Dr Palmiro Poltronieri is researcher at the Agrofood Department of the Italian National Research Council. He is co-founder of Biotecgen SME - a service company involved in European projects, such as RIBOREG, NANOMYC, ABSTRESS, and TOMGEM. He has also tutored researchers for another start up, Bioesplora, in the EU project TRANS-BIO. He is Associate Editor to BMC Research Notes and is editor-in-chief for Challenges, an MDPI journal. He holds a Ph.D. in Molecular and Cellular Biology from Verona University. His current interest is on abiotic stress response in roots of tolerant and sensitive chickpea varieties, on activation of the jasmonic acid synthesis, and in the biotic stress response in model plants.
Applied plant genomics and biotechnology reviews the recent advancements in the post-genomic era, discussing how different varieties respond to abiotic and biotic stresses, investigating epigenetic modifications and epigenetic memory through analysis of DNA methylation states, applicative uses of RNA silencing and RNA interference in plant physiology and in experimental transgenics, and plants modified to produce high-value pharmaceutical proteins. The book provides an overview of research advances in application of RNA silencing and RNA interference, through Virus-based transient gene expression systems, Virus induced gene complementation (VIGC), Virus induced gene silencing (Sir VIGS, Mr VIGS) Virus-based microRNA silencing (VbMS) and Virus-based RNA mobility assays (VRMA); RNA based vaccines and expression of virus proteins or RNA, and virus-like particles in plants, the potential of virus vaccines and therapeutics, and exploring plants as factories for useful products and pharmaceuticals are topics wholly deepened. The book reviews and discuss Plant Functional Genomic studies discussing the technologies supporting the genetic improvement of plants and the production of plant varieties more resistant to biotic and abiotic stresses. Several important crops are analysed providing a glimpse on the most up-to-date methods and topics of investigation. The book presents a review on current state of GMO, the cisgenesis-derived plants and novel plant products devoid of transgene elements, discuss their regulation and the production of desired traits such as resistance to viruses and disease also in fruit trees and wood trees with long vegetative periods. Several chapters cover aspects of plant physiology related to plant improvement: cytokinin metabolism and hormone signaling pathways are discussed in barley; PARP-domain proteins involved in Stress-Induced Morphogenetic Response, regulation of NAD signaling and ROS dependent synthesis of anthocyanins. Apple allergen isoforms and the various content in different varieties are discussed and approaches to reduce their presence. Euphorbiaceae, castor bean, cassava and Jathropa are discussed at genomic structure, their diseases and viruses, and methods of transformation. Rice genomics and agricultural traits are discussed, and biotechnology for engineering and improve rice varieties. Mango topics are presented with an overview of molecular methods for variety differentiation, and aspects of fruit improvement by traditional and biotechnology methods. Oilseed rape is presented, discussing the genetic diversity, quality traits, genetic maps, genomic selection and comparative genomics for improvement of varieties. Tomato studies are presented, with an overview on the knowledge of the regulatory networks involved in flowering, methods applied to study the tomato genome-wide DNA methylation, its regulation by small RNAs, microRNA-dependent control of transcription factors expression, the development and ripening processes in tomato, genomic studies and fruit modelling to establish fleshy fruit traits of interest; the gene reprogramming during fruit ripening, and the ethylene dependent and independent DNA methylation changes. - provides an overview on the ongoing projects and activities in the field of applied biotechnology- includes examples of different crops and applications to be exploited- reviews and discusses Plant Functional Genomic studies and the future developments in the field- explores the new technologies supporting the genetic improvement of plants
Front Cover 1
Applied Plant Genomics and Biotechnology 4
Copyright Page 5
Contents 6
List of figures 10
List of tables 16
About the editors 18
About the contributors 20
List of abbreviations 32
Introduction 38
1 Transgenic, cisgenic and novel plant products: Challenges in regulation and safety assessment 40
1.1 Genetically modified plant products in the United States 40
1.2 GMP products in Europe 41
1.2.1 Novel GMP producing methods and risk mitigation 42
1.2.2 Targeted genome modification using site-specific nucleases 43
1.2.3 New technologies applied to plant genome editing 44
1.2.3.1 Transient introduction of recombinant DNA 46
1.2.3.2 Stable introduction of recombinant DNA during an intermediate step in the development of NPPs 47
1.2.3.3 Stable integration of recombinant DNA 47
1.2.4 RNA, RNA-mediated control of gene expression and post-translational modification: From transgenic plants to NPP and c... 48
1.2.5 Cisgenesis 49
1.2.6 Modification of trees, stone fruit trees and plants with long vegetative periods 50
1.2.7 Product-based regulatory frameworks 51
References 53
2 What turns on and off the cytokinin metabolisms and beyond 56
Acronyms 56
2.1 Introduction 56
2.2 Regulation of cytokinin biosynthesis 57
2.2.1 The role of cytokinins in plant development 57
2.2.2 Nitrogen and cytokinin metabolism 58
2.2.3 Defence response, development and cytokinin 59
2.2.4 Regulatory mechanism of cytokinin degradation 60
2.2.5 Transcription factors regulating cytokinin metabolisms 60
2.2.6 Regulation of grain yield and seed size by cytokinin 65
2.2.7 Establishment of symbiosis, cluster root formation and CKX 66
2.2.8 Crosstalk with other hormones 66
2.3 Application of altered cytokinin metabolisms to improve agricultural traits 67
Acknowledgement 68
References 68
3 Apple allergens genomics and biotechnology: Unravelling the determinants of apple allergenicity 74
3.1 Introduction: Fruit and apple allergies 74
3.1.1 Apple allergy symptoms and clinical studies 75
3.1.2 Genomics and biochemistry 77
3.1.2.1 Mal d 1 – PR-10 ribonuclease-like 77
3.1.2.2 Mal d 2 – PR-5 thaumatins 79
3.1.2.3 Mal d 3 – PR-14 nsLTPs 80
3.1.2.4 Mal d 4 – Profilins 81
3.2 Abiotic factors: Influence of environment and cultivation techniques 82
3.3 Biotic factors: Pathogen infection and allergens content 83
3.4 Post-harvest, food processing and breeding strategies towards allergenic content decrease 85
3.4.1 Post-harvest and food processing 85
3.4.2 Breeding programs 86
3.5 Conclusion 87
References 88
4 Non-food interventions: Exploring plant biotechnology applications to therapeutic protein production 94
4.1 Introduction 94
4.2 Plant as heterologous expression system for molecular farming 95
4.3 Stable transformation 96
4.4 Transient transformation 98
4.5 Limits on the use of plants as expression systems for molecular farming 99
4.6 Plant-made recombinant pharmaceuticals 100
4.6.1 Plant-made vaccines 100
4.6.2 Plant-made antibodies 101
4.6.3 Plant-made therapeutics 102
4.6.4 Production of recombinant human acid ß-glucosidase stored in tobacco seed 103
4.6.5 Transgenic expression, accumulation and recovery of dimer human apolipoprotein A-IMilano in rice seeds 103
4.6.6 Production of a functional human acid maltase in tobacco seeds 104
4.7 Regulatory aspects and clinical status of PMPs 105
References 106
5 In planta produced virus-like particles as candidate vaccines 112
5.1 Introduction 112
5.2 Papillomaviruses 113
5.3 Hepatitis B virus 116
5.4 Human immunodeficiency virus-1 118
5.5 Influenza A virus 120
References 121
6 Biotechnology of Euphorbiaceae (Jatropha curcas, Manihot esculenta, Ricinus communis) 126
6.1 Euphorbiaceae crops 126
6.2 Genetic diversity 128
6.2.1 Genetic diversity in Jatropha 128
6.2.2 Genetic diversity in cassava 129
6.2.3 Genetic diversity in castor bean 131
6.3 Genetic improvement 132
6.3.1 Breeding strategies 133
6.3.1.1 Conventional breeding 133
Jatropha 133
Cassava 134
Castor bean 134
6.3.1.2 Tissue culture and gene transfer technology 134
Jatropha 135
Cassava 136
Castor bean 136
6.4 Phytosanitary improvement 137
6.4.1 Viral diseases of Jatropha, cassava and castor bean 137
6.4.2 Virus detection 137
6.4.3 Host–pathogen interactions 141
6.4.3.1 microRNAs 142
Virus miRNA 142
miRNAs of Euphorbiaceae 142
6.4.4 Utilization of viral sequences to generate virus resistant Euphorbiaceae crops 143
6.5 Concluding remarks 144
Acknowledgement 144
References 145
7 Regulation framework for flowering 154
7.1 Introduction 154
7.2 Getting ready to flower: the juvenile to adult transition 155
7.3 Framework controlling flowering 156
7.4 Flowering sensing the environment 156
7.4.1 The photoperiod and light quality pathways 156
7.4.2 Vernalization pathway 160
7.4.3 Thermosensory pathway 162
7.5 Endogenous cues regulating flowering 163
7.5.1 Autonomous pathway 163
7.5.2 Gibberellic acid pathway 164
7.5.3 Sugar pathway 164
7.5.4 Ageing pathway 165
7.6 Flowering time control and manipulation 166
References 167
8 Epigenetic regulation during fleshy fruit development and ripening 172
8.1 Introduction 172
8.2 An overview of DNA methylation in plants 173
8.2.1 Mechanisms of DNA methylation 173
8.2.2 Targets and distribution of DNA methylation in plants 176
8.2.3 DNA methylation in fruit development 176
8.2.3.1 DNA methylation patterns are highly dynamic during fruit development 176
8.2.3.2 Modifications of methylation pattern impact tomato fruit development and ripening 179
8.2.3.3 DNA methylation might also control fruit quality in other plants 180
8.3 Histone marks are likely to play fundamental role in fruit development 181
8.3.1 Overview 181
8.3.2 Genes involved in histone PTMs are differentially regulated during fruit development 182
8.3.3 DET1 and PRC2s are involved in the control of tomato fruit development 183
8.4 Concluding remarks 184
References 185
9 Tomato fruit quality improvement facing the functional genomics revolution 192
9.1 Introduction 192
9.2 What is meant by fruit quality? 193
9.3 Genomics-assisted breeding for improving fruit quality 194
9.4 Future potential of tomato breeding using omics approaches 196
9.5 Fruit modelling to establish fleshy fruit traits of interest 199
9.6 Concluding remarks 200
References 201
10 Rice genomics and biotechnology 206
10.1 Golden age of genomics, biological engineering and paddy rice 206
10.2 Research on the important agronomic traits in rice biology 208
10.3 Emergence of new technologies will extend the golden age of paddy rice 211
10.4 Rice requires further research development to remain a monocotyledon model plant 212
References 213
11 Genome-wide DNA methylation in tomato 218
11.1 Introduction 218
11.2 Methods to detect and quantify DNA methylation 218
11.2.1 Methylation-sensitive restriction enzymes 218
11.2.2 Immuno-precipitation of methylated DNA 219
11.2.3 Bisulphite sequencing 220
11.3 Distribution of 5-methylcytosine in tomato genome 221
11.3.1 Early studies on tomato genome DNA methylation 221
11.3.1.1 Asymmetric CHH methylation in the PSY1 promoter 221
11.3.1.2 Genome-wide DNA methylation in tomato fruit 221
11.3.2 DNA methylation and transposon 223
11.3.3 DNA methylation and small RNA 223
11.3.3.1 DNA methylation and gene expression 224
11.3.3.2 DNA methylation and histone modification 225
11.4 Genome-wide DNA methylation reprogramming during fruit ripening 225
11.4.1 Ethylene-dependent and -independent fruit ripening control 225
11.4.2 Genome-wide DNA methylation changes in tomato 227
11.4.3 Differential methylation associated with transcription factor-binding sites 228
11.5 Conclusion 229
Acknowledgements 230
References 230
12 Recent application of biotechniques for the improvement of mango research 234
12.1 Introduction 234
12.2 Origin and distribution 235
12.3 Economic importance 236
12.4 Cytology 236
12.5 Molecular biotechniques applied on mango 237
12.5.1 Development of DNA extraction method 237
12.5.2 Molecular markers for genetic diversity analysis 238
12.5.2.1 Isozyme marker 238
12.5.2.2 Restriction fragment length polymorphism 238
12.5.2.3 Random amplified polymorphic DNA 239
12.5.2.4 Amplified fragment length polymorphism 240
12.5.2.5 Simple sequence repeat 241
12.5.2.6 Inter-simple sequence repeats 242
12.5.2.7 Start codon targeted primers 242
12.5.2.8 Developments of CAPS markers 242
12.5.2.9 18S rRNA gene sequence 242
12.6 Application of RAA method on mango 243
12.7 Problems in mango improvement using biotechnology 244
12.8 Conclusion and direction of future research 245
References 246
13 Cotton genomics and biotechnology 252
13.1 Introduction 252
13.2 Cotton genomics 253
13.3 Cotton fibre function genomics 255
13.4 Cotton biotechnology 261
List of abbreviations 262
References 263
14 Virus technology for functional genomics in plants 268
Acronyms 268
14.1 Introduction 268
14.1.1 Virus-based transient gene expression system (Lin et al., 2008 Li et al., 2009)
14.1.2 VIGC – virus-induced gene complementation (Zhou et al., 2012 Kong et al., 2013)
14.1.3 Sir VIGS and Mr VIGS – virus-induced gene silencing (Tang et al., 2010 Chen et al., 2014)
14.1.4 VbMS – virus-based microRNA silencing (Sha et al., 2014) 272
14.2 VRMA – virus-based RNA mobility assay (Li et al., 2009, 2011) 273
14.3 Conclusion 273
References 274
15 PARP proteins, NAD, epigenetics, antioxidative response to abiotic stress 276
15.1 Introduction 276
15.1.1 PARPs in DNA repair 276
15.1.2 Functions of PARP proteins beyond poly(ADP-ribosyl)ation and DNA repair 278
15.1.3 PARP role and activity in the cell reprogramming 278
15.1.4 NAD pool in cell physiology and plant stress response 279
15.1.5 NUDIX hydrolases, pADPr and NAD recycling 280
15.1.6 Plant PARPs and PARP-domain containing proteins 280
15.1.7 PARP-domain proteins: radical induced cell death-1 and SRO1 in stress-induced morphogenetic response 281
15.1.8 Involvement of PARP-domain proteins in control of the flavonoid biosynthesis pathway 283
15.1.9 PARP control of anthocyanin synthesis in stress tolerance 284
15.2 Conclusion 286
Acknowledgement 286
References 286
16 Applied oilseed rape marker technology and genomics 292
16.1 Global importance of oilseed rape 292
16.1.1 Broadening genetic diversity for OSR breeding 292
16.1.2 Current OSR breeding goals, methods and variety types 294
16.2 Rapeseed yield and quality and potential improvements 295
16.3 Future potentials of OSR variety and crop improvement 297
16.3.1 Molecular marker systems 299
16.3.1.1 The forefathers of marker technology: hybridization- and PCR-based markers 299
16.3.1.2 Marker technology coming of age: enzyme- and array-based genotyping-by-hybridization 302
16.3.1.3 Emerging marker technology: GBS 303
16.3.2 SNP marker discovery 304
16.3.3 Molecular marker applications 306
16.3.3.1 Germplasm characterization 307
16.3.3.2 Variety identification 308
16.3.3.3 Genetic linkage mapping 308
16.3.3.4 Fine mapping and map-based cloning 314
16.3.3.5 Association mapping 317
16.3.3.6 MAS and breeding 317
16.3.3.7 Genomic selection 322
16.3.3.8 Genome analyses and comparative genomics 323
16.4 Conclusion 324
References 324
Index 336
About the contributors
Li Bin obtained his MSc degree from the College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, People’s Republic of China. He is now a research associate in a biotechnology company. His main research interest focuses on intercellular RNA silencing and siRNA functions in plant defence against virus infection.
Lisa Boureau did her Ph.D. thesis title “Analyse fonctionnelle de la protéine Enhancer of zeste, SlEZ2, chez la tomate Solanum lycopersicum” collaborating with Philippe Gallusci on topics of tomato fruit ripening, metabolomics and flavonoid studies, at Bordeaux University, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d’Ornon, France. Presently she is post-doc fellow at McGill University, Quebec city, Canada.
Matteo Busconi is an assistant professor at the Institute of Agronomy, Genetics and Field Crops of the Università Cattolica del Sacro Cuore of Piacenza, Italy. He achieved a postdoc in molecular biotechnology at the Università Cattolica del Sacro Cuore in 2005. His scientific activity is mainly focused on food genomics, biodiversity with particular focus on plant biodiversity, molecular marker development, horizontal gene flow of herbicide resistance from cultivated rice to weedy relatives, gene expression, epigenetics and transgenesis. His teaching includes courses on agricultural genetics, biotechnology and plant breeding at the Università Cattolica del Sacro Cuore. He has taught biotechnology for molecular farming at the University of Modena and Reggio-Emilia (Modena, Italy). He is a member of the Società Italiana di Genetica Agraria and the Società di Ortoflorofrutticoltura Italiana. He has experience as a reviewer since 2005 for several indexed journals. He is author and co-author of publications in international and national journals.
Weiwei Chen is a lecturer in the College of Life and Environmental Sciences and a junior research leader in the Research Centre for Plant RNA Signaling, Hangzhou Normal University, Zhejiang, People’s Republic of China, after she obtained her PhD in plant biology from the College of Life Sciences, Zhejiang University, Zhejiang, People’s Republic of China. She is interested in functional dissection of RNA-dependent DNA methylation pathways in the regulation of tomato fruit ripening and plant development. Her research also covers microRNAs and their roles in plants.
Qi Cheng got his bachelor degree in biochemistry at Zhejiang University, Zhejiang, People’s Republic of China, in 1989, master degree in biophysics at Chinese Academy of Agricultural Sciences (CAAS), Beijing, People’s Republic of China, in 1991 and a PhD in biochemistry at University of East Anglia, United Kingdom, in 1999. Over the past two decades of research career, he was employed by CAAS, University of Durham and University of Cambridge among others and has published over 60 papers and 1 book. He has developed his research expertise on various protein catalysts in the fields of nitrogen fixation engineering, lipid degradation, DNA amplification and so on. Since 2010, he is back in China as a professor and CEO, focusing his research and R&D on plant genetics and epigenetics.
Charlotte Degraeve-Guibault has obtained her master degree at Bordeaux University in the field of plant biology and biotechnology. Her work focused on the analysis of DNA demethylation during plant vegetative development.
Corrado Fogher, PhD, has been an associate professor of genetics and was responsible for the transgenic plants sector of the Observatory of Transgenic Organisms in Agriculture at the Università Cattolica del Sacro Cuore of Piacenza, Italy. He was NATO Fellow (1982–83) at the department of biochemistry, University of Missouri, Columbia. Researcher (1984–85) at the department of cellular physiology and molecular genetics of the Pasteur Institute, Paris, and visiting scientist at The Scripps Research Institute, La Jolla, California. He has authored more than 70 peer-reviewed papers. He was director of three SMEs, Plantechno, Incura and SunChem. His SMEs have started extremely interesting partnerships with corporate companies, one patented product will be tested as oral vaccine in a clinical trial, and a second research product will be exploited for the production of kerosene fuels. He died at the end of 2013.
Rupert Fray is an associate professor in plant molecular biology at the University of Nottingham, United Kingdom. He specializes in post-transcriptional gene regulation, focusing on the role of adenosine methylation in mRNA. He also has a long-standing interest in tomato fruit development and ripening regulation, with a particular interest in the synthesis of carotenoids and the control genes encoding the carotenoid biosynthetic genes during the ripening process.
Wolfgang Friedt is a professor emeritus at the Institute of Agronomy and Plant Breeding at the Justus Liebig University of Giessen, Germany. He has previously served as a dean of the faculty for agriculture and environment preservation. In addition, he has been serving as a member of the advisory boards and consulting committees of various scientific organizations and professional associations in the field of agronomy, plant breeding and general agriculture. He has published or co-authored many research papers mainly dealing with the genetic analysis of major complex traits of crop plants such as barley, sorghum, wheat and oilseed rape aiming at the genetic crop enhancement of crops to provide better varieties for agriculture.
Philippe Gallusci is professor at The University of Bordeaux. Since 2007, he has developed a research project focusing on the role of epigenetic mechanisms in plants. He obtained his PhD in Plant Molecular Biology in 1991 at the University of Toulouse and was a post doc at the Max Planck Institut for Züchtungforshung (Cologne, Germany). During this time his work focused on the transcriptional control of maize grain storage proteins. He was hired at the University of Bordeaux 1 in 1994 as an associate professor and studied plant isoprenoids before developing his own research project on the role of epigenetic mechanisms in the control of tomato fruit development and quality.
Juan Hao is a lecturer in College of Life and Environmental Science at the School of Hangzhou Normal University, Hangzhou, Zhejiang, People’s Republic of China. She was awarded a PhD in crop genetics and breeding from the National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, Hubei, People’s Republic of China. She has been engaged in cotton molecular breeding and has mainly focused on the research of the molecular mechanism of cotton fibre development.
Meiling He graduated from College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, People’s Republic of China. She is currently studying RNA and protein signalling in flowering.
Yoshihisa Ikeda is a junior researcher at the Centre of the Region Haná for Biotechnological and Agricultural Research, department of molecular biology, faculty of science, Palacký University in Olomouc, Czech Republic. He obtained a PhD degree in the field of bioscience at Nara Institute of Science and Technology, Japan. He was postdoc at The Rockefeller University, New York; Iowa State University, Ames, Iowa and the Swedish University of Agricultural Science, Sweden. He became a researcher at Umeå University, Sweden and Tohoku University, Japan. He was a Marie Curie Incoming International Fellowship while at the Swedish University of Agricultural Science.
Stephen Jackson is an associate professor since 2009 at the School of Life Sciences, Warwick University, East Anglia, United Kingdom. From 1990 to 1993, he was postdoc at the Institute für Genbiologische Forschung GmbH, Berlin, Germany; from 1993 to 1996, postdoc at the Centro de Investigacion y Desarrollo, C.S.I.C., Barcelona, Spain and from 1996 to 2009, Research leader at HRI, Wellesbourne, Warwick, United Kingdom. His group is investigating the control of plant development by light and photoperiod, a programme to isolate flowering mutants. This programme has identified several mutants that are specifically altered in their response to photoperiod, characterization of these mutants has shown them to represent novel genes in this pathway and work is underway to establish their cellular localization and interaction with known key regulators of the pathway such as CONSTANS. He is working on the role of the FLOWERING LOCUS T (FT) protein which is a component of the mobile flowering signal (florigen) in plants. He showed that FT mRNA is systemically mobile within the plant and may also play a role in the control of flowering time.
Hua Jiang is an associate research fellow at Zhejiang Academy of Agricultural Science, Hangzhou, People’s Republic of China. He received his PhD in genetics and crop breeding from Yangzhou University, Yangzhou, People’s Republic of China, (Supervisor: Qian Qian) in 2008. He has worked as a postdoctoral fellow at Zhejiang Academy of Agricultural Science (2008–10). Jiang’s current research interests are plant pathology and molecular plant pathology, focusing on prevention and control of diseases of rice and functional gene analysis of fungal disease in rice.
Eva Jiskrová graduated in molecular and cell biology from the faculty of science,...
| Erscheint lt. Verlag | 27.1.2015 |
|---|---|
| Sprache | englisch |
| Themenwelt | Informatik ► Weitere Themen ► Bioinformatik |
| Medizin / Pharmazie ► Gesundheitsfachberufe | |
| Medizin / Pharmazie ► Medizinische Fachgebiete ► Pharmakologie / Pharmakotherapie | |
| Naturwissenschaften ► Biologie ► Botanik | |
| Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie | |
| Technik ► Umwelttechnik / Biotechnologie | |
| ISBN-10 | 0-08-100071-5 / 0081000715 |
| ISBN-13 | 978-0-08-100071-7 / 9780081000717 |
| Haben Sie eine Frage zum Produkt? |
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