The Apple Genome

This book covers information on the economics; botany, taxonomy, and origin; germplasm resources; cytogenetics and nuclear DNA; genetic improvement efforts of scion cultivars; genetic and genomic improvement efforts of rootstocks; genetic and physical mapping; genomic resources; genome and epigenome; regulatory sequences; utility of whole-genome sequencing and gene editing in trait dissection; flowering and juvenility; cold hardiness and dormancy; fruit color development; fruit acidity and sugar content; metabolomics; biology and genomics of the microbiome; apple domestication; as well as other ‘omics’ opportunities and challenges for genetic improvement of the apple. The cultivated apple (Malus x domestica Borkh.) is one of the most important tree fruit crops of temperate regions of the world. It is widely cultivated and grown in North America, Europe, and Asia. The apple fruit is a highly desirable fruit due to its flavor, sugar and acid content, metabolites, aroma, as well as its overall texture and palatability. Furthermore, it is a rich source of important nutrients, including antioxidants, vitamins, and dietary fiber.

In The Genome Odyssey, Dr. Euan Ashley, Stanford professor of medicine and genetics, brings the breakthroughs of precision medicine to vivid life through the real diagnostic journeys of his patients and the tireless efforts of his fellow doctors and scientists as they hunt to prevent, predict, and beat disease. Since the Human Genome Project was completed in 2003, the price of genome sequencing has dropped at a staggering rate. It’s as if the price of a Ferrari went from $350,000 to a mere forty cents. Through breakthroughs made by Dr. Ashley’s team at Stanford and other dedicated groups around the world, analyzing the human genome has decreased from a heroic multibillion dollar effort to a single clinical test costing less than $1,000. For the first time we have within our grasp the ability to predict our genetic future, to diagnose and prevent disease before it begins, and to decode what it really means to be human. In The Genome Odyssey, Dr. Ashley details the medicine behind genome sequencing with clarity and accessibility. More than that, with passion for his subject and compassion for his patients, he introduces readers to the dynamic group of researchers and doctor detectives who hunt for answers, and to the pioneering patients who open up their lives to the medical community during their search for diagnoses and cures. He describes how he led the team that was the first to analyze and interpret a complete human genome, how they broke genome speed records to diagnose and treat a newborn baby girl whose heart stopped five times on the first day of her life, and how they found a boy with tumors growing inside his heart and traced the cause to a missing piece of his genome. These patients inspire Dr. Ashley and his team as they work to expand the boundaries of our medical capabilities and to envision a future where genome sequencing is available for all, where medicine can be tailored to treat specific diseases and to decode pathogens like viruses at the genomic level, and where our medical system as we know it has been completely revolutionized.

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 is a new edition of the book published under the title Story of the apple, 2006"--Title page verso.

The crop plants cater not only to our basic F5 (food, feed, fiber, fuel, and furniture) needs but also provide a number of nutraceuticals with potential nutritional, safety and therapeutic properties. Many crop plants provide an array of minerals, vitamins, and antioxidant-rich bioactive phytochemicals. Increasing incidences of chronic diseases such as cancer, diabetes and HIV, and malnutrition necessitate global attention to health and nutrition security with equal emphasis to food security. This compendium compiles results of researches on biochemical, physiological and genetic mechanisms underlying biosynthesis of the health and nutrition related nutraceuticals. It also explores the precise breeding strategies for augmentation of their content and amelioration of their quality in crop plants under all commodity categories including cereals and millets, oilseeds, pulses, fruits and nuts, and vegetables. The compendium comprise 5 sections dedicated to these 5 commodity groups and presents enumeration on the concepts, strategies, tools and techniques of nutraceutomics. These sections include 50 chapters devoted to even number of major crop plants. These chapters present deliberations on the biochemistry and medicinal properties of the nutracuticals contained; genetic variation in their contents; classical genetics and breeding for their quantitative and qualitative improvement; tissue culture and genetic engineering for augmentation of productivity and quality; and sources of genes underlying their biosynthesis. They also include comprehensive enumeration on genetic mapping of the genes and QTLs controlling the contents and profile of the nutraceuticals and molecular breeding for their further improvement through marker assisted selection and backcross breeding tools. Prospects of post-genomic precise breeding strategies including genome-wide association mapping, genomic selection, allele mining, and genome editing are also discussed. This compendium fills the gap in academia, and research and development wings of the private sector industries interested in an array of subjects including genetics, genomics, tissue culture, genetic engineering, molecular breeding, genomics-assisted breeding, bioinformatics, biochemistry, physiology, pathology, entomology, pharmacognosy, IPR, etc., and will also facilitate understanding of the policy making agencies and people in the socio-economic domain and research sponsoring agencies.

This book presents deliberations on the molecular and genomic mechanisms underlying the interactions of crop plants with the biotic stresses caused by insects, bacteria, fungi, viruses, and oomycetes, etc. important to develop resistant crop varieties. Knowledge on the advanced genetic and genomic crop improvement strategies including molecular breeding, transgenics, genomic-assisted breeding and the recently emerging genome editing for developing resistant varieties in fruit crops is imperative for addressing FPNEE (food, health, nutrition. energy and environment) security. Whole genome sequencing of these crops followed by genotyping-by-sequencing have facilitated precise information about the genes conferring resistance useful for gene discovery, allele mining and shuttle breeding which in turn opened up the scope for 'designing' crop genomes with resistance to biotic stresses. The nine chapters, each dedicated to a fruit crop in this volume, deliberate on different types of biotic stress agents and their effects on and interaction with the crop plants; enumerate the available genetic diversity with regard to biotic stress resistance among available cultivars; illuminate on the potential gene pools for utilization in interspecific gene transfer; present brief on the classical genetics of stress resistance and traditional breeding for biotic stress resistance; depict the success stories of genetic engineering for developing biotic stress resistant varieties; discuss on molecular mapping of genes and QTLs underlying biotic stress resistance and their marker-assisted introgression into elite varieties; enunciate different emerging genomics-aided techniques including genomic selection, allele mining, gene discovery and gene pyramiding for developing resistant crop varieties with higher quantity and quality of yield; and also elaborate some case studies on genome editing focusing on specific genes for generating disease and insect resistant crops.

A major new book overturning our assumptions about how evolution works Earth’s natural history is full of fascinating instances of convergence: phenomena like eyes and wings and tree-climbing lizards that have evolved independently, multiple times. But evolutionary biologists also point out many examples of contingency, cases where the tiniest change—a random mutation or an ancient butterfly sneeze—caused evolution to take a completely different course. What role does each force really play in the constantly changing natural world? Are the plants and animals that exist today, and we humans ourselves, inevitabilities or evolutionary flukes? And what does that say about life on other planets? Jonathan Losos reveals what the latest breakthroughs in evolutionary biology can tell us about one of the greatest ongoing debates in science. He takes us around the globe to meet the researchers who are solving the deepest mysteries of life on Earth through their work in experimental evolutionary science. Losos himself is one of the leaders in this exciting new field, and he illustrates how experiments with guppies, fruit flies, bacteria, foxes, and field mice, along with his own work with anole lizards on Caribbean islands, are rewinding the tape of life to reveal just how rapid and predictable evolution can be. Improbable Destinies will change the way we think and talk about evolution. Losos's insights into natural selection and evolutionary change have far-reaching applications for protecting ecosystems, securing our food supply, and fighting off harmful viruses and bacteria. This compelling narrative offers a new understanding of ourselves and our role in the natural world and the cosmos.

This is the first book on Rosaceae genomics. It covers progress in recent genomic research among the Rosaceae, grounding this firmly in the historical context of genetic studies and in the application of genomics technologies for crop development.