Genetics and Genomics of the Triticeae (Plant Genetics and Genomics: Crops and Models, 7)

**Genetics and Genomics of Triticeae** Edited by Catherine Feuillet and Gary Muehlbauer Domestication of cereals in the Fertile Crescent 10,000 years ago ushered in the beginning of agriculture, and signified a remarkable breakthrough in the advancement of civilization. Today, the crops of the Triticeae tribe, wheat, barley, and rye, 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. The economic importance of the Triticeae has triggered intense cytogenetic and genetic studies over the past few decades, and has resulted in a breadth of information and tools for developing wheat, barley, and rye varieties. Hampered by the size and complexity of their genomes, however, research regarding the genomics of the Triticeae has lagged behind. But, the recent convergence of several technology developments has enabled dramatic breakthroughs in genomic research and led to the development of a robust "Genomic toolbox." These new capabilities permit a better understanding of the biology of the Triticeae plants and support the improvement of agronomically important traits in these essential species. Comprised of the work of internationally recognized experts, Genetics and Genomics of Triticeae provides an in depth summary of the advances of the past decades, synthesizes the current state of knowledge of the structure, function, and evolution of the Triticeae genomes, and describes progress in the application of this knowledge to the improvement of wheat, barley, and rye. This book explores both the fundamentals of genetic and genomic research of the Triticeae and the applications of state of the art technology that have led to improvements in agronomically important traits such as biotic and abiotic stress resistance, plant development, and quality. Genetics and Genomics of Triticeae opens perspectives into the deployment of new genetic approaches to identify traits and create a better understanding of the organization of the Triticeae genome, and the ongoing development of new sequencing technologies that will support future genome sequencing of these essential crops. **Catherine Feuillet** is research director and leader of the group "Structure, function and evolution of the wheat genomes" at the INRA, Clermont-Ferrand (France). She was educated as a geneticist and molecular biologist and worked for 10 years in Switzerland on the genomics of disease resistance in wheat and barley before moving to France. She is one of the co-chairs of the International Wheat Genome Sequencing Consortium (IWGSC), the International Triticeae Mapping Initiative (ITMI), and the European Triticeae Genomics Initiative (ETGI). **Gary J. Muehlbauer** is an Associate Professor and Endowed Chair in Molecular Genetics of Crop Improvement in the Department of Agronomy and Plant Genetics at the University of Minnesota. He studied maize genetics during his Ph.D. at the University of Minnesota and his postdoctoral work at the University of California at Berkeley. He has been on the faculty at the University of Minnesota for eleven years working on barley and wheat genomics. He is the vice chair of the International Barley Sequencing Consortium. 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... Front Matter....Pages i-xxi Front Matter....Pages 1-1 Scientific Names in the Triticeae ....Pages 3-30 Triticeae Genetic Resources in ex situ Genebank Collections....Pages 31-79 Domestication of the Triticeae in the Fertile Crescent....Pages 81-119 Cytogenetic Analysis of Wheat and Rye Genomes....Pages 121-135 Applying Cytogenetics and Genomics to Wide Hybridisations in the Genus Hordeum ....Pages 137-162 Methods for Genetic Analysis in the Triticeae ....Pages 163-199 Genetic Mapping in the Triticeae....Pages 201-235 Early Stages of Meiosis in Wheat- and the Role of Ph1 ....Pages 237-252 Front Matter....Pages 253-253 A Toolbox for Triticeae Genomics....Pages 255-283 Chromosome Genomics in the Triticeae....Pages 285-316 Physical Mapping in the Triticeae....Pages 317-335 Map-Based Cloning of Genes in Triticeae (Wheat and Barley)....Pages 337-357 Functional Validation in the Triticeae ....Pages 359-385 Genomics of Transposable Elements in the Triticeae....Pages 387-405 Gene and Repetitive Sequence Annotation in the Triticeae....Pages 407-425 Brachypodium distachyon , a New Model for the Triticeae....Pages 427-449 Comparative Genomics in the Triticeae....Pages 451-477 Front Matter....Pages 479-479 Genomics of Tolerance to Abiotic Stress in the Triticeae....Pages 481-558 Genomics of Biotic Interactions in the Triticeae....Pages 559-589 Developmental and Reproductive Traits in the Triticeae....Pages 591-609 Front Matter....Pages 479-479 Genomics of Quality Traits....Pages 611-652 Front Matter....Pages 653-653 Linkage Disequilibrium and Association Mapping in the Triticeae....Pages 655-683 Triticeae Genome Structure and Evolution....Pages 685-711 Wheat and Barley Genome Sequencing....Pages 713-742 Back Matter....Pages 743-757 Reviews the progress in the development of structural and functional genomics tools in the Triticeae species. This volume also reviews the understanding of wheat, barley, and rye biology that has resulted from these new resources as well as to illuminate how this knowledge can be applied for the improvement of these essential species