The Tomato Genome

This book describes the strategy used for sequencing, assembling and annotating the tomato genome and presents the main characteristics of this sequence with a special focus on repeated sequences and the ancestral polyploidy events. It also includes the chloroplast and mitochondrial genomes. Tomato (Solanum lycopersicum) is a major crop plant as well as a model for fruit development, and the availability of the genome sequence has completely changed the paradigm of the species’ genetics and genomics. The book describes the numerous genetic and genomic resources available, the identified genes and quantitative trait locus (QTL) identified, as well as the strong synteny across Solanaceae species. Lastly, it discusses the consequences of the availability of a high-quality genome sequence of the cultivated species for the research community. It is a valuable resource for students and researchers interested in the genetics and genomics of tomato and Solanaceae.

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.

This book gathers the latest information on the organization of genomes in wild Solanum species and emphasizes how this information is yielding direct outcomes in the fields of molecular breeding, as well as a better understanding of both the patterns and processes of evolution. Cultivated Solanums, such as potato, tomato, and pepper, possess a high number of wild relatives that are of great importance for practical breeding and evolutionary studies. Their germplasm is often characterized by allelic diversity, as well as genes that are lacking in the cultivated species. Wild Solanums have not been fully exploited by breeders. This is mainly due to the lack of information regarding their genetics and genomics. However, the genome of important cultivated Solanaceae such as potato, tomato, eggplant, and pepper has already been sequenced. On the heels of these recent developments, wild Solanum genomes are now becoming available, opening an exciting new era for both basic research and varietal development in the Solanaceae.

The present volume includes the large majority of papers given at the symposium entitled "Fundamental Approaches to Plant and Animal Improvement," held at Cali, Colombia, in November, 1972. The primary focal points were on various genetic mechanisms, including gene action and mutation, the development of phenotypic attributes, and on evolution, including that controlled by man for agricultural purposes. In fact, very little referring in any particular way to animal improvement was included, while a great deal of attention was paid to higher plants and to microorganisms. On the other hand, both the population genetics of insects and insect control were considered. Thus Genes, Enzymes, and Populations, the title given to this published work, seems to me to represent somewhat more fairly the contents than does the original symposium title. Given the intent of the symposium, which is expressed in the original title, the published record cannot be expected to be a neatly packaged presentation of some highly defined subject matter. Indeed the diverse subjects represent some, but by no means all, of the varied and dynamic scientific activities that need to be components in the improvement and production of agriculturally Significant plants at a time when world populations are rapidly increasing and shortages of food occurring. In any case, the organizers of the symposium wisely decided that considerations of environment as well as of genetics should be introduced into the thinking of the group and that physiology and molecular biology could not be ignored.

The use of homologous recombination to precisely modify plant genomes has been challenging, due to the lack of efficient methods for delivering DNA repair templates to plant cells. Even with the advent of sequence-specific nucleases, which stimulate homologous recombination at predefined genomic sites by creating targeted DNA double-strand breaks, there are only a handful of studies that report precise editing of endogenous genes in crop plants. More efficient methods are needed to modify plant genomes through homologous recombination, ideally without randomly integrating foreign DNA. High-frequency, precise modification of the tomato genome was achieved using geminivirus replicons, suggesting that these vectors can overcome the efficiency barrier that has made gene targeting in plants challenging. This work provides a foundation for efficient genome editing of crop genomes without the random integration of foreign DNA.

PlantOmics: The Omics of Plant Science provides a comprehensive account of the latest trends and developments of omics technologies or approaches and their applications in plant science. Thirty chapters written by 90 experts from 15 countries are included in this state-of-the-art book. Each chapter describes one topic/omics such as: omics in model plants, spectroscopy for plants, next generation sequencing, functional genomics, cyto-metagenomics, epigenomics, miRNAomics, proteomics, metabolomics, glycomics, lipidomics, secretomics, phenomics, cytomics, physiomics, signalomics, thiolomics, organelle omics, micro morphomics, microbiomics, cryobionomics, nanotechnology, pharmacogenomics, and computational systems biology for plants. It provides up to date information, technologies, and their applications that can be adopted and applied easily for deeper understanding plant biology and therefore will be helpful in developing the strategy for generating cost-effective superior plants for various purposes. In the last chapter, the editors have proposed several new areas in plant omics that may be explored in order to develop an integrated meta-omics strategy to ensure the world and earth’s health and related issues. This book will be a valuable resource to students and researchers in the field of cutting-edge plant omics.

Recent major advances in the field of comparative genomics and cytogenomics of plants, particularly associated with the completion of ambitious genome projects, have uncovered astonishing facets of the architecture and evolutionary history of plant genomes. The aim of this book was to review these recent developments as well as their implications in our understanding of the mechanisms which drive plant diversity. New insights into the evolution of gene functions, gene families and genome size are presented, with particular emphasis on the evolutionary impact of polyploidization and transposable elements. Knowledge on the structure and evolution of plant sex chromosomes, centromeres and microRNAs is reviewed and updated. Taken together, the contributions by internationally recognized experts present a panoramic overview of the structural features and evolutionary dynamics of plant genomes.This volume of Genome Dynamics will provide researchers, teachers and students in the fields of biology and agronomy with a valuable source of current knowledge on plant genomes.

For the last eighteen years we have been deeply involved in a cooperative effort with our Latin American colleagues in genetics, biochemistry, physiology, and molecular biology. We have been in close contact with scientists in a number of centers and have helped to organize symposia, workshops, and so forth, in an effort to accelerate their development and make their substantial work known. These symposia in Latin America have been quite successful. The fifteenth will take place in Brasilia in 1977. At the request of colleagues, we are in the process of developing a similar series in Asia. The first very successful symposium was held in Calcutta in 1973. We were most pleased when Dr. Amir Muhammed, Vice Chancellor of the University of Agriculture, Lyallpur suggested that we hold a symposium on a topic of great importance to Pakistan, Genetic Control of Diversity in Plants, under the auspices of the University of Agriculture. It is our hope that this symposium will be followed by additional ones in Pakistan as well as in other countries in the Far East. Leadership is quickly developing in the hands of outstanding scientists in these countries, and we appreciate the opportunity to cooperate with them. We are especially grateful to the Natiohal Science Foundation for makingPL- 480 funds available which made this symposium possible.