Principles and practices of plant genomics. Volume 1, Genome mapping / editors, Chittaranjan Kole, Albert G. Abbott.

Format:

Book

Contributor:

Abbott, Albert G.

Kole, Chittaranjan.

Language:

English

Subjects (All):

Plant genetics.

Plant genomes.

Physical Description:

xxvi, 393 p. : ill. (some col.)

Edition:

1st ed.

Place of Publication:

Enfield, NH : Science Publishers, c2008.

Language Note:

English

Summary:

Genome of an organism is depicted by genetic linkage mapping and physical mapping. Genome mapping stated with genetic linkage mapping and contributed enormously in genome analysis and its improvement. Physical mapping emerged later and is the prelude to structural and functional genomics. Volume One of Principles and Practices of Plant Genomics introduces the historical background of genome mapping, and delineates modern methods in the field. This volume briefly introduces the historical background and overview on genome mapping. Chapters deliberating on different types of molecular markers, their detection, relative merits, shortcomings and applications; types of mapping populations, methods of their generation, applications; basic concepts and schematic depiction of construction of genetic linkage maps; concepts and strategies of mapping genes controlling qualitative and quantitative traits on framework genetic linkage maps; rationale, methodologies and implications of comparative mapping; principles, strategies, and outcome of map-based cloning; overviews on the recent advances on plant genomics and genome initiatives; and finally computer strategies and software.

Contents:

Intro

The Prologue

Foreword

Preface to the Series

Preface to the Volume

Contents

List of Contributors

List of Abbreviations

1. Fundamentals of Plant Genome Mapping

1. THE GENOME CONCEPTS

1.1 Types of Genomes

1.2 Nuclear DNA Content in Plant Genomes

1.3 Genome or Chromosome Mapping

Genetic Map

Physical Map

2. GENETIC MAPPING AND MARKERS IN THE ERA OF CLASSICAL GENETICS

3. GENETIC MAPPING AND MARKERS IN THE ERA OF MOLECULAR GENETICS

3.1 Isoenzyme Markers

3.2 Historical Background of DNA Markers

3.3 The DNA Markers

3.4 Molecular Genetic Mapping: New Concepts, Tools and Strategies

3.5 Mapping Populations and Genetic Stocks

3.6 Computer Programs for Molecular Mapping

4. APPLICATIONS OF GENETIC MAPPING

4.1 Marker-Assisted Crop Improvement

4.2 Map-Based Cloning of Genes and QTLs

4.3 Elucidation of Phylogenetic Relationships and Evolutionary Pathways

4.4 Construction of Third Generation Chromosome Maps

4.5 Role of Genetic Mapping in Genomics Arena

5. CONTRIBUTORY DISCIPLINES AND BENEFICIARIES

6. CONCERNS AND CAUTIONS

6.1 Selection of Crop

6.2 Selection of Traits

6.3 Selection of Base Materials

6.4 Converging Approach

References

2. Molecular Markers-History, Features and Applications

1. INTRODUCTION

1.1 Genetic Markers

1.2 Molecular Markers

2. THE MAJOR CATEGORIES OF MOLECULAR MARKERS

Restriction Fragment Length Polymorphism (RFLP)

Dot Blot Assay

PCR-based Markers

Random Amplified Polymorphic DNA (RAPD)

Amplified Fragment Length Polymorphism (AFLP)

Sequence Characterized Amplified Region (SCAR)

Simple Sequence Repeat (SSR)

Expressed Sequence Tag-derived SSR (EST-SSR)

Inter-Simple Sequence Repeat (ISSR)

Cleaved Amplified Polymorphic Sequence (CAPS)

Sequence-Specific Amplified Polymorphism (S-SAP).

Inter-Retrotransposon Amplified Polymorphism (IRAP)

Retrotransposon-Microsatellite Amplified Polymorphism (REMAP)

Retrotransposon-Based Insertional Polymorphism (RBIP)

Sequence Related Amplification Polymorphism (SRAP)

Target Region Amplification Polymorphism (TRAP)

Single Nucleotide Polymorphism (SNP)

3. FEATURES OF MOLECULAR MARKERS

4. FUTURE PERSPECTIVES

3. Mapping Populations: Development, Descriptions and Deployment

2. MAPPING POPULATIONS

3. SELECTION OF PARENTS

4. POPULATIONS DERIVED FROM HOMOZYGOUS PARENTS

4.1 F2, Population

Advantages

Disadvantages

4.2 F2-derived F3 (F2:3) Population

4.3 Backcross (BC) Population

4.4 Doubled Haploid Lines (DHL)

Aduantages

4.5 Recombinant Inbred Lines (RIL)

4.6 Near-lsogenic Lines (NIL)

5. CONSIDERATIONS FOR QTL MAPPING FROM HETEROZYGOUS PARENTS

5.1 Genetic Load, Heterozygosity and Mating Type

6. ESTIMATION OF ADDITIVITY AND DOMINANCE

7. MAPPING ACCURACY

7.1 Segregation Distortion in Linkage Mapping

8. COMBINING MARKERS AND POPULATIONS

Conclusions

4. Construction of Genetic Linkage Maps

Overview

2. FROM MARKERS TO LINKAGE MAPPING

2.1 Basic Concepts

2.2 Two- and Three-point Analysis

2.3 Genetic Distance and Mapping Functions

2.4 Estimating Genetic Distance from Experimental Data

2.5 Formation of Linkage Groups

2.6 Ordering of Markers within a Linkage Group

2.7 Special Considerations

3. MAPPING OUTBREEDING SPECIES

4. MAPPING WITH A REDUCED POPULATION SIZE

4.1 The Deterministic Approach

Greedy Algorithm

4.2 The Stochastic Approach

Application.

5. HIGH- AND ULTRA HIGH-DENSITY MAPS

5.1 Construction of High-Density Linkage Maps

5.2 Ultra High-Density Maps (UHD-maps)

Construction of UHD maps

6. LINKAGE MAPS IN POLYPLOIDS

7. CONCLUDING REMARKS

5. Mapping and Tagging of Genes Controlling Simple-inherited Traits

1.1 Simple-Inherited Traits

1.2 The Early History of Genetic Maps

1.3 The Evolution of Genetic Maps

1.4 Integrated Cytogenetic Maps

1.5 Generating Cytogenetic Maps

2. IDENTIFICATION OF MARKERS LINKED TO TRAITS OF INTEREST

2.1 Use of NILs to Identify Linkage with Molecular Markers

2.2 Use of Bulked Segregant Analysis (BSA) to Identify Linkage with Molecular Markers

2.3 Targeting Disease Resistance Genes by NBS Profiling

3. CONVERSION OF DOMINANT TO CO-DOMINANT MARKERS

4. USE OF GENOMICS TOOLS FOR MAPPING

5. STATISTICAL CONSIDERATIONS

6. APPLICATION OF GENETIC MAPPING

6. Genetic Mapping of Quantitative Trait Loci

2. NATURE OF QUANTITATIVE VARIATION

3. MAPPING POPULATIONS

3.1 Controlled Crosses

3.2 Structured Pedigrees

3.3 Natural Populations

3.4 Joint linkage and linkage disequilibrium mapping

4. STATISTICAL MODELS, METHODS AND ALGORITHMS

4.1 Models

4.2 The QTL. Model

4.3 The Marker Model

4.4 Marker-conditional QTL. Model

4.5 Methods and Algorithms

4.5.1 Marker Analysis

4.5.1.1 Testing

4.5.1.2 Linkage analysis

4.5.2 Interval Mapping

4.5.2.1 Mixture model

4.5.2.2 Conditional probabilities

4.5.2.3 Likelihood and algorithm

4.5.2.4 Hypothesis testing

4.5.2.5 Example

4.5.3 Composite and Multiple Interval Mapping

5. CONCLUDING REMARKS

Acknowledgements

7. Comparative Mapping

2. METHODOLOGY AND HISTORY

3. APPLICATIONS OF COMPARATIVE MAPPING.

3.1 Development of Linkage Maps

3.2 Predicting Gene Location and Function

3.3 Gene Cloning

3.4 Analysis of Genome Evolution

4. COMPARATIVE MAPPING IN GRASSES (POACEAE)

5. THE SOLANACEAE

6. THE BRASSICACEAE

7. THE FABACEAE

8. COMPARATIVE MAPPING BEYOND FAMILIES

8. Map-based Cloning of Genes and Quantitative Trait Loci

2. DETAILED PROCEDURE OF W-BASED CLONING

2.1 Genetic Mapping or Tagging of the Targeted Genes or QTLs with DNA Markers

2.1.1 Genome-wide Interval Mapping

Bulked Segregant Analysis (BSA)

Near-Isogenic Line (NIL) Analysis

2.2 Physical Mapping of the Targeted Region

2.3 High-Resolution or Fine-Mapping of Targeted Gene Locus

2.4 Chromosome Walking or Landing

2.5 Gene Identification

BLAST Search

Comparative Sequence Analysis

Gene Expression Analysis

Genomic DNA Transformation

cDNA Transformation

RNA Interference (RNAi)

3. EXAMPLES OF MAP-BASED CLONING IN PLANTS

3.1 Map-based Cloning of Genes Controlling Mendelian Traits

3.2 Map-based Cloning of QTLs

4. NOTES OF MAP-BASED CLONING

4.1 Phenotyping Accuracy

4.2 Variation of Genetic Recombination Rate along a Chromosome

4.3 Use of Plant-Transformation-Competent BIBAC and TAC Libraries

4.4 Chromosome Walking versus Whole-Genome Physical Mapping and Sequencing

4.5 Targeted Gene Source Genotypes and Source Libraries

9. Bioinformatics: Fundamentals and Applications in Plant Genetics, Mapping and Breeding

1. WHAT IS BIOINFORMATICS?

2. UNDERSTANDING THE GENOME

3. GENE AND GENOME SEQUENCE DATABASES

4. GENE EXPRESSION INFORMATION

5. GENE EXPRESSION DATABASES

6. THE PROTEOME AND METABOLOME

7. THE PHENOME

8. FROM GENETICS AND GENOMICS TO PHENOMICS

9. MOLECULAR GENETIC MARKERS: SSRs AND SNPs.

10. MOLECULAR MARKER DATABASES

11. MOLECULAR MARKER APPLICATIONS

12. POPULATION GENETIC SOFTWARE PACKAGES

13. GENETIC DIVERSITY

14. HARDY-WEINBERG EQUILIBRIUM (HWE)

15. LINKAGE DISEQUILIBRIUM

16. POPULATION SUBDIVISION

17. PHYLOGENETIC ANALYSIS

17.1 Phylogenetic Analysis Software Packages

18. APPLICATION OF GENOTYPIC DATA TO GENETIC MAPPING ANALYSIS

19. QTL ANALYSIS

20. GENETIC MAPPING AND QTL SOFTWARE PACKAGES

21. INTEGRATED BIOINFORMATICS FOR CROP BREEDING

10. An Overview on Plant Genome Initiatives

1.1 What is a Plant Genome Initiative?

1.2 Plant Nuclear DNA Content

1.3 Molecular Maps

1.4 Molecular Markers

2. GENOME SEQUENCING INITIATIVES

3. EXAMPLES OF GENOME INITIATIVES

3.1 The Maize Sequencing Project

3.2 Wheat Genome Initiative

4. NON-GENOME SEQUENCING ACTIVITIES

4.1 The Identification of Genes

4.2 The Identification of Gene Function

5. FUTURE EXTENDED SEQUENCING OF PLANT GENOMES

6. CONCLUDING REMARKS

11. Computing Strategies and Software for Gene Mapping

2. QTL ANALYSIS WITH INBRED LINES

2.1 Single QTL Mapping

2.1.1 Missing Genotypes

2.1.2 Detection of QTL

2.1.3 Model Selection for Multiple QTL

2.1.4 Multiple QTL Estimation Approaches

2.1.5 Detailed Analysis of Multiple QTL Simulated Cross

2.1.6 Covariates and Gene-Environment Interactions

2.1.7 Overview of Available Packages

2.1.8 QTL Analysis with Outbred Lines

3. ASSOCIATION ANALYSIS

3.1 Association Analysis Examples

Index.

Notes:

Bibliographic Level Mode of Issuance: Monograph

Includes bibliographical references and index.

ISBN:

1-04-027730-6

1-003-57929-9

1-281-94848-9

9786611948481

1-57808-620-5

9781003579298

OCLC:

646770490