This book celebrates the dawn of the rye genomics era with concise, comprehensive, and accessible reviews on the current state of rye genomic research, written by experts in the field for students, researchers and growers. To most, rye is the key ingredient in a flavoursome bread or their favourite American whisky. To a farmer, rye is the remarkable grain that tolerates the harshest winters and the most unforgiving soils, befitting its legacy as the life-giving seed that fed the ancient civilisations of northern Eurasia. Since the mid-1900s, scientists have employed genetic approaches to better understand and utilize rye, but only since the technological advances of the mid-2010s has the possibility of addressing questions using rye genome assemblies become a reality. Alongside the secret of its unique survival abilities, rye genomics has accelerated research on a host of intriguing topics such as the complex history of rye’s domestication by humans, the nature of genes that switch fertility on and off, the function and origin of accessory chromosomes, and the evolution of selfish DNA.

Owing to its considerable winter hardiness, rye is a cereal that played a major role in the feeding of European populations throughout the Middle Ages. Recent data shows that rye is grown on about 5.4 million hectares, with a world production of approximately 13 million tons. While still an important bread food in many countries, rye produced for bread making has decreased or stagnated, whereas production is increasing for other market segments. Particularly, rye for feeding, ethanol processing, and biogas is promoted in Europe. The first comprehensive monograph on rye, Rye: Genetics, Breeding, and Cultivation gathers all the relevant and historic information from botany and genetics to utilization and sustainability of rye. The book covers taxonomy, morphology, and other botany-related aspects of rye. It describes its physiology, cytology, and genetics, including use for genetic improvement of other cereals. The author addresses various types of breeding such as population, hybrid, and molecular breeding. He also discusses rye cropping, including seeding techniques, fungal and viral diseases, and predators. The book examines the various uses for rye beyond bread making. This includes feeding, biomass and biogas production, ethanol production, and other important characteristics such as phytosterol content and antioxidant activity. It also explores the nutritional value of rye. Written by a leading expert in the field, this monograph compiles the most important facets of rye research, past and present.

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.

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.

This proceedings is a collection of 46 selected papers that were presented at the 12th International Wheat Genetics Symposium (IWGS). Since the launch of the wheat genome sequencing project in 2005, the arrival of draft genome sequences has marked a new era in wheat genetics and genomics, catalyzing rapid advancement in the field. This book provides a comprehensive review of the forefront of wheat research, across various important topics such as germplasm and genetic diversity, cytogenetics and allopolyploid evolution, genome sequencing, structural and functional genomics, gene function and molecular biology, biotic stress, abiotic stress, grain quality, and classical and molecular breeding. Following an introduction, 9 parts of the book are dedicated to each of these topics. A final, 11th part entitled “Toward Sustainable Wheat Production” contains 7 excellent papers that were presented in the 12th IWGS Special Session supported by the OECD. With rapid population growth and radical climate changes, the world faces a global food crisis and is in need of another Green Revolution to boost yields of wheat and other widely grown staple crops. Although this book focuses on wheat, many of the newly developed techniques and results presented here can be applied to other plant species with large and complex genomes. As such, this volume is highly recommended for all students and researchers in wheat sciences and related plant sciences and for those who are interested in stable food production and food security.

Applications of Genetic and Genomic Research in Cereals covers new techniques for practical breeding, also discussing genetic and genomic approaches for improving special traits. Additional sections cover drought tolerance, biotic stress, biomass production, the impact of modern techniques on practical breeding, hybrid breeding, genetic diversity, and genomic selection. Written by an international team of top academics and edited by an expert in the field, this book will be of value to academics working in the agricultural sciences and essential reading for professionals working in plant breeding. - Provides in-depth and comprehensive coverage of a rapidly developing field - Presents techniques used in genetic and genomics research, with coverage of genotyping, gene cloning, genome editing and engineering and phenotyping in various cereals - Includes the latest genetic and genomic approaches for improving special traits - drought tolerance, biotic stress and biomass production - Covers breeding practices, with chapters on the genetic diversity of wheat, hybrid breeding and the potential of rye and barley crops

Summarizing landmark research, Volume 2 of this essential series furnishes information on the availability of germplasm resources that breeders can exploit for producing high-yielding cereal crop varieties. Written by leading international experts, this volume offers the most comprehensive and up-to-date information on employing genetic resources t

Written by an international team of experts, Somatic Genome Variation presents a timely summary of the latest understanding of somatic genome development and variation in plants, animals, and microorganisms. Wide-ranging in coverage, the authors provide an updated view of somatic genomes and genetic theories while also offering interpretations of somatic genome variation. The text provides geneticists, bioinformaticians, biologist, plant scientists, crop scientists, and microbiologists with a valuable overview of this fascinating field of research.

Mapping the genomic landscapes is one of the most exciting frontiers of science. We have the opportunity to reverse engineer the blueprints and the control systems of living organisms. Computational tools are key enablers in the deciphering process. This book provides an in-depth presentation of some of the important computational biology approaches to genomic sequence analysis. The first section of the book discusses methods for discovering patterns in DNA and RNA. This is followed by the second section that reflects on methods in various ways, including performance, usage and paradigms.

Maize is used in an endless list of products that are directly or indirectly related to human nutrition and food security. Maize is grown in producer farms, farmers depend on genetically improved cultivars, and maize breeders develop improved maize cultivars for farmers. Nikolai I. Vavilov defined plant breeding as plant evolution directed by man. Among crops, maize is one of the most successful examples for breeder-directed evolution. Maize is a cross-pollinated species with unique and separate male and female organs allowing techniques from both self and cross-pollinated crops to be utilized. As a consequence, a diverse set of breeding methods can be utilized for the development of various maize cultivar types for all economic conditions (e.g., improved populations, inbred lines, and their hybrids for different types of markets). Maize breeding is the science of maize cultivar development. Public investment in maize breeding from 1865 to 1996 was $3 billion (Crosbie et al., 2004) and the return on investment was $260 billion as a consequence of applied maize breeding, even without full understanding of the genetic basis of heterosis. The principles of quantitative genetics have been successfully applied by maize breeders worldwide to adapt and improve germplasm sources of cultivars for very simple traits (e.g. maize flowering) and very complex ones (e.g., grain yield). For instance, genomic efforts have isolated early-maturing genes and QTL for potential MAS but very simple and low cost phenotypic efforts have caused significant and fast genetic progress across genotypes moving elite tropical and late temperate maize northward with minimal investment. Quantitative genetics has allowed the integration of pre-breeding with cultivar development by characterizing populations genetically, adapting them to places never thought of (e.g., tropical to short-seasons), improving them by all sorts of intra- and inter-population recurrent selection methods, extracting lines with more probability of success, and exploiting inbreeding and heterosis. Quantitative genetics in maize breeding has improved the odds of developing outstanding maize cultivars from genetically broad based improved populations such as B73. The inbred-hybrid concept in maize was a public sector invention 100 years ago and it is still considered one of the greatest achievements in plant breeding. Maize hybrids grown by farmers today are still produced following this methodology and there is still no limit to genetic improvement when most genes are targeted in the breeding process. Heterotic effects are unique for each hybrid and exotic genetic materials (e.g., tropical, early maturing) carry useful alleles for complex traits not present in the B73 genome just sequenced while increasing the genetic diversity of U.S. hybrids. Breeding programs based on classical quantitative genetics and selection methods will be the basis for proving theoretical approaches on breeding plans based on molecular markers. Mating designs still offer large sample sizes when compared to QTL approaches and there is still a need to successful integration of these methods. There is a need to increase the genetic diversity of maize hybrids available in the market (e.g., there is a need to increase the number of early maturing testers in the northern U.S.). Public programs can still develop new and genetically diverse products not available in industry. However, public U.S. maize breeding programs have either been discontinued or are eroding because of decreasing state and federal funding toward basic science. Future significant genetic gains in maize are dependent on the incorporation of useful and unique genetic diversity not available in industry (e.g., NDSU EarlyGEM lines). The integration of pre-breeding methods with cultivar development should enhance future breeding efforts to maintain active public breeding programs not only adapting and improving genetically broad-based germplasm but also developing unique products and training the next generation of maize breeders producing research dissertations directly linked to breeding programs. This is especially important in areas where commercial hybrids are not locally bred. More than ever public and private institutions are encouraged to cooperate in order to share breeding rights, research goals, winter nurseries, managed stress environments, and latest technology for the benefit of producing the best possible hybrids for farmers with the least cost. We have the opportunity to link both classical and modern technology for the benefit of breeding in close cooperation with industry without the need for investing in academic labs and time (e.g., industry labs take a week vs months/years in academic labs for the same work). This volume, as part of the Handbook of Plant Breeding series, aims to increase awareness of the relative value and impact of maize breeding for food, feed, and fuel security. Without breeding programs continuously developing improved germplasm, no technology can develop improved cultivars. Quantitative Genetics in Maize Breeding presents principles and data that can be applied to maximize genetic improvement of germplasm and develop superior genotypes in different crops. The topics included should be of interest of graduate students and breeders conducting research not only on breeding and selection methods but also developing pure lines and hybrid cultivars in crop species. This volume is a unique and permanent contribution to breeders, geneticists, students, policy makers, and land-grant institutions still promoting quality research in applied plant breeding as opposed to promoting grant monies and indirect costs at any short-term cost. The book is dedicated to those who envision the development of the next generation of cultivars with less need of water and inputs, with better nutrition; and with higher percentages of exotic germplasm as well as those that pursue independent research goals before searching for funding. Scientists are encouraged to use all possible breeding methodologies available (e.g., transgenics, classical breeding, MAS, and all possible combinations could be used with specific sound long and short-term goals on mind) once germplasm is chosen making wise decisions with proven and scientifically sound technologies for assisting current breeding efforts depending on the particular trait under selection. Arnel R. Hallauer is C. F. Curtiss Distinguished Professor in Agriculture (Emeritus) at Iowa State University (ISU). Dr. Hallauer has led maize-breeding research for mid-season maturity at ISU since 1958. His work has had a worldwide impact on plant-breeding programs, industry, and students and was named a member of the National Academy of Sciences. Hallauer is a native of Kansas, USA. José B. Miranda Filho is full-professor in the Department of Genetics, Escola Superior de Agricultura Luiz de Queiroz - University of São Paulo located at Piracicaba, Brazil. His research interests have emphasized development of quantitative genetic theory and its application to maize breeding. Miranda Filho is native of Pirassununga, São Paulo, Brazil. M.J. Carena is professor of plant sciences at North Dakota State University (NDSU). Dr. Carena has led maize-breeding research for short-season maturity at NDSU since 1999. This program is currently one the of the few public U.S. programs left integrating pre-breeding with cultivar development and training in applied maize breeding. He teaches Quantitative Genetics and Crop Breeding Techniques at NDSU. Carena is a native of Buenos Aires, Argentina. http://www.ag.ndsu.nodak.edu/plantsci/faculty/Carena.htm