Geminivirus: Detection, Diagnosis and Management

1st Edition - May 28, 2022
Editors: R.K. Gaur, Pradeep Sharma, Henryk Czosnek
Language: English
Paperback ISBN:
9 7 8 - 0 - 3 2 3 - 9 0 5 8 7 - 9
eBook ISBN:
9 7 8 - 0 - 3 2 3 - 9 0 7 1 1 - 8

Geminivirus: Detection, Diagnosis and Management focuses on the latest techniques for managing diseases caused by these circular, single-stranded (ss) DNA genomes. The most sign… Read more

Purchase options

LIMITED OFFER

Save 50% on book bundles

Immediately download your ebook while waiting for your print delivery. No promo code is needed.

Institutional subscription on ScienceDirect

Request a sales quote

Geminivirus: Detection, Diagnosis and Management focuses on the latest techniques for managing diseases caused by these circular, single-stranded (ss) DNA genomes. The most significant impact of plant diseases in host populations is often caused by emerging diseases, whose incidence in a plant host is increasing as a result of long-term changes in their underlying epidemiology. Genetic changes in pathogen and host populations, as well as changes in host ecology and environment, are major factors contributing to disease emergence. Understanding plant virus evolution is crucial for modeling the within-host and between-host dynamics and genetics of virus populations.

The book presents a comprehensive review of how these viruses develop, including contributing factors such as population bottlenecks during cell-to-cell movement, systemic colonization, or between-host transmission by different procedures.

Presented in five sections—Detection and Diagnosis, Emergence and Diversity, Vector and Transmission, Virus–Host Interaction, and Disease Management, the book includes host range determinant and virulence factors involved in pathogenesis, virus–vector interactions during acquisition, retention, and transmission and evaluating management strategies to control Geminivirus.

The book is an essential reference for students and researchers interested in plant virology, particularly begomoviruses, geminiviruses, and vector transmission biology.

Introduces identification and characterization of geminiviruses that infect agricultural crops, their wild relatives, and weed hosts

Discusses recombination and reassortment mechanisms influencing viral genetic diversity, virulence, and vector transmission

Explores the origin, evolution, and bottlenecks of Geminiviruses

Cover image
Title page
Table of Contents
Copyright
List of contributors
About the editors
Foreword
Preface
A journey of Geminivirus
1 Introduction
2 Factors driving the geminivirus evolution
3 Conclusion
Section I: Detection and Diagnosis
Chapter 1. Current challenges and future perspectives on detection of geminiviruses
Abstract
1.1 An introduction to ssDNA viruses
1.2 Exploring the vast diversity of geminiviruses
1.3 Wild plants: invisible sources of emerging and reemerging geminiviral infections
1.4 Vectors as vehicles for geminivirus dissemination and diversity
1.5 Human activities and the importance of fast and accurate detection of geminiviruses
1.6 Classic and current methods used for detecting geminiviruses and their challenges
1.7 New approaches developed for geminivirus detection: pros and cons
1.8 Different sources for detecting geminiviruses
1.9 A challenging question: what is the best approach for geminivirus detection?
1.10 Future steps
Acknowledgments
References
Chapter 2. Molecular detection and characterization of begomoviruses infecting Amaranthus, a protein-rich crop
Abstract
2.1 Introduction
2.2 Viruses of Amaranthus
2.3 Begomoviruses
2.4 Detection of begomoviruses from Amaranth
2.5 Characterization of begomoviruses from Amaranth
2.6 Conclusion
References
Chapter 3. Recent developments in the diagnosis of geminiviruses
Abstract
3.1 Introduction
3.2 Thermal cycling based amplification—polymerase chain reaction
3.3 Polymerase chain reaction variants
3.4 Isothermal nucleic acid amplification
3.5 Rolling circle amplification
3.6 Loop-mediated isothermal amplification
3.7 Recombinase polymerase amplification
3.8 Next-generation sequencing
3.9 Clustered regularly interspaced short palindromic repeats diagnostics
3.10 Conclusion
References
Chapter 4. Viral metagenomics for the analysis of the Begomovirus genome
Abstract
4.1 Introduction
4.2 Begomovirus and its genome
4.3 Conclusion
References
Chapter 5. In silico detection tools for begomoviruses causing leaf curl disease in crops and its management through RNA interference
Abstract
5.1 Introduction
5.2 Leaf curl disease: a threat to agriculture
5.3 Genomic organization of begomovirus
5.4 Infection cycle of begomovirus
5.5 Circulative pathway of begomovirus in whitefly
5.6 In silico design of detection tools
5.7 RNA interference
5.8 Conclusion
Acknowledgments
References
Section II: Emergence and Diversity
Chapter 6. Origin, evolution and bottlenecks of geminiviruses
Abstract
6.1 Introduction
6.2 Origin, evolutionary factors, and prevalence of geminiviruses
6.3 Classification, taxonomy, and distribution of geminiviruses
6.4 Genetic composition of geminiviruses
6.5 Epidemiological dynamics of geminiviruses
6.6 Hosts of geminiviruses (crop plants and weed species)
6.7 Mode of transmission of geminiviruses
6.8 Economic importance of geminiviruses on crop plants
6.9 Management of geminiviruses
6.10 Conclusion
References
Chapter 7. Spotlight on the recently discovered aphid-transmitted geminiviruses
Abstract
7.1 Background and overview
7.2 Transmission features of Alfalfa leaf curl virus
7.3 Low transmission rate seems a generic feature of capulaviruses
7.4 Ecology of capulaviruses
7.5 Clarifying the etiology of capulaviruses for an efficient control
References
Chapter 8. Emergence of begomoviruses in cucurbits as a menace for its cultivation
Abstract
8.1 Introduction
8.2 Genome organization of Begomoviruses
8.3 Symptomatology
8.4 Distribution of begomoviruses on cucurbits
8.5 Host range of begomoviruses
8.6 Diversity
8.7 Diagnostics of begomovirus
8.8 Epidemiology and transmission
8.9 Mixed infection
8.10 Management of begomoviruses
References
Chapter 9. Begomoviruses in crops with economic interest for North and Central America
Abstract
9.1 Begomoviruses present in main crops of North and Central America
9.2 Expansion of Tomato yellow leaf curl disease in North and Central America
9.3 Tomato yellow leaf curl virus in the insular Caribbean
9.4 Current distribution of B. tabaci species in North and Central America and the Caribbean islands
9.5 Concluding remarks
References
Chapter 10. Diversity of begomoviruses infecting crops and weeds in the Caribbean and Latin America
Abstract
10.1 Introduction
10.2 Diversity of begomoviruses
10.3 Whitefly vectors in the Caribbean and Latin America
10.4 Evolution in begomoviruses
10.5 Conclusion
References
Chapter 11. Diversity of geminiviruses occurring on jatropha (Jatropha curcus), a biodiesel crop
Abstract
11.1 Introduction
11.2 Disease incidence and natural symptoms on Jatropha curcas
11.3 Whitefly transmission
11.4 PCR detection of virus using begomovirus-specific primers
11.5 Rolling circle amplification for full-length genome
11.6 Cloning and sequencing of RCA amplicons
11.7 Genome organization and sequence analysis
11.8 Sequence analysis of begomovirus isolate
11.9 Recombination analysis
11.10 Possible disease management strategies
11.11 Conclusions
11.12 Scope and application potential of the study
References
Chapter 12. Geminiviruses occurrence in the middle east and their impact on agriculture in Iraq
Abstract
12.1 Introduction
12.2 Current status of agriculture in Iraq
12.3 The status of geminiviruses in the Middle East
12.4 Geminiviruses in Iraq
12.5 Transmission and host range of geminiviruses
12.6 Epidemiology and control
12.7 Phylogenetic relatedness
12.8 Conclusion
References
Chapter 13. Diversity of begomoviruses associated with gourds
Abstract
13.1 Introduction
13.2 Symptomatology of begomoviruses on different gourd crops
13.3 Begomoviruses and satellite molecules associated with different gourd crops
13.4 Phylogenetics and recombination among the begomoviruses and satellites in gourds
13.5 Neighbor-net and recombination analysis
References
Chapter 14. Characterization of begomoviruses and DNA satellites associated with tomato
Abstract
14.1 Introduction
14.2 The Geminivirideae family
14.3 Distribution of Old and New World begomovirus
14.4 Detection and diagnosis of the virus
14.5 Transmission of begomovirus
14.6 Emergence of novel whitefly transmitted virus
14.7 Conclusions
References
Section III: Vector and Transmission
Chapter 15. Replication and transovarial transmission of tomato yellow leaf curl virus in its whitefly vector: myth or reality?
Abstract
15.1 Introduction
15.2 Tomato yellow leaf curl viruses, a group of begomoviruses transmitted by whitefly (Bemisia tabaci) species (or biotypes)
15.3 Tomato yellow leaf curl viruses outside the circulative transmission pathway
15.4 Tomato yellow leaf curl viruses replication, transcription, and translation in Bemisia tabaci
15.5 Whitefly defense systems that may restrain tomato yellow leaf curl viruses replication
15.6 Transovarial transmission of tomato yellow leaf curl viruses; does it depend on the age of the female?
15.7 Discussion
Acknowledgment
References
Chapter 16. The other face of pollinating insects and their relationship to geminivirus transmission
Abstract
16.1 Importance of stingless bees in pollination
16.2 Insect vectors of Begomovirus
References
Chapter 17. Behavioral manipulation for managing Bemisia tabaci as a virus vector
Abstract
17.1 Introduction
17.2 The problem
17.3 Some conceptual concerns
17.4 A preventative managing scheme based on Bemisia tabaci behavior
17.5 Conclusion
Acknowledgments
References
Chapter 18. Enigmatic emergence of seed transmission of geminiviruses
Abstract
18.1 Introduction
18.2 Importance of seed transmission of viruses
18.3 Seed-transmitted gemininiruses
18.4 Mechanism of seed transmission
18.5 Factors governing seed transmission
18.6 Conclusion
18.7 Future perspectives
References
Section IV: Virus-Host Interaction
Chapter 19. The diverse roles of the multifunctional C4/AC4 protein in geminivirus infection
Abstract
19.1 Introduction
19.2 Symptom development
19.3 Suppression of RNA silencing—the viral counter defense
19.4 Cell cycle regulation
19.5 Viral DNA accumulation and movement
19.6 Disruption of disease resistance signaling
19.7 Role of C4/AC4 sequence variability on function
19.8 Conclusion
Acknowledgments
References
Chapter 20. Geminivirus DNA replication in plants
Abstract
20.1 Introduction
20.2 The geminiviral origin of replication
20.3 Geminivirus-encoded proteins involved in geminivirus DNA replication
20.4 Reactivation of the cell cycle mediated by geminiviruses
20.5 Plant proteins required for geminivirus DNA replication: toward the viral replisome
20.6 Current model of geminiviral replication
20.7 Open questions and future perspectives
References
Chapter 21. Begomovirus–host protein-protein interactions in intracellular virus movement
Abstract
21.1 Introduction
21.2 The Begomovirus genus of the Geminiviridae family
21.3 Host–NSP protein–protein interactions
21.4 Host–MP protein–protein interactions
21.5 Models for intra- and intercellular movement of bipartite begomoviruses: putting the pieces together
References
Chapter 22. Geminivirus promoters: a breakthrough in transgenic research
Abstract
22.1 Introduction
22.2 Geminiviruses and their genomes
22.3 Nuclear hijack/takeover by geminiviruses
22.4 Constitutive, tissue-specific, and inducible geminivirus promoters
22.5 Early and late promoters
22.6 Transactivation by AC2/C2 gene
22.7 Promoter silencing
References
Chapter 23. Molecular evaluation of geminiviruses and their interaction with host plants
Abstract
23.1 Introduction
23.2 Geminiviruses and RNA silencing
23.3 Geminivirus and small noncoding RNAs
23.4 Geminivirus and counter-RNA silencing
23.5 Geminiviruses and host cellular reprogramming
23.6 Implications for engineered resistance
23.7 Future directions and conclusions
References
Chapter 24. Molecular insights into pathogenicity determinant proteins of geminiviruses
Abstract
24.1 Introduction
24.2 Pathogenicity determinants
24.3 Takeover of plant defense by geminiviruses: unfolding the role of pathogenicity proteins
24.4 Conclusion
Acknowledgments
Conflict of interest
References
Chapter 25. The begomovirus–host interplay in viral replication and movement
Abstract
25.1 Introduction
25.2 Genome organization
25.3 Begomoviral replication
25.4 Cellular trafficking of begomoviruses in hosts
25.5 Conclusion
References
Chapter 26. Role of plant viral satellites association in geminivirus infection
Abstract
26.1 Introduction
26.2 Discovery/history
26.3 Satellite DNAs associated with geminiviruses
26.4 Origin, evolution, and phylogenetic relationship of geminivirus satellites
26.5 Conclusion
26.6 Future perspectives
References
Chapter 27. Geminivirus infections co-opt posttranslational modification of proteins during viral pathogenesis
Abstract
27.1 Introduction
27.2 The silent artillery of geminiviruses
27.3 Types of posttranslational modification of proteins
27.4 Phosphorylation
27.5 Ubiquitination
27.6 Sumoylation
27.7 Acetylation
27.8 Lipidation
27.9 Conclusion
References
Further reading
Chapter 28. Exploring the functional interactions between geminivirus and host during viral replication, assembly, and movement
Abstract
28.1 Introduction
28.2 Genome organization
28.3 Geminiviruses replication
28.4 Role of viral proteins in replication
28.5 Role of host proteins in replication
28.6 Geminivirus–host interactions during viral assembly
28.7 Intracellular and intercellular movement of geminiviruses
28.8 Trafficking of bipartite begomoviruses
28.9 Movement of monopartite geminiviruses
28.10 Conclusion
References
Chapter 29. Molecular arms race between geminiviruses and host plants during infection cycle—a transcriptomics overview
Abstract
29.1 Introduction
29.2 Transcriptomics
29.3 Transcriptomics approaches in plant–geminivirus interactions
29.4 Current challenges and future prospects
29.5 Conflict of interest
References
Section V: Disease Management
Chapter 30. Resistance to geminivirus infections: natural and induced by controlled elicitation
Abstract
30.1 Introduction
30.2 Geminivirus resistance sources in Mexican chili peppers
30.3 Biochemical and molecular characterization of a natural resistance source to geminiviruses
30.4 Induced resistance to geminiviruses using controlled elicitation
30.5 Defense mechanisms
30.6 Elicitors and geminiviruses
References
Chapter 31. Invasive tomato yellow leaf curl virus recombinants challenge virus diagnosis and disease management
Abstract
31.1 Overview
31.2 Background
31.3 The emergence scenario of the resistance-driven recombinant TYLCV-IS76
31.4 An invading TYLCV recombinant shed new light on an underexplored region of the viral genome
31.5 Perspective on detection and management of tomato yellow leaf curl virus recombinants
References
Chapter 32. Natural and engineered host resistance for geminivirus management
Abstract
32.1 Geminivirus—an introduction
32.2 Crop losses due to geminiviruses
32.3 Cultural/conventional methods
32.4 Management using insecticides
32.5 Natural resistance
32.6 Engineered resistance
32.7 Difficulties in achieving resistance against geminiviruses
32.8 Conclusions
Acknowledgment
References
Chapter 33. Natural and engineered resistance: implications for managing the cassava mosaic disease
Abstract
33.1 The crop cassava and its importance
33.2 Productivity, production areas, and limitations of cassava production
33.3 Cassava mosaic disease
33.4 Genome of geminiviruses infecting cassava
33.5 Management of cassava mosaic disease
33.6 Disease free planting materials
33.7 Vector control
33.8 Cultural practices
33.9 Extensive surveillance of disease
33.10 Resistant varieties
33.11 Natural resistance
33.12 Engineered resistance
33.13 Concluding remarks
References
Chapter 34. Host immunity and viral counter defense
Abstract
34.1 Introduction
34.2 Molecular biology of host–pathogen interaction: entry and transport
34.3 Molecular biology of host–pathogen interaction: balance between host response and viral effects
34.4 Exploiting host–pathogen interactions for future prospects: generation of virus-resistant plants
References
Chapter 35. Disease rating scale for the resistant screening against begomoviruses causing yellow mosaic disease in different crops
Abstract
35.1 Introduction
35.2 Disease measurement: the beginning
35.3 Existing rating scale for the yellow mosaic diseases in different crops
35.4 Different disease rating scale: observation and analysis
35.5 Standard operating protocol
35.6 Case study
35.7 Summary
35.8 Disease rating scales for the case study
References
Chapter 36. Overview of host factors and geminivirus proteins involved in virus pathogenesis and resistance
Abstract
36.1 Geminiviruses—a serious threat to food security
36.2 Two-layered plant antiviral immunity—pattern-triggered immunity and effector-triggered immunity
36.3 RNA silencing—a potent plant defense response
36.4 Suppression of RNA silencing by geminviruses
36.5 Virus symptom recovery
36.6 Hormone signaling during geminivirus infection
36.7 Hypersensitive response
36.8 Autophagy during geminivirus infection
36.9 Conclusion
References
Chapter 37. Application of virus-induced gene silencing in crops: mechanism, assessment of risk factors and ecological advantages
Abstract
37.1 Introduction
37.2 Mechanism of virus-induced gene silencing
37.3 Relationship with small RNAs
37.4 Applications
37.5 Probable roles in crop improvement, nutritional improvement
37.6 Risks, main emphasis on ecological risk
37.7 Advantages over other methods
37.8 Future perception
37.9 Conclusion
Acknowledgment
References
Chapter 38. Peptide aptamers: selection strategies, mechanisms, and applications in engineered geminivirus resistance
Abstract
38.1 Introduction
38.2 Peptide aptamers
38.3 Peptide aptamers selection strategies
38.4 Peptide aptamers: plant viral diseases controlling tool
38.5 Applications of peptide aptamers in engineered geminivirus resistance
38.6 Conclusion
Conflict of interest
References
Chapter 39. Geminiviruses infecting tomato: genetic diversity, distribution, natural and genetically engineered resistance
Abstract
39.1 Introduction
39.2 Diversity and distribution of geminiviruses infecting tomato
39.3 Resistance development through a breeding approach
39.4 Resistance development through a biotechnological approach
39.5 Conclusion
Acknowledgment
References
Chapter 40. Evaluating management strategies to control geminivirus
Abstract
40.1 Introduction
40.2 Strategies for geminiviruses management
References
Index

R.K. Gaur

Prof. (Dr.) R.K. Gaur earned his Ph.D. in 2005, and is now a Professor at the Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh, India. His Ph.D. was on the molecular characterization of sugarcane viruses, i.e., mosaic, streak mosaic, and yellow luteovirus. He received a MASHAV fellowship of the Israeli government for his postdoctoral studies and joined The Volcani Center, Israel and Ben-Gurion University, Negev, Israel. In 2007 he received the Visiting Scientist Fellowship from the Swedish Institute, Sweden to work at Umea˚ University, Umea˚, Sweden. He received a postdoc fellowship from ICGEB, Italy in 2008. He has made significant contributions on sugarcane viruses and has pub lished 130 national/international papers, authored 17 edited books and presented about 50 papers at national and international conferences. He has been honored as a Fellow of Linnean Society, a Fellow of the Royal Society of Biology, a Fellow of the Society of Plant Research, a Fellow of the Society of Applied Biology (FSAB), and a Fellow of the International Society of Biotechnology (FISBT). He has received many other awards, including the Prof. B.M. Johri memorial Award, Society of Plant Research (SPR); Excellent Teaching Award by Astha Foundation, Meerut; UGC-Research Teacher Award; Young Scientist Award in 2012 in Biotechnology by the Society of Plant Research (SPR), Meerut; and Scientific and Applied Research Center Gold Medal Award in 2011 for outstanding contribution in the field of Biotechnology. He has visited several laborato ries in the United States, Canada, New Zealand, United Kingdom, Thailand, Sweden, and Italy. Currently, he is han dling many national and international grants and international collaborative projects on plant viruses and disease management

Affiliations and expertise

Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh, India

Pradeep Sharma

Dr. Pradeep Sharma received his Ph.D. in 2002 on the cloning and characterization of cotton leaf curl viruses. He performed his postdoctoral research (2006 2008) at Tohoku University, Japan with Prof M Ikegami as a JSPS fellow, where he worked on RNA silencing. He also undertook postdoctoral work at the ARO Volcani Center, Israel with Prof Y Gafni (2006 2006), focusing on the nuclear import of genes using yeast one hybrid system, as a DST scientist (2006), as a visiting scientist at South Dakota State University (2011) investigating allele mining and comparative genomics in rice, and at Oklahoma State University (2016) on small noncoding RNAs. In 2008, Dr. Sharma joined the faculty in the Department of Crop Improvement at ICAR-Indian Institute of Wheat and Barley Research, Karnal, where he is the Principal Scientist. He directs a research group studying the role of sRNAs and epigenetics for biotic and abiotic stresses, molecular dynamics simulation, and NGS-based marker discovery in wheat. His group also decoded Karnal bunt genomes, the development of SSR markers for population structure, and diversity analysis of bunts and smut fungi. He teaches courses in Molecular Biology and Computational Biology to graduate students. Dr. Sharma has published more than 110 national and international research papers, 25 invited chap ters, eight scientific review articles, and he has edited seven books on biotic and abiotic stresses including RNAi tech nology. Dr. Sharma was conferred the Young Scientist’s Award (biannual 2005 2006) of the National Academy of Agricultural Sciences; the Pran Vohra Award (2008 2009) of the Indian Science Congress Association; a Fellow of the National Academy of Biological Sciences (2015); a Fellow of the Indian Virological Society (2012); and a Fellow of the Society for Advancement of Wheat and Barley Research (2019). He has worked at and visited many pioneering lab oratories of the United States, the United Kingdom, Japan, France, China, the Netherlands, Indonesia, Turkey, and Israel.

Affiliations and expertise

Principle Scientist, 201A Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India

Henryk Czosnek

Prof. (Dr.) Henryk Czosnek earned his Ph.D. in 1978 from the Hebrew University of Jerusalem, working on protein synthesis in the liver. He took a postdoctoral position of Senior Research Scientist at the NY State Institute for Basic Research in Mental Disabilities, New York, USA, working on the biochemistry of brain degenerative diseases. He joined the Weizmann Institute in 1980, Rehovot, Israel, and worked on the cloning and expression of mammalian muscle genes. In 1985 Dr. Czosnek joined the Faculty of Agriculture of the Hebrew University of Jerusalem, Rehovot, Israel. He was on sabbatical leave in 1990 at the CNRS at Gif sur Yvette, France, working with Dr. Bruno Gronenborn on begomoviruses, and in 2000 at the University of Arizona, Tucson, USA working with Prof. Judith Brown on the transcriptome of the whitefly Bemisia tabaci. He was a full Professor from 1996 and emeritus from 2017. Prof. Czosnek has investigated the relationships between begomoviruses, their whitefly vector, and the host plants. He has led funded collaborative projects with many countries in the Middle East, Southern Africa, the Maghreb, Europe, the United States, Central America and the Caribbean, India, and China, on the topics of plants’ viral diseases and their management. Prof. Czosnek is teaching courses on Genetic Engineering, Plant Molecular Biology, and Molecular Genetics.

Affiliations and expertise

Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Israel