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.
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. Unlimited access to a high-quality reference sequence is removing one of the major constraints in basic and applied research. This book summarizes the advanced knowledge of the composition of the barley genome, its genes and the much larger non-coding part of the genome, and how this information facilitates studying the specific characteristics of barley. One of the oldest domesticated crops, barley is the small grain cereal species that is best adapted to the highest altitudes and latitudes, and it exhibits the greatest tolerance to most abiotic stresses. With comprehensive access to the genome sequence, barley’s importance as a genetic model in comparative studies on crop species like wheat, rye, oats and even rice is likely to increase.
This detailed book presents recent methodologies for the task of inspecting the genomic world of plants, extracting valuable information, and presenting it in a readable way. With a focus on bioinformatics tools, the volume explores phylogenetics and evolution, Omics analysis, as well as experimental procedures for trait characterization. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of vital expert implementation advice that will lead to successful results. Authoritative and practical, Plant Comparative Genomics serves as an ideal resource for researchers looking to implement comparative tools in order to explore their genomic data for their daily scientific work.
Marking the change in focus of tree genomics from single species to comparative approaches, this book covers biological, genomic, and evolutionary aspects of angiosperm trees that provide information and perspectives to support researchers broadening the focus of their research. The diversity of angiosperm trees in morphology, anatomy, physiology and biochemistry has been described and cataloged by various scientific disciplines, but the molecular, genetic, and evolutionary mechanisms underlying this diversity have only recently been explored. Excitingly, advances in genomic and sequencing technologies are ushering a new era of research broadly termed comparative genomics, which simultaneously exploits and describes the evolutionary origins and genetic regulation of traits of interest. Within tree genomics, this research is already underway, as the number of complete genome sequences available for angiosperm trees is increasing at an impressive pace and the number of species for which RNAseq data are available is rapidly expanding. Because they are extensively covered by other literature and are rapidly changing, technical and computational approaches—such as the latest sequencing technologies—are not a main focus of this book. Instead, this comprehensive volume provides a valuable, broader view of tree genomics whose relevance will outlive the particulars of current-day technical approaches. The first section of the book discusses background on the evolution and diversification of angiosperm trees, as well as offers description of the salient features and diversity of the unique physiology and wood anatomy of angiosperm trees. The second section explores the two most advanced model angiosperm tree species (poplars and eucalypts) as well as species that are soon to emerge as new models. The third section describes the structural features and evolutionary histories of angiosperm tree genomes, followed by a fourth section focusing on the genomics of traits of biological, ecological, and economic interest. In summary, this book is a timely and well-referenced foundational resource for the forest tree community looking to embrace comparative approaches for the study of angiosperm trees.
Applied plant genomics and biotechnology reviews the recent advancements in the post-genomic era, discussing how different varieties respond to abiotic and biotic stresses, investigating epigenetic modifications and epigenetic memory through analysis of DNA methylation states, applicative uses of RNA silencing and RNA interference in plant physiology and in experimental transgenics, and plants modified to produce high-value pharmaceutical proteins. The book provides an overview of research advances in application of RNA silencing and RNA interference, through Virus-based transient gene expression systems, Virus induced gene complementation (VIGC), Virus induced gene silencing (Sir VIGS, Mr VIGS) Virus-based microRNA silencing (VbMS) and Virus-based RNA mobility assays (VRMA); RNA based vaccines and expression of virus proteins or RNA, and virus-like particles in plants, the potential of virus vaccines and therapeutics, and exploring plants as factories for useful products and pharmaceuticals are topics wholly deepened. The book reviews and discuss Plant Functional Genomic studies discussing the technologies supporting the genetic improvement of plants and the production of plant varieties more resistant to biotic and abiotic stresses. Several important crops are analysed providing a glimpse on the most up-to-date methods and topics of investigation. The book presents a review on current state of GMO, the cisgenesis-derived plants and novel plant products devoid of transgene elements, discuss their regulation and the production of desired traits such as resistance to viruses and disease also in fruit trees and wood trees with long vegetative periods. Several chapters cover aspects of plant physiology related to plant improvement: cytokinin metabolism and hormone signaling pathways are discussed in barley; PARP-domain proteins involved in Stress-Induced Morphogenetic Response, regulation of NAD signaling and ROS dependent synthesis of anthocyanins. Apple allergen isoforms and the various content in different varieties are discussed and approaches to reduce their presence. Euphorbiaceae, castor bean, cassava and Jathropa are discussed at genomic structure, their diseases and viruses, and methods of transformation. Rice genomics and agricultural traits are discussed, and biotechnology for engineering and improve rice varieties. Mango topics are presented with an overview of molecular methods for variety differentiation, and aspects of fruit improvement by traditional and biotechnology methods. Oilseed rape is presented, discussing the genetic diversity, quality traits, genetic maps, genomic selection and comparative genomics for improvement of varieties. Tomato studies are presented, with an overview on the knowledge of the regulatory networks involved in flowering, methods applied to study the tomato genome-wide DNA methylation, its regulation by small RNAs, microRNA-dependent control of transcription factors expression, the development and ripening processes in tomato, genomic studies and fruit modelling to establish fleshy fruit traits of interest; the gene reprogramming during fruit ripening, and the ethylene dependent and independent DNA methylation changes. - provides an overview on the ongoing projects and activities in the field of applied biotechnology - includes examples of different crops and applications to be exploited - reviews and discusses Plant Functional Genomic studies and the future developments in the field - explores the new technologies supporting the genetic improvement of plants
A comprehensive account of genomic rearrangement, focusing on the mechanisms of inversion, translocation, gene and genome duplication and gene transfer and on the patterns that result from them in comparative maps. Includes analyses of genomic sequences in organelles, prokaryotes and eukaryotes as well as comparative maps of the nuclear genomes in higher plants and animals. The book showcases a variety of algorithmic and statistical approaches to rearrangement and map data.
The Genetics and Genomics of the Brassicaceae provides a review of this important family (commonly termed the mustard family, or Cruciferae). The family contains several cultivated species, including radish, rocket, watercress, wasabi and horseradish, in addition to the vegetable and oil crops of the Brassica genus. There are numerous further species with great potential for exploitation in 21st century agriculture, particularly as sources of bioactive chemicals. These opportunities are reviewed, in the context of the Brassicaceae in agriculture. More detailed descriptions are provided of the genetics of the cultivated Brassica crops, including both the species producing most of the brassica vegetable crops (B. rapa and B. oleracea) and the principal species producing oilseed crops (B. napus and B. juncea). The Brassicaceae also include important “model” plant species. Most prominent is Arabidopsis thaliana, the first plant species to have its genome sequenced. Natural genetic variation is reviewed for A. thaliana, as are the genetics of the closely related A. lyrata and of the genus Capsella. Self incompatibility is widespread in the Brassicaceae, and this subject is reviewed. Interest arising from both the commercial value of crop species of the Brassicaceae and the importance of Arabidopsis thaliana as a model species, has led to the development of numerous resources to support research. These are reviewed, including germplasm and genomic library resources, and resources for reverse genetics, metabolomics, bioinformatics and transformation. Molecular studies of the genomes of species of the Brassicaceae revealed extensive genome duplication, indicative of multiple polyploidy events during evolution. In some species, such as Brassica napus, there is evidence of multiple rounds of polyploidy during its relatively recent evolution, thus the Brassicaceae represent an excellent model system for the study of the impacts of polyploidy and the subsequent process of diploidisation, whereby the genome stabilises. Sequence-level characterization of the genomes of Arabidopsis thaliana and Brassica rapa are presented, along with summaries of comparative studies conducted at both linkage map and sequence level, and analysis of the structural and functional evolution of resynthesised polyploids, along with a description of the phylogeny and karyotype evolution of the Brassicaceae. Finally, some perspectives of the editors are presented. These focus upon the Brassicaceae species as models for studying genome evolution following polyploidy, the impact of advances in genome sequencing technology, prospects for future transcriptome analysis and upcoming model systems.
Pan-genomics: Applications, Challenges, and Future Prospects covers current approaches, challenges and future prospects of pan-genomics. The book discusses bioinformatics tools and their applications and focuses on bacterial comparative genomics in order to leverage the development of precise drugs and treatments for specific organisms. The book is divided into three sections: the first, an "overview of pan-genomics and common approaches, brings the main concepts and current approaches on pan-genomics research; the second, “case studies in pan-genomics, thoroughly discusses twelve case, and the last, “current approaches and future prospects in pan-multiomics , encompasses the developments on omics studies to be applied on bacteria related studies. This book is a valuable source for bioinformaticians, genomics researchers and several members of biomedical field interested in understanding further bacterial organisms and their relationship to human health. Covers the entire spectrum of pangenomics, highlighting the use of specific approaches, case studies and future perspectives Discusses current bioinformatics tools and strategies for exploiting pangenomics data Presents twelve case studies with different organisms in order to provide the audience with real examples of pangenomics applicability
This book examines the application of soybean genome sequences to comparative, structural, and functional genomics. Since the availability of the soybean genome sequence has revolutionized molecular research on this important crop species, the book also describes how the genome sequence has shaped research on transposon biology and applications for gene identification, tilling and positional gene cloning. Further, the book shows how the genome sequence influences research in the areas of genetic mapping, marker development, and genome-wide association mapping for identifying important trait genes and soybean breeding. In closing, the economic and botanical aspects of the soybean are also addressed.
Sequencing of the model plant genomes such as those of A. thaliana and rice has revolutionized our understanding of plant biology but it has yet to translate into the improvement of major crop species such as maize, wheat, or barley. Moreover, the comparative genomic studies in cereals that have been performed in the past decade have revealed the limits of conservation between rice and the other cereal genomes. This has necessitated the development of genomic resources and programs for maize, sorghum, wheat, and barley to serve as the foundation for future genome sequencing and the acceleration of genomic based improvement of these critically important crops. Cereals constitute over 50% of total crop production worldwide (http://www.fao.org/) and cereal seeds are one of the most important renewable resources for food, feed, and industrial raw materials. Crop species of the Triticeae tribe that comprise wheat, barley, and rye are essential components of human and domestic animal nutrition. With 17% of all crop area, wheat is the staple food for 40% of the world’s population, while barley ranks fifth in the world production. Their domestication in the Fertile Crescent 10,000 years ago ushered in the beginning of agriculture and signified an important breakthrough in the advancement of civilization. Rye is second after wheat among grains most commonly used in the production of bread and is also very important for mixed animal feeds. It can be cultivated in poor soils and climates that are generally not suitable for other cereals. Extensive genetics and cytogenetics studies performed in the Triticeae species over the last 50 years have led to the characterization of their chromosomal composition and origins and have supported intensive work to create new genetic resources. Cytogenetic studies in wheat have allowed the identification and characterization of the different homoeologous genomes and have demonstrated the utility of studying wheat genome evolution as a model for the analysis of polyploidization, a major force in the evolution of the eukaryotic genomes. Barley with its diploid genome shows high collinearity with the other Triticeae genomes and therefore serves as a good template for supporting genomic analyses in the wheat and rye genomes. The knowledge gained from genetic studies in the Triticeae has also been used to produce Triticale, the first human made hybrid crop that results from a cross between wheat and rye and combines the nutrition quality and productivity of wheat with the ruggedness of rye. Despite the economic importance of the Triticeae species and the need for accelerated crop improvement based on genomics studies, the size (1.7 Gb for the bread wheat genome, i.e., 5x the human genome and 40 times the rice genome), high repeat content (>80%), and complexity (polyploidy in wheat) of their genomes often have been considered too challenging for efficient molecular analysis and genetic improvement in these species. Consequently, Triticeae genomics has lagged behind the genomic advances of other cereal crops for many years. Recently, however, the situation has changed dramatically and robust genomic programs can be established in the Triticeae as a result of the convergence of several technology developments that have led to new, more efficient scientific capabilities and resources such as whole-genome and chromosome-specific BAC libraries, extensive EST collections, transformation systems, wild germplasm and mutant collections, as well as DNA chips. Currently, the Triticeae genomics "toolbox" is comprised of: - 9 publicly available BAC libraries from diploid (5), tetraploid (1) and hexaploid (3) wheat; 3 publicly available BAC libraries from barley and one BAC library from rye; - 3 wheat chromosome specific BAC libraries; - DNA chips including commercially available first generation chips from AFFYMETRIX containing 55’000 wheat and 22,000 barley genes; - A large number of wheat and barley genetic maps that are saturated by a significant number of markers; - The largest plant EST collection with 870’000 wheat ESTs, 440’000 barley ESTs and about 10’000 rye ESTs; - Established protocols for stable transformation by biolistic and agrobacterium as well as a transient expression system using VIGS in wheat and barley; and - Large collections of well characterized cultivated and wild genetic resources. International consortia, such as the International Triticeae Mapping Initiative (ITMI), have advanced synergies in the Triticeae genetics community in the development of additional mapping populations and markers that have led to a dramatic improvement in the resolution of the genetic maps and the amount of molecular markers in the three species resulting in the accelerated utilization of molecular markers in selection programs. Together, with the development of the genomic resources, the isolation of the first genes of agronomic interest by map-based cloning has been enabled and has proven the feasibility of forging the link between genotype and phenotype in the Triticeae species. Moreover, the first analyses of BAC sequences from wheat and barley have allowed preliminary characterizations of their genome organization and composition as well as the first inter- and intra-specific comparative genomic studies. These later have revealed important evolutionary mechanisms (e.g. unequal crossing over, illegitimate recombination) that have shaped the wheat and barley genomes during their evolution. These breakthroughs have demonstrated the feasibility of developing efficient genomic studies in the Triticeae and have led to the recent establishment of the International Wheat Genome Sequencing Consortium (IWGSC) (http//:www.wheatgenome.org) and the International Barley Sequencing Consortium (www.isbc.org) that aim to sequence, respectively, the hexaploid wheat and barley genomes to accelerate gene discovery and crop improvement in the next decade. Large projects aiming at the establishment of the physical maps as well as a better characterization of their composition and organization through large scale random sequencing projects have been initiated already. Concurrently, a number of projects have been launched to develop high throughput functional genomics in wheat and barley. Transcriptomics, proteomics, and metabolomics analyses of traits of agronomic importance, such as quality, disease resistance, drought, and salt tolerance, are underway in both species. Combined with the development of physical maps, efficient gene isolation will be enabled and improved sequencing technologies and reduced sequencing costs will permit ultimately genome sequencing and access to the entire wheat and barley gene regulatory elements repertoire. Because rye is closely related to wheat and barley in Triticeae evolution, the latest developments in wheat and barley genomics will be of great use for developing rye genomics and for providing tools for rye improvement. Finally, a new model for temperate grasses has emerged in the past year with the development of the genetics and genomics (including a 8x whole genome shotgun sequencing project) of Brachypodium, a member of the Poeae family that is more closely related to the Triticeae than rice and can provide valuable information for supporting Triticeae genomics in the near future. These recent breakthroughs have yet to be reviewed in a single source of literature and current handbooks on wheat, barley, or rye are dedicated mainly to progress in genetics. In "Genetics and Genomics of the Triticeae", we will aim to comprehensively review the recent progress in the development of structural and functional genomics tools in the Triticeae species and review the understanding of wheat, barley, and rye biology that has resulted from these new resources as well as to illuminate how this new found knowledge can be applied for the improvement of these essential species. The book will be the seventh volume in the ambitious series of books, Plant Genetics and Genomics (Richard A. Jorgensen, series editor) that will attempt to bring the field up-to-date on the genetics and genomics of important crop plants and genetic models. It is our hope that the publication will be a useful and timely tool for researchers and students alike working with the Triticeae.
