Liedl B.E., Labate J.A., Stommel J.R., Slade A., Kole C. (eds.) Genetics, Genomics, and Breeding of Tomato

CRC Press, 2013. — 520 p. — (Series: Genetics, Genomics and Breeding of Crop Plants).
ISBN-13: 978-1-4665-6325-4 (eBook - PDF)This volume covers the advances in the study of tomato diversity and taxonomy. It examines the mapping of simple and complex traits, classical genetics and breeding, association studies, molecular breeding, positional cloning, and structural and comparative genomics. The contributors also discuss transcriptomics, proteomics, metabolomics, and bioinformatics. The information in this book will be useful to researchers working on other Solanaceaous crops as well as those interested in using the tomato as a model crop species.Contents:
Basic Information about Tomatoes and the Tomato Group (Ana Caicedo and Iris Peralta).Economic and Nutritional Importance of Tomato.
Academic Importance of Tomato and its Wild Relatives.
Taxonomy and Evolution.
Botanical Descriptions.
Ecology and Biodiversity of the Tomato Clade.
Tomato Domestication and Dissemination.
Tomato Breeding and Research Resources.
Classical Genetics and Traditional Breeding (John W. Scott, James R. Myers, Peter S. Boches, Courtland G. Nichols and Frederic F. Angell).Classical Mapping Efforts with Morphological and Isozyme Markers.
Limitations of Classical Endeavors and Utility of Molecular Mapping.
Classical Tomato Breeding Achievements.
Breeding Objectives Positive and Negative.
Limitations of Traditional Breeding and Rationale for Molecular Breeding.
Diversity within Cultivated Tomato (Esther van der Knaap, Claire Anderson and Gustavo Rodriguez).Phenotypic Analysis of Tomato Fruit.
The Effect of the Tomato Shape Genes on Fruit Morphology.
Genotype-Based Diversity Analysis.
Genetic Diversity within Cultivated Tomato Germplasm.
Future Prospects.
Molecular Markers, Genetic Maps and Association Studies in Tomato (Martin W. Ganal).Molecular Markers for Tomato Genome Mapping and Marker/Trait Association Studies.
Genetic Maps and Available Markers.
Population Structure, Linkage Disequilibrium and Association of Markers and Traits.
Future Developments.
Mapping and Tagging of Simply Inherited Traits (Ilan Levin and Arthur A. Schaffer).Importance of the Simply Inherited Traits.
Genetic and Molecular Dissection of Simply Inherited Traits.
Identification of Markers Linked to Traits of Interest.
Use of Genomics Tools for Mapping.
Simply Inherited Traits Associated with Fruit Nutritional Quality.
Simply Inherited Traits Associated with Fruit Taste: Brix, Sugars, Acids and Aroma Volatiles.Molecular Mapping of Complex Traits in Tomato (Silvana Grandillo, Pasquale Termolino and Esther van der Knaap).Populations used for QTL Mapping.
Framework Maps and Markers.
QTL Mapping Approaches and Software.
Introgression Line Mapping and Breeding Approach.
Interactions between QTL and Genetic Background.
MAS and QTL Pyramiding.
Mendelizing QTLs.
QTL Mapping on a Trait Basis.
Conclusions and Future Prospects.
Molecular Breeding (Emidio Sabatini, Massimiliano Beretta, Tea Sala, Nazareno Acciarri, Justyna Milc and Nicola Pecchioni).Germplasm Characterization and Exploitation.
Marker-Assisted Trait Introgression.
Advantages, Limitations and Prospects of MAS.
Transgenic Breeding.
Concluding Remarks.
Positional Cloning Strategies in Tomato (Cornelius S. Barry).Mutant Collections.
Strategies for Generating Mapping Populations.
Strategies for Extracting DNA for Genetic Mapping.
Molecular Markers.
Assigning Loci to Chromosomal Regions.
Fine Genetic Mapping.
Resources for Generating Physical Maps.
Identification and Confirmation of Candidate Genes.
The Impact of an Emerging Genome Sequence.
Alternative Strategies for Identification of Mutant Loci.
Future Perspectives.
Structural Genomics: Studying Variation in Gene Sequences (Allen E. Van Deynze, Theresa Hill and Hamid Ashrafi).Sources of Sequence.
Targeted Marker Discovery.The Tomato Genome Sequencing Project (Lukas A. Mueller).Sequencing Strategy.
Genome Annotation by ITAG.Comparative Genome Sequencing of Tomato and Potato: Methods and Analysis (Sanwen Huang and Zhong-hua Zhang).A Pipeline for the Comparative Sequencing of Tomato and Potato Genomes.
Advantages of Comparative Genome Sequencing.
Comparative Analysis of Syntenic Clones Obtained from Comparative Sequencing.
Limitations and Opportunities.
Developments in Tomato Transcriptomics (Antonio J. Matas, Zhangjun Fei, James J. Giovannoni and Jocelyn K.C. Rose).Transcriptomics Tools Developed.
Advances in Sequencing Technologies.
Bioinformatic Challenges and Data Analysis.
Use of Related Species Resources.
Application of Functional Genomics in Genomics-Assisted Breeding.Proteomics and Metabolomics (Mireille Faurobert, Yoko Iijima and Koh Aoki).Tomato Proteomics: Techniques, Applications, and QTL Analyses.
Tomato Metabolomics: Techniques, Applications, and QTL Analyses.
Application in Phenomics-Assisted Breeding.
Role of Bioinformatics as a Tool in Tomato Research (Catherine M. Ronning).Gene and Genome Databases.
Comparative Genome Databases.
Gene Expression Databases.
Molecular Marker and Genetic Map Databases.
Protein and Metabolome Databases.
Integration of Different Data Types.