Methods of Genome Analysis in Plants: Current Topics in Plant Molecular Biology

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.

Table of Contents:
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