Bücher der Reihe Compendium of Plant Genomes

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 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 sheds new light on the chickpea genome sequencing and resequencing of chickpea germplasm lines and provides insights into classical genetics, cytogenetics, and trait mapping.

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 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 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.

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 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.

Pigeonpea (Cajanus cajan) is a crop of small land holding farmers in arid and semi-arid regions of the world. It has a number of usages starting from protein rich food to vegetarian families; fuel wood; nitrogen supplier to soil; recycling minerals in soil to animal feed etc. Pigeonpea has been considered to be originated and domesticated in central India from where it travelled to different parts of the world such as Africa and Latin America. In ongoing scenario of climate change, biotic and especially abiotic stresses will make the conditions more challenging for entire agriculture. This volume focusing on the pigeonpea genome will collate the information on the genome sequencing and its utilization in genomics activities, with a focus on the current findings, advanced tools and strategies deployed in pigeonpea genome sequencing and analysis, and how this information is leading to direct outcomes for plant breeders and subsequently to farmers.

This book describes the sequencing efforts for Neem (Azadirachta indica A. Juss), one of the most versatile tropical evergreen tree species. The neem tree is a source of various natural products, including the potent biopesticide azadirachtin and limonoids, which have a broad spectrum of activity against insect pests and microbial pathogens. To identify genes and pathways in neem, three neem genomes and several transcriptomes are studied using next-generation sequencing technologies.Neem has been extensively used in Ayurveda, Unani and homoeopathic medicine and is often referred to as the 'village pharmacy' by natives due to its wealth of medicinal properties.Besides the description of the genome, this book discusses the neem microbiome and its role in the production of neem metabolites like salanin, nimbin and exopy-azadirachtin under in vitro conditions. It also highlights cell and tissue culture using various neem explants including the leaf, root, shoot, cambium, etc.

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.

The carrot genome was sequenced in 2016, and its relatively small diploid genome, combined with the fact that it is the most complete root crop genome released to date and the first-ever Euasterid II genome to be sequenced, mean the carrot has an important role in the study of plant development and evolution.

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 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.

The book discusses the importance of eggplant (Solanum melongena L.) as a crop, highlighting the potential for eggplant to serve as a model for understanding several evolutionary and taxonomic questions. It also explores the genomic make-up, in particular in comparison to other Solanaceous crops, and examines the parallels between eggplant and tomato domestication as well as between the most common eggplant species and two related eggplants native to Africa (Ethiopian eggplant [Solanum aethiopicum L.] and African eggplant [Solanum macrocarpon L.]).The eggplant genome was first sequenced in 2014, and an improved version was due to be released in 2017. Further investigations have revealed the relationships between wild species, domesticated eggplant, and feral weedy eggplant (derived from the domesticate), as well as targets of selection during domestication. Parallels between eggplant and tomato domestication loci are well known and the molecular basis is currently being investigated.Eggplant is a source of nutrition for millions of people worldwide, especially in Southeast Asia where it is a staple food source. Domesticated in the old world, in contrast to its congeners tomato and potato, the eggplant is morphologically and nutritionally diverse. The spread of wild eggplants from Africa is particularly interesting from a cultural point of view. This book brings together diverse fields of research, from bioinformatics to taxonomy to nutrition to allow readers to fully understand eggplant¿s importance and potential.

mume genome with available data, scientists have succeeded in reconstructing nine ancestral chromosomes of the Rosaceae family, as well as the chromosome fusion, fission and duplication history of three major subfamilies.

Further, it describes the current genomics applications of these findings, and efforts to sequence new genomes within the family. These academic and commercial interests have led to international efforts to sequence the Spirodela polyrhiza genome, the smallest and most ancient genome in the family.

Addressing the pear genome, this book covers the current state of knowledge regarding genetic and genomic resources, breeding approaches and strategies, as well as cutting-edge content on how these tools and resources are being / soon will be utilized to pursue genetic improvement efforts that will combine fruit quality, high productivity, precocious fruit bearing, and long postharvest storage life, along with elevated levels of resistance to various major diseases and insect pests. Throughout, the book also explores potential opportunities and challenges in genomic analysis, sequence assembly, structural features, as well as functional studies that will assist in future genetic improvement efforts for pears. The pear (Pyrus), an important tree fruit crop, is grown worldwide, and has several economically relevant cultivars. In recent years, modern genetic and genomic tools have resulted in the development of a wide variety of valuable resources for the pear. In the past few years, completion of whole genome assemblies of 'Dangshansuli', an Asian pear, and 'Bartlett', a European pear, have paved the way for new discoveries regarding for example, the pear's genomic structure, chromosome evolution, and patterns of genetic variation. This wealth of new resources will have a major impact on our knowledge of the pear genome; in turn, these resources and knowledge will have significant impacts on future genetic improvement efforts.

This book is the first comprehensive compilation of deliberations on whole genome sequencing of sesame including genome assembly, annotation, structure and synteny analysis, and sequencing of its chloroplast genome and also its wild species.

This book provides an overview of the Ocimum genus from its genetic diversity to genome sequences, metabolites and their therapeutic utilities. The plants of this genus Ocimum are collectively referred to as Basil and holy basil is worshipped in the Hindu religion.

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 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 contains complete information on Capsicum genetic resources, diversity, evolution, history and advances in capsicum improvement from classical breeding to whole genome sequencing, genomics, databases and its impact on next generation pepper breeding.

cepa and its functional study, scientists in international research collaborations have developed several types of artificially manipulated genetic stocks and analyzed them using modern technologies.The Allium vegetable crop includes garlic, shallot, wakegi onion, Japanese bunching onion, and rakkyo.

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

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.