Genetics and Genomics of Rosaceae

Preface

Contents

Contributors

Introduction

1. Rosaceae: Taxonomy, Economic Importance, Genomics

1 Nomenclature and Taxonomy

2 Economic Importance

3 Rosaceae Genomics

4 The Future

References

2. Genomics Approaches to Crop Improvement in the Rosaceae

1 Use of Genomics in Rosaceae

2 Conclusions

References

3. Genomics Opportunities, New Crops and New Products

1 Introduction

2 Current Use of MAS in Rosaceae Breeding Programs

3 Traits for Which Markers are Currently Available for Use in Developing New Crops

4 Conclusion

References

Part I Apples (Chapters 4 – 7)

4. Introduction to Apple (Malus × domestica)

1 Origin and History

2 Apple Production Worldwide

3 Breeding

4 Genetic Resources

5 Looking Forward

References

5. Apple Structural Genomics

1 Introduction

2 Use of DNA Markers for Evaluating Genetic Diversity in Apple

3 Linkage and PhysicalMaps

4 Genomic Location of Some Monogenic and Polygenic Traits

5 Marker-Assisted Selection

6 Current and Future Developments

References

6. Apple Functional Genomics

1 Malus EST Datasets

2 GC Content and Codon Usage

3 MicroRNAs and Their Targets Identified from EST Databases

4 Global Changes in Apple Gene Expression

5 Heterologous Microarrays

6 Heterologous Expression of Apple Genes in Arabidopsis

7 Transient Assays of Apple Genes in Tobacco

8 Apple Functional Genomics

References

7. Apple Transformation and Translational Genomics

1 Introduction

2 Reverse genetic, Gene Function Validation

3 Conclusions

References

8. Pear Genomics

1 Introduction

2 Structural Genomics

References

9. Genomics of Almond

1 History and Evolution

2 Breeding for Improved Cultivars

3 Development of Molecular Markers and Variability Analysis in Almond

4 Marker Maps: Major Gene and QTL Mapping

5 Gene Cloning and EST Collections

6 Genetic Transformation

7 Main Agronomic Characters, and Their Genetic Basis

8 Future Prospects

References

Part II Peach (Chapters 10 – 13)

10. An Introduction to Peach (Prunus persica)

1 Introduction

2 Traits of Primary Interest for Traditional Breeding Programs

References

11. Peach Structural Genomics

1 Molecular Markers and Breeding in Peach

2 Comparative Genomics in Prunus

3 Mapping Polygenic Traits in Peach

4 Functional Markers in Peach

5 Marker Assisted Selection (MAS) in Peach

6 Peach Physical Mapping

References

12. Functional Genomics in Peach

1 Introduction

2 Proteomics Analysis

3 Functional Genomics Tools in Rosaceae

4 Functional Genomics Candidate Gene Databases

5 The Transcriptome

6 The Peach Integrated Genetic/Physical/EST Functional Genomics Database

7 The Prunus Resistance Gene Map as a Functional Genomics Tool

8 The Peach Proteome

9 Perspectives

References

13. Genetic Engineering of Plum (Prunusdomestica L.) for Plant Improvement andGenomics Research in Rosaceae

1 Introduction

2 The Plum System

3 Future Applications

4 Conclusions

References

14. Sweet and Sour Cherries: Linkage Maps, QTL Detection and Marker Assisted Selection

1 Introduction

2 Construction of Genetic Maps

3 Gene Mapping and QTLs Detected

4 Analysis of Self Incompatibility

5 Conclusion and Future Scope of Work

References

15. Genomics-Based Opportunities in Apricot

1 Introduction

2 Molecular Markers

3 Significant Traits

4 Genomics Resources

5 Regeneration and Transformation

6 Conclusions

References

Part III Rose (Chapters 16 – 19)

16. Introduction to Rosa

1 Major Economic Use/Value of Roses and Limitations to Production

2 Garden Roses (Including Landscape Roses)

3 CutRoses

4 PotRoses

5 Rose Oil Production

6 Ornamental Fruits

7 Culinary and Medicinal Fruits

8 Rootstocks

9 Taxonomy and Classification

10 Available Genetic Resources

11 Major Features of Rose Genetics

12 Cross Breeding

References

17. Rose Structural Genomics

1 DNA Markers Available and Future Developments

2 Use of Markers for Identification and Studies of Rose Population Structure, Taxonomy, Domestication, and Diversity Studies

3 Current Situation for Linkage Maps

4 Inheritance of Known Characters

5 Flower Traits

6 PlantTraits

7 Adaptation Traits

8 Physical Maps, BAC Libraries and Current Situation for Positional Cloning

9 Synteny to Other Rosaceous Crops

References

18. Functional Genomics in Rose

1 Introduction

2 The Tools Available for the Genomic Approaches

3 Ethylene Signaling and Metabolism and Its Involvement in Rose Opening and Senescence

4 Cloning of Genes Involved in Ethylene Signaling and Synthesis

5 Ethylene and Flower Opening

6 Ethylene and Flower Senescence

7 Anthocyanin Biosynthesis in Flower Color

References

19. Genetic Engineering and Tissue Culture of Roses

1 Introduction

2 Regeneration

3 Genetic Transformation

4 Gene Function Studies by Expression in Model Organisms

References

Part IV Strawberry (Chapters 20 – 23)

20. Strawberry Genomics: Botanical History, Cultivation, Traditional Breeding, and New Technologies

1 Origin, Speciation, and Evolution

2 Diploid Species

3 Higher Ploidy Species

4 Cultivated Octoploid Strawberries

5 Intergeneric Hybrid

6 History of Cultivation

7 Traditional Breeding

8 Structural Genomics

9 Functional Genomics

10 Biotechnological Approaches to Genetic Improvement

References

21. Strawberry (Fragaria spp.) StructuralGenomics

1 Cytology and Interfertility

2 Phylogenetic Analyses

3 Molecular Markers

4 Resistance Gene Analogues

5 Linkage and PhysicalMaps-Diploid

6 Whole Genome Sequencing

References

22. Functional Molecular Biology Research in Fragaria

1 Introduction

2 Fruit-Related Traits

3 Volatile Compounds

4 Polyphenol Compounds

5 Fruit Firmness

6 Hormone Metabolism

7 Vitamins

8 Sugar and Acid Composition

9 Allergens

10 Control of Flowering

11 Resistance to Abiotic Stress

12 Resistance to Biotic Agents

References

23. GMO Strawberry: Methods, Risk and Benefits

1 Introduction

2 Strawberry Regeneration and Agrobacterium Transformation

3 Genes for Strawberry Improvement

4 Biotechnology for Berry Nutritional Quality

5 GM Strawberry Field Trials and Risk Assessment

6 Conclusions

References

24. Raspberries and Blackberries:The Genomics of Rubus

1 Taxonomy

2 Diversity

3 Breeding Objectives

4 Limitations

5 Structural Genomics

6 DNA Markers

7 Linkage Mapping

8 Physical Mapping

9 Functional Genomics

10 Future Strategies

References

25. Loquat (Eriobotrya Lindl.)

1 Origin and Botany

2 Genetic Resources and Diversity

3 Genetic Mapping

4 Biotechnology Techniques Applied in Loquat Breeding

References

26. Genomics Tools Across Rosaceae Species

1 Introduction – Toward a Rosaceae Genome as a Unique System?

2 The Genome Structure of Rosaceae

3 Tools for Genomics Analyses in Rosaceae

4 Challenges for the Future

References

27. Application of Genetic Markers in Rosaceous Crops

1 Introduction

2 The Cost/Benefit of Marker Assisted Selection

3 Marker Applications in the Rosaceae

4 Marker Assisted Selection

5 Prunus

6 Fragaria

7 Rubus

8 Background Selection

9 Conclusion and Perspectives

References

28. Rosaceaous Genome Sequencing: Perspectives and Progress

1 Plant Genome Sequencing Overview and History

2 Sequencing Technologies

3 Next Generation Technologies

4 Peach Genome Sequencing

5 Apple Genome Sequencing

6 Fragaria Genome Sequencing

References

Index