Omics in Horticultural Crops

1st Edition - July 16, 2022
Editors: Gyana Ranjan Rout, K.V. Peter
Language: English
Paperback ISBN:
9 7 8 - 0 - 3 2 3 - 8 9 9 0 5 - 5
eBook ISBN:
9 7 8 - 0 - 3 2 3 - 8 9 9 1 3 - 0

Omics in Horticulture Crops presents a comprehensive view of germplasm diversity, genetic evolution, genomics, proteomics and transcriptomics of fruit crops (temperate, tropic… Read more

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Omics in Horticulture Crops presents a comprehensive view of germplasm diversity, genetic evolution, genomics, proteomics and transcriptomics of fruit crops (temperate, tropical and subtropical fruits, fruit nuts, berries), vegetables, tuberous crops, ornamental and floricultural crops and medicinal aromatic plants. Information covering phenomics, genetic diversity, phylogenetic studies, genome sequencing, and genome barcoding through the utilization of molecular markers plays an imperative role in the characterization and effective utilization of diverse germplasm are included in the book. This is a valuable reference for researchers and academics seeking to improve cultivar productivity through enhanced genetic diversity while also retaining optimal traits and protecting the growing environment.

Cover image
Title page
Table of Contents
Copyright
Contributors
Foreword
Preface
Chapter 1: State of the art of omics technologies in horticultural crops
Abstract
1: Introduction
2: Preliminary remarks
3: Genomics
4: Transcriptomics
5: Applications of combined genomic and transcriptomic data
References
Chapter 2: Small RNA-omics: Decoding the regulatory networks associated with horticultural traits
Abstract
1: Introduction
2: Classification and biogenesis of small RNAs
3: Identification and validation of small RNAs
4: Small RNA target prediction and validation
5: Development of sRNA research in horticultural crops
6: Conclusion and future perspectives
References
Chapter 3: Multiomics bioinformatics approaches in horticultural crops
Abstract
1: Introduction
2: Biological databases: A global perspective
3: Next-generation sequencing (NGS) data analysis and its applications in agriculture
4: De novo genome assembly
5: Genome annotation and gene prediction
6: Impact of NGS in agriculture
7: Molecular evolutionary analysis
8: Protein structure prediction
9: Subtractive genomics and molecular docking
10: Primer designing
11: Promoter prediction
12: Restriction enzyme analysis
13: High-performance computing in agricultural/horticultural research
References
Chapter 4: Application of omics in arid fruit crops: Present status, challenges, and future perspectives
Abstract
1: Introduction
2: Genomics and its application in arid fruit crops
3: Transcriptomics in arid fruit crops
4: Proteomics in arid horticultural crops
5: Metabolomics in arid horticultural crops
6: Future thrust
7: Conclusions
References
Further reading
Chapter 5: Omics technologies and breeding of horticultural crops
Abstract
1: Introduction
2: Breeding methodologies
3: Plantomics techniques
4: Improvement of horticulture crops using omics approaches
5: Exploitation of omics approaches in breeding functional traits
6: Breeding through genome editing in horticultural crops
7: Conclusions and future prospects
References
Chapter 6: Cryobiomics in tropical and subtropical horticultural crops
Abstract
1: Introduction
2: Importance and general principles of cryopreservation
3: Tropical and subtropical ornamental and fruit plants
4: Cryopreservation of endangered ornamental plants
5: Cryopreservation of endangered fruit plants
6: Thawing and recovery
7: Cryopreservation and omics technologies
8: Conclusions and future perspectives
References
Further reading
Chapter 7: Application of ’omics technologies in tropical and subtropical fruit crops
Abstract
1: Introduction
2: Transcriptome studies in other tropical and subtropical fruit crops
3: Metabolomics for quality traits in fruits
4: Conclusions
References
Further reading
Chapter 8: Understanding grape berry development and response to environmental factors through omics approaches
Abstract
1: Introduction
2: Biochemical changes during grape berry development
3: Genomics of grape berry development
4: Transcriptomics of grape berry development
5: Role of GA3 response
6: Effect of stress conditions
7: Metabolomics and proteomics of grape berry development
8: Abiotic stress response
9: Conclusion and future perspectives
References
Chapter 9: Application of “omics” in banana improvement
Abstract
1: Introduction
2: Genomics
3: Transcriptomics
4: Proteomics
5: Metabolomics
6: Phenomics
7: Epigenomics
8: Cytogenomics
9: Pathogenomics
10: Metagenomics
11: Role of molecular markers on genetic diversity
12: Bioinformatic tools
13: Pan genomics
14: Integrated omics
15: Conclusion
References
Chapter 10: Recent advances in pomegranate genomics: Status and prospects
Abstract
1: Introduction
2: Economic significance and production constraints
3: Genomic resources in pomegranate
4: Trait mapping through linkage analysis and association mapping
5: Future prospects for trait breeding in pomegranate
6: Conclusion
References
Chapter 11: Role of “Omics” approaches in sustainable development and improvement of oil palm (Elaeis guineensis Jacq)
Abstract
1: Introduction
2: Genomics
3: Metabolomics
4: Role of proteomics in oil palm physiological processes
5: Transcriptomics
6: Phenomics
7: Conclusion and future perspectives
References
Further reading
Chapter 12: Omics studies for vegetable improvement
Abstract
Acknowledgment
1: Introduction
2: Genomics applications in vegetable plants
3: Pan-genome in vegetables
4: Transcriptomics
5: Proteomics applications
6: Metabolomics
7: Phenomics
8: Conclusion and future perspectives
References
Chapter 13: Omics in vegetable crops: Cucurbitaceae and Amaryllidaceae
Abstract
1: Introduction
2: Cucurbitaceous vegetables
3: Amaryllidaceous vegetables
4: Conclusion
References
Chapter 14: Omics in leafy vegetables: Genomics, transcriptomics, proteomics, metabolomics, and multiomics approaches
Abstract
1: Introduction
2: Phenomics approaches in leafy vegetables
3: Genomics approaches in leafy vegetables
4: Transcriptomics approaches in leafy vegetables
5: Proteomics approaches in green vegetables
6: Metabolomics approaches in leafy vegetables
7: Multiomics approaches in leafy vegetables
8: Future perspectives
9: Conclusions and future perspectives
References
Chapter 15: Omics in vegetable crops under the family Solanaceae
Abstract
1: Introduction
2: Traits for crop improvement
3: Mapping of traits associated with biotic stress tolerances
4: Mapping of traits associated with abiotic stress tolerances
5: Transcriptome analysis for biotic stress tolerances
6: Transcriptome analysis of abiotic stress tolerances
7: Proteome
8: Metabolome
9: Conclusions
References
Further reading
Chapter 16: Omics-driven advances in plantation crops and cashew: A perspective and way forward
Abstract
1: Introduction
2: Application of molecular tools in plantation crops
3: Transcriptomics
4: Proteomics
5: Metabolomics
6: Way forward
References
Chapter 17: Omics advances in tea research
Abstract
1: Introduction
2: Various omics approaches in tea
3: Conclusion
References
Chapter 18: Applications of omics technologies in Coffea
Abstract
1: Introduction
2: Genome structure and organization
3: Genomics in coffee
4: Coffee QTL omics
5: Transcriptomics
6: Proteomics
7: Metabolomics
8: Conclusion
References
Chapter 19: Omics of mango: A tropical fruit tree
Abstract
Acknowledgments
1: Introduction
2: Genomic studies in mango
3: Transcriptomics
4: Metabolomics
5: Proteomics
6: Conclusion and future prospect
References
Chapter 20: Omics in sugarcane
Abstract
1: Introduction
2: Sugarcane genomics
3: Marker-assisted breeding in sugarcane
4: Sugarcane transcriptomics, impacts, and genetic gains regarding sugarcane genome complexity
5: Sugarcane proteomics and metabolomics
6: A new approach based on complex networks and systems biology in sugarcane
7: Conclusion and future prospect
References
Chapter 21: Omics research for crop improvement in spices
Abstract
1: Introduction
2: Genomics research in spices
3: Transcriptomics research for crop improvement in spices
4: Proteomics research for crop improvement in spices
5: Metabolomics research for crop improvement in spices
6: Conclusion and future perspectives
References
Chapter 22: Application of omics technologies in Rubber, Cocoa, and Betel nut
Abstract
1: Omics based research in Hevea brasiliensis
2: Omics-based research in cocoa
3: Omics-based research in Arecanut
4: Conclusion
References
Further reading
Chapter 23: Omics in tuber crops: Cassava and sweet potato
Abstract
1: Introduction
2: Next-generation sequencing
3: Databases (DB)
4: Transcriptomics
5: Molecular markers and variant analysis
6: QTL analysis and genome-wide association maping (GWAS)
7: Small and long noncoding RNAs (miRNAs and lncRNAs)
8: Interaction networks
9: Metabolomics
10: Data integration
11: Conclusion and future prospects
References
Chapter 24: Omics in commercial flowers: Applications and prospects
Abstract
1: Introduction
2: Advantage of omics technology
3: Omic research in major floricultural crops
4: Multiomic integration facilitates the understanding of biological systems
5: Future prospects
References
Further reading
Chapter 25: Omics in medicinal plants
Abstract
1: Introduction
2: Ancient importance of medicinal plants
3: Genomic approaches in medicinal plants
4: Secondary metabolic pathway and genomics
5: Transcriptomics in medicinal plants
6: Proteomic studies in medicinal plants
7: Metabolomics in medicinal plants
8: Lipidomics in medicinal plants
9: Conclusions and future challenges
References
Further reading
Chapter 26: Omics in saffron (Crocus sativus L.): A spice of immense medicinal value
Abstract
1: Introduction
2: Saffron omics
3: Saffron genomics
4: Saffron transcriptomics
5: Saffron miRNomics
6: Saffron metabolomics
7: Saffron proteomics
8: Conclusion
Authors' contribution
References
Chapter 27: Multiomics approach in medicinal plants
Abstract
1: Introduction
2: Medicinal plants and their importance
3: Omics data layers for medicinal plant research in the postgenomic era
4: Integration of omics data sets for holistic understanding of systems biology
5: Current challenges and future prospects
6: Conclusion
References
Chapter 28: Omics databases in horticultural crops
Abstract
1: Introduction
2: Application of omics for improvement of horticultural crop
3: Omics and system biology
4: Omics database for vegetable crops
5: Omics databases in vegetable crops
6: CarrotDB: A genomic and transcriptomic database for carrot
7: Coriander genomics database
8: Sol genomics network
9: Radish genome database (RadishGD)
10: Omic database for fruit crops
11: Genome database for family Rosaceae
12: Citrus genome database
13: Database for grape
14: Omics database for medicinal plants
15: Database for plantation crops
16: OMIC database for ornamental crops
17: Conclusion and future prospectives
References
Further reading
Chapter 29: Multiomics approaches in walnut
Abstract
1: Introduction
2: Genomics
3: Transcriptomics
4: Proteomics
5: Metabolomics
6: Epigenomics
7: Conclusion and future prospect
References
Index

Gyana Ranjan Rout

Prof. Gyana Ranjan Rout (b. 30 December,1962), Ph.D, D.Sc (Utkal University), Professor & Head, Department of Agricultural Biotechnology & Coordinator P.G teaching programme in Agricultural Biotechnology, Orissa University of Agriculture & Technology, Bhubaneswar, India. He worked as a Post-Doctoral Fellow at the Department of Life Sciences, Cellular and Molecular Biology Research Unit, University of East London, United Kingdom, 1996. He got SERC fellowship and BOYSCAST fellowship in 1997 funded by Ministry of Science & Technology, Govt. of India to work at Chiba University, Japan. He was selected to work at University of Leuven, Belgium under FAO/IAEA/BADA fellowship. He worked at Federal Centre for Ornamental and Plant Breeding, Ahrensburg, Germany in 2004 under the DBT Overseas fellowship funded by Department of Biotechnology, Govt. of India. He has made significant contributions in the field of plant improvement & propagation of various plant species including horticultural crops and genetic diversity analysis. Prof. Rout is elected as a Fellow of National Academy of Sciences, India (FNASc) in the field of Plant Biotechnology and Molecular Biology. He is awarded Samanta Chandra Shekhar award in 2005 honoured by Orissa Bigyan Academy, Govt. of Odisha for contributions to Life Sciences. He is also elected Fellow of National Academy of Agril. Sciences (NAAS) and Fellow of Indian Society of Plant Genetic Resources (FISPGR). Prof. Rout has 27 years research and teaching experience in the field of Plant Biotechnology. He has published 200 research papers and 18 review articles published in National & International peer reviewed journals and 22 book chapters. He has been Principal Investigator of 10 major research projects funded by ICAR, DBT & NMPB. He is routinely reviewing papers for over 12 international journals and 4 National journals and also life members in number of learned society. He has guided 9 Ph.D students and 35 post graduate students in the field of plant sciences.

Affiliations and expertise

Professor, Department of Agricultural Biotechnology, College of Agriculture, Orissa University of Agriculture and Technology, Odisha, India

K.V. Peter

Prof. K.V.Peter (b. 17th May, 1948), Ph. D. in Plant Breeding & Genetics in G.B. Pant University, Pantnagar, Director, World Noni Research Foundation, Perungudi,Chennai, India. He worked as Post Doctoral Fellow in the Vegetable laboratory BARC-W, Beltsvillae MD, USA. Prof. Peter worked assiduously in various aspects of horticultural sciences for over 35 years. He worked as a Professor of Horticulture, Kerala Agricultural University (KAU), India; Director of Research, KAU; Director, Indian Institute of Spices Research, Calicut, India and Vice-Chancellor, Kerala Agricultural University, He has made significant contributions in the field of Horticultural Sciences. He has identified source(s) of resistance to bacterial wilt in tomato, chilli and brinjal and these sources are used globally for resistance breeding programmes. He has handled externally funded projects from ICAR and DBT. He is member of editorial board of international journals of reputes. Prof. Peter is elected as a Fellow of National Academy of Sciences, India (FNASc), Fellow of National Academy of Agricultural Sciences (NAAS), Fellow of Indian Society of Vegetable Sciences, Fellow of National Academy of Biological Sciences and Fellow of Horticulture Society of India. He has published more than 150 research papers in National & International peer reviewed journals and many edited books. He is a recipient of number of National Awards from ICAR. He has guided number of students of for PG & Ph.D degree.

Affiliations and expertise

Director, World Noni Research Foundation, Perungudi, Chennai, India