Analysis in Diploid and Cultivated Polyploid Wheats, B. Friebe and B.S. Gill
Introduction
Constitutive Heterochromatin and the Development of Chromosome Banding Techniques
The Origin of Cultivated Wheat
Equilocal C-Heterochromatin Distribution and the Evolution of C-Banding Patterns
References
Numerical Meiotic Models for the Inference of Genomic Affinity in Polyploids, C.F. Crane
Introduction
Background
Principles of Model Construction
Choice of Objective Function and Data to be Evaluated
Solution Algorithms
Interpretation of Model Results
Abstract
References
Limitations and Pitfalls in the Use of Quantitative Polyploid Meiotic Models for Genome Analysis, J. Sybenga
Introduction
Limitations of Meiotic Affinity Models
Summary
References
Molecular-Meiotic Analysis of Cotton, D.M. Stelly, C. F. Crane, R.E. Hanson, T.D. McKnight, and H. J. Price
Introduction
Localization to a Chromosome
Subchromosomal Localization
"Ring"-IV Analysis
Open "Chain"-IV Analysis
"Barbell"-IV Analysis
TeNT-IV Analysis
Summary and Outlook
References
CHARACTERISTICS OF NUCLEAR DNA AND GENOME ANALYSIS
Analysis of Plant DNA Content by Feulgen Microspectrophotometry and Flow Cytometry, H.J. Price and J.S. Johnston
Introduction
Methods of DNA Content Determination in Plants
Additional Uses of Flow Cytometry for Plant Genome Analysis
References
Genome Analysis of Polyploid Species Employing Variation in Repeated Nucleotide Sequences, J. Dvorak and J. Dubcovsky
Repeated Nucleotide Sequences
Repeated Sequence Correspondence
Method Comparisons
Modification of Genomes by Introgressive Hybridization
Summary
References
Development and Application of Simple Sequence Repeat (SSR) Loci for Plant Genome Analysis, S.M. Brown, A.K. Szewc-McFadden, and S. Kresovich
Introduction
Characteristics and Use of SSR Markers
Theory of SSR Hypervariability
Applications of SSR Markers in Human Genetics
Applications of SSR Markers in Plant Genetics
Future Developments in SSR Marker Analysis of Plant Genomes
References
In situ HYBRIDIZATION AND GENOMIC PAINTING
Genomic Southern and In situ Hybridization for Plant Genome Analysis, J.S. Heslop-Harrison and T. Schwarzacher
Introduction
Genomic Hybridization-The Methods
Genomic In situ Hybridization to Look at Genomes in Hybrid and Polyploid Species
Genomic In situ Hybridization to Examine Species Relationships
Genomic Southern Hybridization to Examine Species Relationships
What Types of DNA Sequence are Probed by Genomic Hybridization and In situ Hybridization?
Conclusions
References
Multicolor Fluorescence In situ Hybridization: A New Tool for Genome Analysis, Y. Mukai
Introduction
Principle and Methods of Multicolor FISH
Genome Analysis Revealed by Fluorescent Probes
Physical Ordering of DNA Sequences
Other Applications in Cytogenetics
Concluding Remarks
References
ISOZYME AND MOLECULAR MARKERS IN GENOME ANALYSIS
Genome Analysis in the Triticeae Using Isozymes, G. Hart
Introduction
Methods
Homoeologous Relationships Among Chromosomes
Summary
References
Genome Analysis in Polyploids Using Molecular Markers, J.A.G. da Silva and M.E. Sorrells
Introduction
Terminology
Mapping Populations
Segregation Analyses
Power of Linkage Detection
Identification of Homologous Groups
Conclusions
References
Barley Genome Mapping and Its Applications, P.M. Hayes, F.Q. Chen, A. Kleinhofs, A. Kilian, and D. Mather
Background
Map Construction
Quantitative Trait Locus (QTL) Analysis
Dissection of the Components of Winterhardiness
QTLs as a Tool for Exotic Germplasm Introgression
QTL Effects in Elite Germplasm
Summary of QTL Effects in Several Reference Populations
References
RAPD Analysis of Plant Genomes, G. Penner
Introduction
Techniques
Reproducibility
Mendelian Segregation
Statistical Considerations
Applications
Summary
References
CYTOPLASMIC GENOME ANALYSIS: PHYLOGENETIC INFERENCES
Plasmon Analysis as the Counterpart of Genome Analysis, K. Tsunewaki
Introduction
Plasmon Analysis
Plastome and Chondriome Analysis
Discussion and Conclusion
References
Chloroplast DNA Analysis of the Monogenomic Triticeae: Phylogenetic Implications and Genome-Specific Markers, R.J. Mason-Gamer and E.A. Kellogg
Introduction
Materials and Methods
Results
Discussion
References
SPECIALIZED TECHNIQUES OF GENOME ANALYSIS
Chromosome Microdissection and Microcloning: Application to Genome Analysis, F-T. Kao
Origin of Chromosome Microdissection and Microcloning
Microdissection and Microcloning Prior to Using PCR
Microdissection and PCR-Assisted Microcloning
Importance of Minimizing DNA Contamination
Evaluation of a Microdissection Library
Variations in Microdissection and Microcloning Techniques
Technical Aspects in Microdissection and Microcloning
Application to Genome Analysis
Application to Plants
Conclusion
References
Numerical Taxonomy and Genome Analysis, B.R. Baum and P.K. Gupta
Introduction
Numerical Taxonomy
Genome Analysis Data for Numerical Analysis
Application of Numerical Taxonomy to Genome Analysis
Conclusion and Perspectives
References
GENOMIC CONSTITUTION OF AN IMPORTANT CROP PLANT AS REVEALED BY DIFFERENT TECHNIQUES
Genomic Constitution of Bread Wheat: Current Status, Y. Yen, P.S. Baenziger, R. Morris,
Introduction
Historical Aspects of Genome Analysis in Wheat
Speciation of Bread Wheat
General Evolutionary Patterns of Wheat Nuclear Genomes
The Nuclear Genomes and Chromosome Organization of Wheat
Molecular-Genetic Organization of Bread Wheat Genomes
Organellar Genomes of Bread Wheat
Introgression of Alien Germplasm into Wheat
Homoeologies Between Bread Wheat and Other Gramineae Species
Future Prospects
References