BookDario Cantu, M. Andrew Walker, editors.
Summary: This book describes the current state of international grape genomics, with a focus on the latest findings, tools and strategies employed in genome sequencing and analysis, and genetic mapping of important agronomic traits. It also discusses how these are having a direct impact on outcomes for grape breeders and the international grape research community. While V. vinifera is a model species, it is not always appreciated that its cultivation usually requires the use of other Vitis species as rootstocks. The book discusses genetic diversity within the Vitis genus, the available genetic resources for breeding, and the available genomic resources for other Vitis species. Grapes (Vitis vinifera spp. vinifera) have been a source of food and wine since their domestication from their wild progenitor (Vitis vinifera ssp. sylvestris) around 8,000 years ago, and they are now the worlds most valuable horticultural crop. In addition to being economically important, V. vinifera is also a model organism for the study of perennial fruit crops for two reasons: Firstly, its ability to be transformed and micropropagated via somatic embryogenesis, and secondly its relatively small genome size of 500 Mb. The economic importance of grapes made V. vinifera an obvious early candidate for genomic sequencing, and accordingly, two draft genomes were reported in 2007. Remarkably, these were the first genomes of any fruiting crop to be sequenced and only the fourth for flowering plants. Although riddled with gaps and potentially omitting large regions of repetitive sequences, the two genomes have provided valuable insights into grape genomes. Cited in over 2,000 articles, the genome has served as a reference in more than 3,000 genome-wide transcriptional analyses. Further, recent advances in DNA sequencing and bioinformatics are enabling the assembly of reference-grade genome references for more grape genotypes revealing the exceptional extent of structural variation in the species.
Contents:
Intro; Preface to the Series; Preface; Contents; Abbreviations; 1 Grapes in the World Economy; Abstract; 1.1 Grapes in the World Economy; 1.1.1 Grape Production and Utilization; 1.1.2 Many Diverse Varieties; 1.1.3 The Value of Diverse Varieties; 1.1.4 The Demand for Varieties; 1.1.5 Government Intervention; 1.2 Conclusion; Acknowledgements;
Appendix 1: Data Resources; References; 2 Grape Taxonomy and Germplasm; Abstract; 2.1 Introduction; 2.2 North American Vitis; 2.2.1 Series Labruscae; 2.2.2 Series Aestivales; 2.2.3 Series Cinerascentes; 2.2.4 Series Vulpinae; 2.2.5 Series Precoces 2.2.6 Series Occidentales2.3 Subgenus Muscadinia; References; 3 Evolutionary Genomics and the Domestication of Grapes; Abstract; 3.1 Introduction; 3.2 Four Stages of Domestication; 3.2.1 Stage 1: Management Prior to Cultivation; 3.2.2 Stage 2: Purposeful Cultivation; 3.2.3 Stage 3: Geographic Expansion with Introgression as a Means of Local Adaptation; Acknowledgements; References; 4 Grape Archaeology and Ancient DNA Sequencing; Abstract; 4.1 Grape Archaeology; 4.1.1 Archaeological Evidences of the Wine Culture in the Near East and Mediterranean Region; 4.1.2 Wine Culture in Ancient Egypt 4.1.3 Grape and Wine Iconography from Ancient Egypt4.1.4 Wine Archaeology from Ancient Egypt; 4.2 Chemical and Morphometric Analyses of Grapes and Wine Samples; 4.3 Ancient DNA Sequencing; 4.3.1 DNA Preservation of Archaeological Material; 4.3.2 Ancient DNA Studies in Plant Archaeology; 4.4 Future Perspectives; Acknowledgements; References; 5 Strategies for Sequencing and Assembling Grapevine Genomes; Abstract; 5.1 Introduction; 5.2 Major Factors Influencing Nucleic Acids Isolation from Grapevine; 5.2.1 Tissue Collection; 5.2.2 Tissue Disruption; 5.2.3 Removal of Contaminants 5.2.4 Nucleic Acid Precipitation5.2.5 Nucleic Acids Quantity and Quality Evaluation; 5.3 Sequencing and Assembly of Grape Genomes; 5.3.1 Sequencing Methods Used in Grape Genomics; 5.3.2 Assembly Methods Used in Grape Genomics; 5.4 Conclusions; Acknowledgements; References; 6 The Grapevine Genome Annotation; Abstract; 6.1 Introduction; 6.2 Automatic Annotation in Grapevine; 6.3 New Gene Discovery Through Manual Curation; 6.4 Gene Nomenclature for Improving Data Description and Interoperability; 6.5 Proteogenomics-Based Annotation; 6.6 Annotation of Non-coding Transcriptome 6.7 Future Perspective for Improving the Annotation6.8 Conclusions; References; 7 Molecular Mapping of Grapevine Genes; Abstract; 7.1 Introduction; 7.2 The Variety of Genetic Markers: Development and Screening; 7.2.1 Genetic Variant Discovery; 7.2.2 Molecular Marker Localization; 7.2.3 Genotyping Tools; 7.3 Parental, Consensus and Integrated Genetic Maps; 7.3.1 General Map Building Principles and Implementation; 7.3.2 Specificities for Outbred Species; 7.3.3 An Overview of Published Vitis Genetic Maps; 7.4 Quantitative Trait Loci (QTLs) Mapping Studies; 7.4.1 QTL Detection Approaches