From Plant Genomics to Plant Biotechnology

With the appearance of methods for the sequencing of genomes and less expensive next generation sequencing methods, we face rapid advancements of the -omics technologies and plant biology studies: reverse and forward genetics, functional genomics, transcriptomics, proteomics, metabolomics, the movement at distance of effectors and structural biology. From plant genomics to plant biotechnology reviews the recent advancements in the post-genomic era, discussing how different varieties respond to abiotic and biotic stresses, understanding the epigenetic control and epigenetic memory, the roles of non-coding RNAs, applicative uses of RNA silencing and RNA interference in plant physiology and in experimental transgenics and plants modified to specific aims. In the forthcoming years these advancements will support the production of plant varieties better suited to resist biotic and abiotic stresses, for food and non-food applications.

This book covers these issues, showing how such technologies are influencing the plant field in sectors such as the selection of plant varieties and plant breeding, selection of optimum agronomic traits, stress-resistant varieties, improvement of plant fitness, improving crop yield, and non-food applications in the knowledge based bio-economy.

• Discusses a broad range of applications: the examples originate from a variety of sectors (including in field studies, breeding, RNA regulation, pharmaceuticals and biotech) and a variety of scientific areas (such as bioinformatics, -omics sciences, epigenetics, and the agro-industry)
• Provides a unique perspective on work normally performed 'behind closed doors'. As such, it presents an opportunity for those within the field to learn from each other, and for those on the 'outside' to see how different groups have approached key problems
• Highlights the criteria used to compare and assess different approaches to solving problems. Shows the thinking process, practical limitations and any other considerations, aiding in the understanding of a deeper approach

Contenu

List of figures

List of tables

Abbreviations

About the contributors

Introduction

Chapter 1: From plant genomics to -omics technologies

Abstract:

1.1 SuperSAGE

1.2 CAGE - cap analysis of gene expression

1.3 -Omics and new advances in plant functional genomics

Chapter 2: Plant microRNAs

Abstract:

2.1 Introduction

2.2 Transcription of miRNA genes

2.3 MicroRNA processing

2.4 Modes of action

2.5 Evolution of miRNA genes

2.6 Differences from animal miRNAs

2.7 miRNA functions

2.8 The potential roles of microRNAs in crop improvement

Chapter 3: Epigenetic control by plant Polycomb proteins: new perspectives and emerging roles in stress response

Abstract:

3.1 Introduction

3.2 Conserved multi-protein complexes with histone post-translational modifying activities

3.3 Polycomb functions in plant development

3.4 Non-coding RNAs as regulatory cofactors of Polycomb complexes

3.5 Emerging roles of PcG and ncRNAs in responses to environmental stress

3.6 PcG protein functions in three-dimensional nuclear organization

3.7 Perspectives: the role of Polycomb in abiotic and biotic stress response

Chapter 4: Metabolite profiling for plant research

Abstract:

4.1 Introduction

4.2 Methodological approach

4.3 Metabolomic platform

4.4 Metabolomics in plant science

4.5 The future role of metabolomics in crop improvement

4.6 Conclusion

Chapter 5: The uniqueness of conifers

Abstract:

5.1 Introduction

5.2 Functional differentiation

5.3 Genome structure and composition

5.4 Genome function

5.5 Chemical divergence

5.6 Meeting the challenge: the system biology approach to unraveling the conifer genome

Chapter 6: Cryptochrome genes modulate global transcriptome of tomato

Abstract:

6.1 Introduction

6.2 Cryptochrome functions

6.3 Role of cryptochromes in mediating light-regulated gene expression in plants

6.4 Cryptochromes influence the diurnal global transcription profiles in tomato

Chapter 7: Genomics of grapevine: from genomics research on model plants to crops and from science to grapevine breeding

Abstract:

7.1 Use of genetic and molecular markers for studies of genetic diversity and genome selection in grapevine

7.2 Grapevine breeding

7.3 Transgene silencing

7.4 Identification and characterization of transgene insertion loci

7.5 Integration of vector backbone

7.6 Stability of inserted transgenes

7.7 Conclusions

7.8 Acknowledgement

Chapter 8: Grapevine genomics and phenotypic diversity of bud sports, varieties and wild relatives

Abstract:

8.1 Introduction

8.2 Origin of Vitis vinifera, domestication, and early selection for fruit characters

8.3 Sources of phenotypic variation in present-day grapevines

8.4 Genomic tools in the genome sequencing era

8.5 Current activities in grapevine genome analysis

8.6 Bud organogenesis, somatic mutations, and DNA typing of somatic chimeras

8.7 Phenotypically divergent clones and the underlying DNA variation

8.8 Transposon insertion-site profiling using NGS

8.9 Large structural variation using NGS

8.10 Copy number variation, gene redundancy, and subtle specialisation in secondary metabolism

8.11 Conclusions

Chapter 9: Peach ripening transcriptomics unveils new and unexpected targets for the improvement of drupe quality

Abstract:

9.1 Introduction

9.2 The fruit

9.3 Peach development and ripening

9.4 Microarray Transcript Profiling in peach

9.5 New players in the control of peach ripening

9.6 Conclusions

9.7 Acknowledgements

Chapter 10: Application of doubled haploid technology in breeding of Brassica napus

Abstract:

10.1 Introduction

10.2 Technique of isolated microspore culture

10.3 Doubled haploid method in breeding of Brassica napus

10.4 In vitro mutagenesis

10.5 Utilization of double haploidy in selection for resistance

10.6 Selection for modified seed oil composition

10.7 Selection for improved seed meal

10.8 Selection for cold tolerance

10.9 Concluding remarks

Chapter 11: Plant biodiversity and biotechnology

Abstract:

11.1 Biodiversity

11.2 Biotechnology

11.3 Heat stress tolerance in cereals

11.4 Modern approaches in cereals for yield and food security under temperature stress

11.5 Future perspectives

11.6 Acknowledgment

Chapter 12: Natural resveratrol bioproduction

Abstract:

12.1 Stilbenes and resveratrol

12.2 Health benefits of resveratrol

12.3 trans-resveratrol production through plant cell cultures

12.4 Introducing new pathway branches to crop plants: trans-resveratrol synthesis in tomato fruits

12.5 Concluding remarks

Index