The introduction of semi-dwarf wheat and rice varieties since the 1960s contributed to unprecedented yield gains by improving lodging tolerance and harvest index in high-input environments. In wheat, Rht-B1b and Rht-D1b (encoding DELLA proteins) provided the main genetic source for the short stature of modern varieties cultivated worldwide. Despite the yield advantages in optimal conditions, undesirable pleiotropic effects (e.g. poor seedling vigor) associated with these alleles can cause yield loss in adverse environments such as dry/hot climates. Therefore, searching alternative height genes and dwarfing alleles has been an important goal in wheat breeding programs. This dissertation explores natural and induced variation to identify new genetic resources for modulating plant height in wheat. In Chapter 1, I describe the identification of a quantitative trait locus (QHt.ucw-6AS) for plant height in a hexaploid wheat recombinant inbred line population, and its precise mapping as a Mendelian gene officially designated as Rht25. Rht25 confers a mild dwarfing effect (~50% of Rht-B1b and Rht-D1b), exhibits pleiotropic effects on coleoptile length, heading time, and spike development, and presents a potential dwarfing source for fine-tuning wheat plant height. In Chapter 2, I describe a mapping-by-exome-sequencing approach and use it to identify candidate causal mutations associated with increased height in a tetraploid wheat mutant population. The proposed strategy provides a cost-efficient and rapid mapping procedure to identify causative induced mutations associated with a target phenotype in species with large genomes. In Chapter 3, I describe the transcriptomic changes induced by a missense mutation (E529K) in the GRAS functional domain of the RHT-B1b protein causing increased height, and provide distinct sets of potential GA-response genes regulated directly or indirectly by DELLA in a highly tissue-specific manner.

Researchers in the field of ecological genomics aim to determine how a genome or a population of genomes interacts with its environment across ecological and evolutionary timescales. Ecological genomics is trans-disciplinary by nature. Ecologists have turned to genomics to be able to elucidate the mechanistic bases of the biodiversity their research tries to understand. Genomicists have turned to ecology in order to better explain the functional cellular and molecular variation they observed in their model organisms. We provide an advanced-level book that covers this recent research and proposes future development for this field. A synthesis of the field of ecological genomics emerges from this volume. Ecological Genomics covers a wide array of organisms (microbes, plants and animals) in order to be able to identify central concepts that motivate and derive from recent investigations in different branches of the tree of life. Ecological Genomics covers 3 fields of research that have most benefited from the recent technological and conceptual developments in the field of ecological genomics: the study of life-history evolution and its impact of genome architectures; the study of the genomic bases of phenotypic plasticity and the study of the genomic bases of adaptation and speciation.

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.

This book serves the teachers, researchers and the students as a handy and concise reference as well as guidebook while designing and planning for use of the advanced technologies for crop improvement. The content of the book is designed to cover the latest genome engineering techniques for crop improvement. The conventional breeding has got its limitations such as non-availability of desired genes within the genepool. In many cases, breeding has been highly used and it has nearly reached its highest limit so far as the productivity and production of crops are concerned. However, with increasing need of food and decreasing resources, including water, land, labour, etc., to feed the growing population, the alternative available ways of increasing crop productivity need to be explored and exploited. Genome engineering has a wide scope that includes technologies such as genetic engineering and transgenesis, RNA technologies, CRISPR, cisgenics and subgenics for better productivity and more efficient biotic and abiotic stress management. Therefore, the book is planned to enlighten the readers with the advanced technologies with examples and case studies, whenever possible. Efforts will be made to emphasize on general efforts on various major food crops; however, it would also be made clear that such efforts could be taken as proofs of concepts and that this could be extrapolated keeping the demand in mind.

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. Maize is an extremely important crop, providing a large proportion of the world’s human caloric intake and animal feed, and serving as a model species for basic and applied research. The exceptionally high level of genetic diversity within maize presents opportunities and challenges in all aspects of maize genetics, from sequencing and genotyping to linking genotypes to phenotypes. Topics covered in this timely book range from (i) genome sequencing and genotyping techniques, (ii) genome features such as centromeres and epigenetic regulation, (iii) tools and resources available for trait genomics, to (iv) applications of allele mining and genomics-assisted breeding. This book is a valuable resource for researchers and students interested in maize genetics and genomics.

Climate Change and Food Security with Emphasis on Wheat is the first book to present the full scope of research in wheat improvement, revealing the correlations to global issues including climate change and global warming which contribute to food security issues. Wheat plays a key role in the health of the global economy. As the world population continuously increases, economies modernize, and incomes rise, wheat production will have to increase dramatically to secure it as a reliable and sustainable food source. Since covering more land area with wheat crops is not a sustainable option, future wheat crops must have consistently higher yields and be able to resist and/or tolerate biotic and abiotic stresses that result from climate change. Addressing the biophysical and socioeconomic constraints of producing high-yielding, disease-resistant, and good quality wheat, this book will aid in research efforts to increase and stabilize wheat production worldwide. Written by an international team of experts, Climate Change and Food Security with Emphasis on Wheat is an excellent resource for academics, researchers, and students interested in wheat and grain research, especially as it is relevant to food security. Covers a wide range of disciplines, including plant breeding, genetics, agronomy, physiology, pathology, quantitative genetics and genomics, biotechnology and gene editing Explores the effect of climate change on biotic stresses (stripe rust, stem rust, leaf rust, Karnal bunt, spot blotch) on wheat production and utilization of biotechnology Focuses on whole genome sequencing and next-generation sequencing technologies to improve wheat quality and address the issue of malnutrition in developing world

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.