Bücher der Reihe Compendium of Plant Genomes

This book describes the historical importance of potato (Solanum tuberosum L.),potato genetic resources and stocks (including S. tuberosum group Phureja DM1-3 516 R44, a unique doubled monoploid homozygous line) used for potato genome sequencing. It also discusses strategies and tools for high-throughput sequencing, sequence assembly, annotation, analysis, repetitive sequences and genotyping-by-sequencing approaches. Potato (Solanum tuberosum L.; 2n = 4x = 48) is the fourth most important food crop of the world after rice, wheat and maize and holds great potential to ensure both food and nutritional security. It is an autotetraploid crop with complex genetics, acute inbreeding depression and a highly heterozygous nature. Further, the book examines the recent discovery of whole genome sequencing of a few wild potato species genomes, genomics in management and genetic enhancement of Solanum species, new strategies towards durable potato late blight resistance, structural analysis of resistance genes, genomics resources for abiotic stress management, as well as somatic cell genetics and modern approaches in true-potato-seed technology. The complete genome sequence provides a better understanding of potato biology, underpinning evolutionary process, genetics, breeding and molecular efforts to improve various important traits involved in potato growth and development.

This book collates the most up to date information on Fragaria, and Rubus genomes. It focuses on the latest advances in the model system Fragaria vesca, along with the allied advances in economically important crops. Covering both basic and applied aspects of crop genomics, it illustrates strategies and resources for the study and utilization of genome sequences and aligned functional genomics resources.Rosaceous berries are collectively an increasingly important set of high-value global crops, with a trade value of over £2 billion dollars per annum. The rosaceous berries strawberry, raspberry and blackberry share some common features at the genome scale, namely a range of ploidy levels in each genus and high levels of heterozygosity (and associated inbreeding depression) due to self-incompatibility systems, dioecy, or multispecies hybridization events. Taken together, although the genomes are relatively compact, these biological features lead to significant challenges in the assembly and analysis of berry genomes, which until very recently have hampered the progress of genome-level studies.The genome of the woodland strawberry, Fragaria vesca, a self-compatible species with a homozygous genome was first sequenced in 2011 and has served as a foundation for most genomics work in Fragaria and to some extent Rubus. Since that time, building upon this resource, there have been significant advances in the development of genome sequences for related crop species. This, coupled with the revolution in affordable sequencing technology, has led to a suite of genomics studies on Fragaria and more recently Rubus, which undoubtedly aid crop breeding and production in future years.

This book presents an overview of the state-of-the-art in barley genome analysis, covering all aspects of sequencing the genome and translating this important information into new knowledge in basic and applied crop plant biology and new tools for research and crop improvement.

This book addresses various aspects of the current castor bean research, including genetics, biotechnology, comparative genomics, and more specific topics such as oil metabolism and the ricin toxin.

This book discusses advances in our understanding of the structure and function of the maize genome since publication of the original B73 reference genome in 2009, and the progress in translating this knowledge into basic biology and trait improvement.

This book offers comprehensive information on the genomics of spruces (Picea spp.), naturally abundant conifer tree species that are widely distributed in the Northern Hemisphere. Due to their tremendous ecological and economic importance, the management of forest genetic resources has chiefly focused on conservation and tree improvement. A draft genome sequence of the 20-gigabase Norway spruce genome was published in the journal Nature in 2013. Continuous efforts to improve the spruce genome assembly are underway, but are hindered by the inherent characteristics of conifer genomes: high amounts of repetitive sequences (introns and transposable elements) in the genome and large gene family expansions with regards to abiotic stress, secondary metabolism and spruces'' defense responses to pathogens and herbivory. This book presents the latest information on the status of genome assemblies, provides detailed insights into transposable elements and methylation patterns, and highlights the extensive genomic resources available for inferring population genomics and climate adaptation, as well as emerging genomics tools for tree improvement programs. In addition, this volume features whole-genome comparisons among conifer species, and demonstrates how functional genomics can be used to improve gene function annotations. The book closes with an outlook on emerging fields of research in spruce genomics.

This book reviews how the release of the citrus genome facilitates the investigation of ancestral species, the study of their complex biological features, and the genetic basis of agronomic traits of paramount importance for their sustainable cultivation. The first chapters discuss citrus origin and distribution, and the economic importance and varietal composition of the cultivated species, providing an overview of citrus and related genera genetic resources. The book then describes the role of traditional breeding techniques (for scion and rootstocks) as well as the potential of genomic breeding and innovative protocols for biotechnological approaches. The second part provides essential information on the genus Citrus, the attributes of pure citrus species, genetic admixtures, hybrids and citrus relatives, and on the horticultural classification of cultivated species, varieties and rootstocks. The third part then focuses on the different molecular mechanisms, covering various aspects of citrus biology, including the role of beneficial compounds of citrus fruits. In addition, it examines the molecular responses of citrus to abiotic stresses and to field and post-harvest diseases. Providing insights gained in recent years, it is a valuable guide for those who are interested in gene discovery, comparative genomics, molecular breeding and new breeding techniques. It is particularly useful for scientists, breeders and students at universities and public sector institutes involved in research for the citrus industry.

This book on lupin genomics primarily focuses on the narrow-leafed lupin (NLL), and details the genomic resources that have been developed and how they are currently being used to help advance both fundamental and applied research on NLL in areas ranging from its domestication to plantΓÇômicrobe interactions and syntenic relationships between NLL and other legume crops. It also reports on genomic efforts being pursued with regard to other lupin crops.Lupins are important ecological ΓÇÿengineersΓÇÖ: they can colonise and thrive in low-nutrient soils due to their ability to fix atmospheric nitrogen in symbiosis with bacteria and efficiently take up phosphorous. Recently, lupins have attracted considerable interest, not only because of their value for sustainable farming as a break crop, but also as a potential ΓÇÿsuper foodΓÇÖ for fighting major health issues in connection with diabetes and obesity.Narrow-leafed lupin is the main grain legume crop, grown primarily in Australia, and was therefore selected for the development of a reference lupin genome and associated genomic resources. Its genome has recently been sequenced with a focus on the gene-rich space, which has advanced the development of new breeding tools for the improvement of NLL and related lupin crops.

This book compiles the fundamental advances resulting from of oil-palm genome and transcriptome sequencing, and describes the challenges faced and strategies applied in sequencing, assembling and annotating oil palm genome sequences.

This book collates the most up to date information on Fragaria, and Rubus genomes. It focuses on the latest advances in the model system Fragaria vesca, along with the allied advances in economically important crops. Covering both basic and applied aspects of crop genomics, it illustrates strategies and resources for the study and utilization of genome sequences and aligned functional genomics resources.Rosaceous berries are collectively an increasingly important set of high-value global crops, with a trade value of over £2 billion dollars per annum. The rosaceous berries strawberry, raspberry and blackberry share some common features at the genome scale, namely a range of ploidy levels in each genus and high levels of heterozygosity (and associated inbreeding depression) due to self-incompatibility systems, dioecy, or multispecies hybridization events. Taken together, although the genomes are relatively compact, these biological features lead to significant challenges in the assembly and analysis of berry genomes, which until very recently have hampered the progress of genome-level studies.The genome of the woodland strawberry, Fragaria vesca, a self-compatible species with a homozygous genome was first sequenced in 2011 and has served as a foundation for most genomics work in Fragaria and to some extent Rubus. Since that time, building upon this resource, there have been significant advances in the development of genome sequences for related crop species. This, coupled with the revolution in affordable sequencing technology, has led to a suite of genomics studies on Fragaria and more recently Rubus, which undoubtedly aid crop breeding and production in future years.

This book presents the first comprehensive compilation of genome research on the Hevea brasiliensis rubber tree.

While genetic maps, transcriptomes, and physical maps of BAC libraries have significantly enhanced our understanding of the tobacco plant, the genome of tobacco and related Nicotiana species has opened a new era in modern tobacco research.

This book describes how the genome sequence contributes to our understanding of allopolyploidisation and the genome evolution, genetic diversity, complex trait regulation and knowledge-based breeding of this important crop.

This book presents an overview of the state-of-the-art in barley genome analysis, covering all aspects of sequencing the genome and translating this important information into new knowledge in basic and applied crop plant biology and new tools for research and crop improvement.

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.

This book presents the current state of the art in peanut genomics, focusing particularly on the latest genomic findings, tools and strategies employed in genome sequencing, transcriptomes and analysis, availability of public and private genomic resources, and ways to maximize the use of this information in peanut breeding programs.

This book provides insights into some of the key achievements made in the study of Lotus japonicus (birdsfoot trefoil), as well as a timely overview of topics that are pertinent for future developments in legume genomics.

The Brassica Rapa Genome

This book describes the basic botanical features of kiwifruit and its wild relatives, reports on the steps that led to its genome sequencing, and discusses the results obtained with the assembly and annotation. The core chapters provide essential insights into the main gene families that characterize this species as a crop, including the genes controlling sugar and starch metabolism, pigment biosynthesis and degradation, the ascorbic-acid pathway, fruit softening and postharvest metabolism, allergens, and resistance to pests and diseases.The book offers a valuable reference guide for taxonomists, geneticists and horticulturists. Further, since information gained from the genome sequence is extraordinarily useful in assessing the breeding value of individuals based on whole-genome scans, it will especially benefit plant breeders. Accordingly, chapters are included that focus on gene introgression from wild relatives and genome-based breeding.

This book describes how the genome sequence contributes to our understanding of allopolyploidisation and the genome evolution, genetic diversity, complex trait regulation and knowledge-based breeding of this important crop.

The advent of affordable whole genome sequencing in combination with existing cereal functional genomics data has enabled the leveraging of the significant novel diversity available in sorghum, the genome of which was fully sequenced in 2009, providing an unmatched resource for the genetic improvement of sorghum and other grass species.

This book presents the genetics and genomics of Jatropha, which is used for biofuel, and shows how plant genomics can be used to improve plant breeding.

This book provides an introduction to the genetics, genomics, and breeding of the olive tree, a multi-functional long-lived crop plant that is relevant not only for culinary olive and oil production, but also for shaping the landscape and history of many rural areas for centuries.

This book provides insights into some of the key achievements made in the study of Lotus japonicus (birdsfoot trefoil), as well as a timely overview of topics that are pertinent for future developments in legume genomics.

This book summarizes the latest information and the status quo of radish genome studies to stimulate innovations and improvements in breeding techniques and to promote further advances in the field. Radish (Raphanus sativus) is a member of the Brassicaceae family and is cultivated worldwide.

This book provides insights into the genetics and the latest advances in genomics research on the common bean, offering a timely overview of topics that are pertinent for future developments in legume genomics.

This book examines the application of soybean genome sequences to comparative, structural, and functional genomics.

This book focuses on the latest genome sequencing of the 25 wild Oryza species, public and private genomic resources, and their impact on genetic improvement research.

This book presents up-to-date information on foxtail millet genomics, with a particular focus on its agronomic importance, genome architecture, marker development, evolutionary and diversity studies, comparative genomics and stress biology.