From Plant Genomics to Plant Biotechnology

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. Dr Natalija Burbulisis currently head of the agrobiotechnology laboratory and professor at the Crop Science and Animal Husbandry Department of the Aleksandr Stulginskis University (Lithuania). She holds a Ph.D. in Agricultural science obtained from the Lithuanian University of Agriculture, and for 10 years performed research in plant biotechnology, physiology and biochemistry. Current studies are in vitro selection of oilseed crops (rapeseed and linseed) - genotypes with important agronomic traits, including disease resistance, cold tolerance and oil quality improvements. Professor Corrado Fogher, Ph.D., is Associate professor of genetics and responsible for the transgenic plants sector at the Observatory on Transgenic Organisms in Agriculture at the Catholic University, 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 is Author or co-author of more than 70 peer-reviewed papers and Research Director of three SMEs, Plantechno, Incura and SunChem.

• List of figuresList of tablesAbbreviationsAbout the contributorsIntroductionChapter 1: From plant genomics to -omics technologiesAbstract:1.1 SuperSAGE1.2 CAGE – cap analysis of gene expression1.3 -Omics and new advances in plant functional genomicsChapter 2: Plant microRNAsAbstract:2.1 Introduction2.2 Transcription of miRNA genes2.3 MicroRNA processing2.4 Modes of action2.5 Evolution of miRNA genes2.6 Differences from animal miRNAs2.7 miRNA functions2.8 The potential roles of microRNAs in crop improvementChapter 3: Epigenetic control by plant Polycomb proteins: new perspectives and emerging roles in stress responseAbstract:3.1 Introduction3.2 Conserved multi-protein complexes with histone post-translational modifying activities3.3 Polycomb functions in plant development3.4 Non-coding RNAs as regulatory cofactors of Polycomb complexes3.5 Emerging roles of PcG and ncRNAs in responses to environmental stress3.6 PcG protein functions in three-dimensional nuclear organization3.7 Perspectives: the role of Polycomb in abiotic and biotic stress responseChapter 4: Metabolite profiling for plant researchAbstract:4.1 Introduction4.2 Methodological approach4.3 Metabolomic platform4.4 Metabolomics in plant science4.5 The future role of metabolomics in crop improvement4.6 ConclusionChapter 5: The uniqueness of conifersAbstract:5.1 Introduction5.2 Functional differentiation5.3 Genome structure and composition5.4 Genome function5.5 Chemical divergence5.6 Meeting the challenge: the system biology approach to unraveling the conifer genomeChapter 6: Cryptochrome genes modulate global transcriptome of tomatoAbstract:6.1 Introduction6.2 Cryptochrome functions6.3 Role of cryptochromes in mediating light-regulated gene expression in plants6.4 Cryptochromes influence the diurnal global transcription profiles in tomatoChapter 7: Genomics of grapevine: from genomics research on model plants to crops and from science to grapevine breedingAbstract:7.1 Use of genetic and molecular markers for studies of genetic diversity and genome selection in grapevine7.2 Grapevine breeding7.3 Transgene silencing7.4 Identification and characterization of transgene insertion loci7.5 Integration of vector backbone7.6 Stability of inserted transgenes7.7 Conclusions7.8 AcknowledgementChapter 8: Grapevine genomics and phenotypic diversity of bud sports, varieties and wild relativesAbstract:8.1 Introduction8.2 Origin of Vitis vinifera, domestication, and early selection for fruit characters8.3 Sources of phenotypic variation in present-day grapevines8.4 Genomic tools in the genome sequencing era8.5 Current activities in grapevine genome analysis8.6 Bud organogenesis, somatic mutations, and DNA typing of somatic chimeras8.7 Phenotypically divergent clones and the underlying DNA variation8.8 Transposon insertion-site profiling using NGS8.9 Large structural variation using NGS8.10 Copy number variation, gene redundancy, and subtle specialisation in secondary metabolism8.11 ConclusionsChapter 9: Peach ripening transcriptomics unveils new and unexpected targets for the improvement of drupe qualityAbstract:9.1 Introduction9.2 The fruit9.3 Peach development and ripening9.4 Microarray Transcript Profiling in peach9.5 New players in the control of peach ripening9.6 Conclusions9.7 AcknowledgementsChapter 10: Application of doubled haploid technology in breeding of Brassica napusAbstract:10.1 Introduction10.2 Technique of isolated microspore culture10.3 Doubled haploid method in breeding of Brassica napus10.4 In vitro mutagenesis10.5 Utilization of double haploidy in selection for resistance10.6 Selection for modified seed oil composition10.7 Selection for improved seed meal10.8 Selection for cold tolerance10.9 Concluding remarksChapter 11: Plant biodiversity and biotechnologyAbstract:11.1 Biodiversity11.2 Biotechnology11.3 Heat stress tolerance in cereals11.4 Modern approaches in cereals for yield and food security under temperature stress11.5 Future perspectives11.6 AcknowledgmentChapter 12: Natural resveratrol bioproductionAbstract:12.1 Stilbenes and resveratrol12.2 Health benefits of resveratrol12.3 trans-resveratrol production through plant cell cultures12.4 Introducing new pathway branches to crop plants: trans-resveratrol synthesis in tomato fruits12.5 Concluding remarksIndex