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Genomics, Transcriptomics, Proteomics and Metabolomics of Crop Plants

1st Edition - July 11, 2023

Editors: Azamal Husen, Altaf Ahmad

Paperback ISBN:

9 7 8 - 0 - 3 2 3 - 9 5 9 8 9 - 6

eBook ISBN:

9 7 8 - 0 - 3 2 3 - 9 5 9 9 0 - 2

Genomics, Transcriptomics, Proteomics and Metabolomics of Crop Plants presents current operational methods applied to model crop plants. Including subcellular organelles, DNA… Read more

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Genomics, Transcriptomics, Proteomics and Metabolomics of Crop Plants presents current operational methods applied to model crop plants. Including subcellular organelles, DNA fingerprinting and barcoding, sRNA, gene expression, rhizosphere engineering, marker assisted and 5G breeding, plant-microorganism interactions, stress signaling and responses, the book highlights important factors that are often overlooked and explores the latest research. The book also explores cutting-edge approaches for immediate application in new research such as OMICS, genome-wide transcriptome profiling, bioinformatics and database, DNA fingerprinting and barcoding, sRNA, gene expression, genome editing, diagnostics, rhizosphere engineering, marker assisted and 5G breeding, crop plant-microorganism interactions, stress signaling and responses.

Additionally, the book describes opportunities to manipulate crop plants genetic and metabolic systems, while also exploring the related bioethical and biosafety issues. These topics are chosen and covered in detail to fill the gap in this understanding of crop molecular biology.

Cover image
Title page
Table of Contents
Copyright
List of contributors
About the editors
Preface
Chapter 1. Genome to phenome: bioinformatics of crop plants
Abstract
Chapter outline
1.1 Introduction
1.2 De novo genome assembly approach
1.3 Genome annotation
1.4 Phenotypes
1.5 Data analysis
1.6 Conclusions
References
Further reading
Chapter 2. Emerging approach of transcriptomics for crop plants improvements
Abstract
Chapter outline
2.1 Introduction
2.2 Transcriptomic approaches applied in plants
2.3 Conclusion
References
Chapter 3. Proteomics as a tool for analyzing plant responses to abiotic and biotic stresses
Abstract
Chapter outline
3.1 Introduction
3.2 Proteomics’ significance for agricultural systems
3.3 Various proteomics approaches used in plant studies
3.4 Proteomics for crop improvement
3.5 Concerns of proteomics in plants for the next decade
3.6 Conclusions and prospects
References
Further reading
Chapter 4. Metabolic engineering of plant primary–secondary metabolism interface
Abstract
Chapter outline
4.1 Introduction
4.2 Metabolic engineering
4.3 Primary and secondary metabolites
4.4 Plant metabolic engineering
4.5 Plant primary–secondary metabolism interface
4.6 Conclusion
References
Chapter 5. Current understanding of genomics, transcriptomics, proteomics, and metabolomics of crop plants under low nutrient stress
Abstract
Chapter outline
5.1 Introduction
5.2 Omics approaches for investigating nutrient response of crop plants
5.3 Nitrogen (N) and its response to plants at omics levels
5.4 Phosphorus (P) and its response to plants at omics levels
5.5 Potassium (K) and its response to plants at omics levels
5.6 Sulfur (S) and its response to plants at omics levels
5.7 Calcium and its response to plants at omics levels
5.8 Magnesium (Mg) and its response to plants at omics levels
5.9 Boron (B) and its response to plants at omics levels
5.10 Manganese (Mn) and its response to plants at omics levels
5.11 Iron (Fe) and its response to plants at omics levels
5.12 Copper (Cu) and its response to plants at omics levels
5.13 Other micronutrients and their responses to plants at omics levels
5.14 Conclusion
References
Further reading
Chapter 6. Perspectives of omics and plant microbiome
Abstract
Chapter outline
6.1 Introduction
6.2 Plant–microbe dynamics and their multiomics studies
6.3 Industrial view of plant–microbial bioactive compounds extraction
6.4 Conclusion and future perspectives
References
Chapter 7. Genome-wide transcriptome profiling of crop plants
Abstract
Chapter outline
7.1 Introduction
7.2 Plant stress-responsive mechanisms
7.3 Transcriptomics
7.4 Genome-wide transcriptome profiling of some crop plants
7.5 Gene ontology and KEGG enrichment analysis of DEGs
7.6 Challenges and prospects in transcriptomics
7.7 Conclusion
References
Chapter 8. Role of noncoding RNA in regulation of biological processes of crop plants
Abstract
Chapter outline
8.1 Introduction
8.2 Classification and function of different types of noncoding RNAs
8.3 Biogenesis of siRNAs
8.4 Function of siRNA in plants
8.5 Housekeeping ncRNAs
8.6 Conclusion
References
Chapter 9. DNA barcoding of crop plants
Abstract
Chapter outline
9.1 Introduction
9.2 Plant species and the barcode
9.3 DNA sequences and barcode
9.4 Herbing of plant species
Acknowledgments
Conflict of interest
Abbreviations
References
Chapter 10. DNA fingerprinting of crop plants
Abstract
Chapter outline
10.1 Introduction
10.2 DNA markers
10.3 Conclusion
References
Chapter 11. Marker assisted selection and breeding of crop plants
Abstract
Chapter outline
11.1 Introduction
11.2 Variations of MAS
11.3 Application of MAS in plant breeding
11.4 Selection of molecular markers
11.5 Conclusion
References
Chapter 12. An overview of gene regulations in crop plants
Abstract
Chapter outline
12.1 Introduction
12.2 Gene and genome
12.3 Are genes steady?
12.4 Regulation of gene expression in plants
12.5 Gene regulation in crop plants under stress conditions
12.6 Tools for analyzing gene expression
References
Chapter 13. Current understanding of proteomics in plants under drought stress conditions
Abstract
Chapter outline
13.1 Introduction
13.2 Approaches to improve the crop production
13.3 Drought stress and crop production
13.4 Proteomics of drought tolerance
13.5 Conclusion
References
Chapter 14. Current understanding of genomics, transcriptomics, proteomics, and metabolomics of crop plants under salt stress
Abstract
Chapter outline
14.1 Introduction
14.2 Response of crop plants to salt stress at genome levels
14.3 Response of crop plants to salt stress at transcriptome levels
14.4 Response of crop plants to salt stress at proteome levels
14.5 Response of crop plants to salt stress at metabolome levels
References
Chapter 15. Current understanding of genomics, transcriptomics, proteomics, and metabolomics of plants upon heavy metal stress
Abstract
Chapter outline
15.1 Introduction
15.2 Genomics
15.3 Transcriptomics
15.4 Proteomics
15.5 Peptides
15.6 Metabolomics
15.7 Phenols
15.8 Heavy metal ATPases
15.9 Amino acids
15.10 (ZIP) transporters ZRT, IRT-like proteins
References
Chapter 16. Safety and ethics associated with genomics, transcriptomics, proteomics, and metabolomics of crop plants
Abstract
Chapter outline
16.1 Introduction
16.2 Background and history
16.3 Use of molecular biogenomics
16.4 Issues in genetic engineering
16.5 Research and development concerning genetic engineering
16.6 Legal concern and update
16.7 Ethical concerns and genetically modified plants
16.8 Conclusion
16.9 Suggestion and a way forward
References
Chapter 17. Food safety and biotechnological products
Abstract
Chapter outline
17.1 Introduction
17.2 History, development, and current status of food safety systems
17.3 Role of biotechnology in the food production and processing
17.4 Role of governments in regulating and enforcing food safety
17.5 Strategies and programs to ensure the safety of the food supply
17.6 Safety of food produced with biotechnology processes
17.7 Benefits and risks of biotechnology in food production
17.8 Future of biotechnology in the food industry
17.9 Concluding remarks and perspectives
References
Index

Azamal Husen

Azamal Husen is a and was previously a Visiting Faculty of the Forest Research Institute, and the Doon College of Agriculture and Forest at Dehra Dun, India. Husen’s research and teaching experience of 20 years encompasses the biogenic nanomaterial fabrication and application, plant responses to nanomaterials, plant adaptation to harsh environments at the physiological, biochemical, and molecular levels, herbal medicine, and clonal propagation for improvement of tree species. He has conducted research sponsored by the World Bank, the National Agricultural Technology Project, the Indian Council of Agriculture Research, the Indian Council of Forest Research Education, and the Japan Bank for International Cooperation. Husen has published extensively and served on the Editorial Board and as reviewer of reputed journals. He is Series Co-Editor of ‘Plant Biology, Sustainability and Climate Change’, Elsevier, USA and is Editor-in-Chief of the American Journal of Plant Physiology.

Affiliations and expertise

Foreign Delegate at Wolaita Sodo University, Wolaita, Ethiopia

Altaf Ahmad

Professor Altaf Ahmad is working in Plant Biotechnology in the Department of Botany, Aligarh Muslim University, Aligarh, India. Dr. Ahmad has 22 years of research experience and has more than 150 publications. Dr. Ahmad handled several research projects funded by various agencies like BBSRS-UK, DST, DBT, CSIR, UGC, CCRUM, ICAR, and INSA. He was a Visiting Scientist at the Virginia Polytechnic and State University, USA University of Freiburg, University of Aberdeen, and the University of Cologne. Based on his research contribution, Dr. Ahmad has been honored with the INSA Medal for Young Scientist (2003) and Professor LSS Kumar Memorial Award (2003) of Indian National Science Academy, Young Scientist Award (2005) of Council of Science & Technology, Govt. of Uttar Pradesh, and elected as Associate of National Academy of Agricultural Sciences

Affiliations and expertise

Department of Botany Nanobiotechnology/Proteomics Aligarh Muslim University, Aligarh, India