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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 the 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 of the most up-to-date methods and topics of investigation. The book presents a review on the current state of GMOs, 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 signalling pathways are discussed in barley; PARP-domain proteins involved in Stress-Induced Morphogenetic Response, regulation of NAD signalling and ROS dependent synthesis of anthocyanins. Apple allergen isoforms and the various content in different varieties and approaches to reduce their presence are discussed. Euphorbiaceae, castor bean, cassava and Jatropha genomic structure, diseases, and viruses are discussed, together with methods of transformation. Rice genomics and agricultural traits are discussed, and biotechnology for engineering and improving 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.
List of figures
List of tables
About the editors
About the contributors
List of abbreviations
Introduction
1. Transgenic, cisgenic and novel plant products: Challenges in regulation and safety assessment
2. What turns on and off the cytokinin metabolisms and beyond
3. Apple allergens genomics and biotechnology: Unravelling the determinants of apple allergenicity
4. Non-food interventions: Exploring plant biotechnology applications to therapeutic protein production
5. In planta produced virus-like particles as candidate vaccines
6. Biotechnology of Euphorbiaceae (Jatropha curcas, Manihot esculenta, Ricinus communis)
7. Regulation framework for flowering
8. Epigenetic regulation during fleshy fruit development and ripening
9. Tomato fruit quality improvement facing the functional genomics revolution
10. Rice genomics and biotechnology
11. Genome-wide DNA methylation in tomato
12. Recent application of biotechniques for the improvement of mango research
13. Cotton genomics and biotechnology
14. Virus technology for functional genomics in plants
15. PARP proteins, NAD, epigenetics, antioxidative response to abiotic stress
16. Applied oilseed rape marker technology and genomics
Index
Dr Palmiro Poltronieri is a 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 startup, 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 PhD 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.
Professor Yiguo Hong is a scientist based at the College of Life and Environmental Sciences, Hangzhou Normal University, China. He has expertise in plant viruses and RNA silencing, having publications in international journals, such as PNAS, eLife and Nature Genetics. He serves as editor for several international journals such as Functional & Integrative Genomics. He also holds long-term visiting professorships at both the University of Warwick and the University of Worcester. His current research covers virus-plant interactions, RNA signalling in plant development, and the development of virus technology in plant functional genomics and crop improvement.
