Plant Genetics and Genomics: Crops and Models – serie

A few members of the Gossypium (cotton) genus are cultivated for the production of elongated single-celled fibers valued worldwide at about $20 billion annually at the farm gate, and which sustain one of the world’s largest industries (textiles) with an annual worldwide economic impact of about $500 billion. In a number of ways, cotton production and the textile industry are closely tied to petrochemical usage. At a practical level, cotton genomics offers both bio-based carbon sequestration alternatives to petrochemical use, and improved sustainability of crop production. The Gossypium (cotton) also genus presents novel opportunities to advance our understanding of the natural world and its organic evolution. In particular, the evolution of cultivated cottons from their wild ancestors has involved a fascinating series of events that offer scientists the opportunity to dissect the evolution of a novel organ, the ‘lint fiber’, and also to unravel the consequences of polyploidy, both for the generation of biodiversity and for crop productivity. In this book, advances of the past decade will be summarized and synthesized to elucidate the current state of knowledge of the structure, function, and evolution of the Gossypium genome, and progress in the application of this knowledge to cotton improvement. This book will address five broad topics. First, as a backdrop for all studies of the genus, it is important to understand the naturally-occurring diversity in the genus, its organization and distribution, and its evolutionary history. Of special importance is the formation of a single polyploid from two (among 8) diploid genome types, the radiation of this polyploid, and the domestication and improvement of two (among 5 extant) polyploid species.

Plant cytogenetics comprises a topic of broad interest and increasing importance in plant science. In keeping with the exciting advances in plant genetics and genomics, we believe that a comprehensive and up-to-date reference on plant cytogenetics would be of great interest and value for researchers, instructors, and students with interests in genetics, plant biology, and plant genomics. The field of cytogenetics is currently expanding at the same fast pace that genome technologies are moving but no reliable reference exists that captures the current state of progress. The goal then of the proposed reference is to provide a scholarly and timely review of plant cytogenetics that covers traditional aspects of plant cytogenetics together with the emerging and exciting new areas of genomics, epigenetics, evolution, and chromosome engineering. Advances in plant genetics and genomics are driving major changes in how we view fundamental concepts such as gene regulation, genome organization, and plant evolution. Plant Cytogenetics: Genome Structure and Chromosome Function provides a unique and critical perspective on these precepts.Our proposed new reference on cytogenetics will be offered in two separate and individual but complementary volumes.This volume will consist of 16 chapters and a glossary, and collectively present a must-have reference for researchers, instructors, students, or breeders whose work on plants can be described as genetics, structural or functional genomics, evolution, or epigenetics. The genome revolution has opened new avenues for understanding and modifying plant genomes. A modern reference book on plant cytogenetics will be a major asset as plant geneticists move from engineering genes and pathways to engineering more complex genetic elements such as whole chromosomes and composite genomes. We expect that this definitive reference would serve just such a role covering the fundamentals of plant cytogenetics on this topic of great historic and contemporary importance.

Having spent most of my life in Academia teaching and carrying out fundam- tal research on plant form and function, I found this collection of essays to be of considerable interest as they expanded my knowledge of genomics to plants - yond the well-studied model systems of Arabidopsis, rice, and temperate maize. It was even more valuable to me in terms of my more recent interest in international agriculture—in particular,my personal interest in promotingthe integration of - ings from the advanced plant sciences into current approaches to crop impro- ment for the bene t of poor, small-scale farmers in the developing world. In my experience, one of the greatest challenges to such integration is the relatively weak interactionamongscientists workingat the forefrontofgenomicsresearchandthose involved in the improvement of crops important to such farmers. Since most of the crops important to the poor are of tropical origin, one hopes that this very readable collection of essays will help bridge that gap as they should be of interest to both types of scientists. My own experience is interesting in this regard—I had thought that it might be useful to read just a few of these essays and ended up wanting to read them all! Reading this collection forced me to consider several important issues.

GeneticsandGenomicsofSoybean,EditedbyProfessorGaryStacey,isaremarkable collection of articles by internationally-recognized experts in the ?eld of soybean genomics – many of whom helped to develop the tools and resources necessary to establish soybean as a powerful crop to investigate important basic and applied questions of plant biology. This collection of articles provides a comprehensive up-to-date review of the ?eld of soybean genomics, and documents how far this ?eld has advanced in the last few years. From the vantage point of someone like myself who ?rst began investigatingthe organizationand expression of the soybean genome thirty years ago, the insights provided by the authors in this book in- cate that soybean has indeed “come of age,” and that decades-old mysteries of the soybean genome are now being illuminated. Genetics and Genomics of Soybean is divided into four sections: (1) soybean genome natural history and diversity – which includes chapters on the genetic variation of the soybean genome and its relationship to other legume genomes; (2) tools, resources, and approaches – which includes reviews of technological advances that are being used to study the s- bean genome – including the ?rst glimpse of how the soybean genome is being sequenced and assembled; (3) investigations of soybean biology – which contains chapters that review how genomics tools have been used to study important qu- tions – such as seed development, host-pathogen interactions, abiotic stress, and metabolic pathways; and (4) how Roundup Ready soybeans, generated by genetic engineering, have made an impact on global soybean agriculture.

The Rosaceae Family is represented by approximately 3,000 species of diverse plants, primarily con?ned to temperate climates. The family has a rich variety of architectural forms and contains herbaceous, tree and shrub species. Many family members are readily recognizable because of their edible seasonal fruits that are prized for their unique ?avors, colors and nutritious properties (e.g. apple, str- berry, raspberry, pear, cherry, plum, apricot, pear), as well as familiar ornamentals (e.g. roses) and nuts (e.g. almonds). Today's rosaceous cultivars have been derived from centuries of careful sel- tion and breeding, using a palette of some of evolution's most curious creations. The careful sculpting that has transformed the germplasm was not trivial, as several of the most coveted fruit species maintain complicated genomes-in some cases among the most complex of cultivated plants (e.g. strawberry). Other species in the family are represented by large perennial tree crops that exhibit substantial juven- ity phases, posing a barrier to standard breeding and genetic analyses.Yet, today's superiorcultivarsfeaturerobustgrowth,substantialyieldsandresistancetocommon biotic and abiotic stresses; traits fostered by human intervention. When the hurdles to ef?cient cultivation, breeding and selection are considered, the quality and qu- tity of rosaceous plant products derived from traditional breeding techniques is little short of amazing.

Genetics and Genomics of Populus provides an indepth description of the genetic and genomic tools and approaches for Populus, examines the biology that has been elucidated using genomics, and looks to the future of this unique model plant. This volume is designed to serve both experienced Populus researchers and newcomers to the field. Contributors to the volume are a blend of researchers, some who have spent most of their research career on Populus and others that have moved to Populus from other model systems. Research on Populus forms a useful complement to research on Arabidopsis. In fact, many plant species found in nature are – in terms of the life history and genetics – more similar to Populus than to Arabidopsis. Thus, the genetic and genomic strategies and tools developed by the Populus community, and showcased in this volume, will hopefully provide inspiration for researchers working in other, less well developed, systems.

Having spent most of my life in Academia teaching and carrying out fundam- tal research on plant form and function, I found this collection of essays to be of considerable interest as they expanded my knowledge of genomics to plants - yond the well-studied model systems of Arabidopsis, rice, and temperate maize. It was even more valuable to me in terms of my more recent interest in international agriculture—in particular,my personal interest in promotingthe integration of - ings from the advanced plant sciences into current approaches to crop impro- ment for the bene t of poor, small-scale farmers in the developing world. In my experience, one of the greatest challenges to such integration is the relatively weak interactionamongscientists workingat the forefrontofgenomicsresearchandthose involved in the improvement of crops important to such farmers. Since most of the crops important to the poor are of tropical origin, one hopes that this very readable collection of essays will help bridge that gap as they should be of interest to both types of scientists. My own experience is interesting in this regard—I had thought that it might be useful to read just a few of these essays and ended up wanting to read them all! Reading this collection forced me to consider several important issues.

GeneticsandGenomicsofSoybean,EditedbyProfessorGaryStacey,isaremarkable collection of articles by internationally-recognized experts in the ?eld of soybean genomics – many of whom helped to develop the tools and resources necessary to establish soybean as a powerful crop to investigate important basic and applied questions of plant biology.

Rising interest in biofuels, concern over a looming global water crisis, a need for precise, environmentally benign weed control: these factors are driving new research on the Saccharinae clade. This book reviews recent progress and anticipates new advances.

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.

This book comprehensively reviews the recent progress in the development of structural and functional genomics tools in the Triticeae species. It attempts to bring the field up-to-date on the genetics and genomics of important crop plants and genetic models.

Genetics and Genomics of Populus provides an indepth description of the genetic and genomic tools and approaches for Populus, examines the biology that has been elucidated using genomics, and looks to the future of this unique model plant. This volume is designed to serve both experienced Populus researchers and newcomers to the field. Contributors to the volume are a blend of researchers, some who have spent most of their research career on Populus and others that have moved to Populus from other model systems. Research on Populus forms a useful complement to research on Arabidopsis. In fact, many plant species found in nature are – in terms of the life history and genetics – more similar to Populus than to Arabidopsis. Thus, the genetic and genomic strategies and tools developed by the Populus community, and showcased in this volume, will hopefully provide inspiration for researchers working in other, less well developed, systems.

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.

Genetics and Genomics of Rice

This book reviews various aspects of papaya genomics, including existing genetic and genomic resources, recent progress on structural and functional genomics, and their applications in papaya improvement.

This reference book provides information on plant cytogenetics for students, instructors, and researchers. Topics covered by international experts include classical cytogenetics of plant genomes; plant chromosome structure; functional, molecular cytology; and genome dynamics. In addition, chapters are included on several methods in plant cytogenetics, informatics, and even laboratory exercises for aspiring or practiced instructors. The book provides a unique combination of historical and modern subject matter, revealing the central role of plant cytogenetics in plant genetics and genomics as currently practiced. This breadth of coverage, together with the inclusion of methods and instruction, is intended to convey a deep and useful appreciation for plant cytogenetics. We hope it will inform and inspire students, researchers, and teachers to continue to employ plant cytogenetics to address fundamental questions about the cytology of plant chromosomes and genomes for years to come.Hank W. Bass is a Professor in the Department of Biological Science at Florida State University.James A. Birchler is a Professor in the Division of Biological Sciences at the University of Missouri.

Rising interest in biofuels, concern over a looming global water crisis, a need for precise, environmentally benign weed control: these factors are driving new research on the Saccharinae clade. This book reviews recent progress and anticipates new advances.

The Rosaceae Family is represented by approximately 3,000 species of diverse plants, primarily con?ned to temperate climates. The family has a rich variety of architectural forms and contains herbaceous, tree and shrub species. Many family members are readily recognizable because of their edible seasonal fruits that are prized for their unique ?avors, colors and nutritious properties (e.g. apple, str- berry, raspberry, pear, cherry, plum, apricot, pear), as well as familiar ornamentals (e.g. roses) and nuts (e.g. almonds). Today's rosaceous cultivars have been derived from centuries of careful sel- tion and breeding, using a palette of some of evolution's most curious creations. The careful sculpting that has transformed the germplasm was not trivial, as several of the most coveted fruit species maintain complicated genomes-in some cases among the most complex of cultivated plants (e.g. strawberry). Other species in the family are represented by large perennial tree crops that exhibit substantial juven- ity phases, posing a barrier to standard breeding and genetic analyses.Yet, today's superiorcultivarsfeaturerobustgrowth,substantialyieldsandresistancetocommon biotic and abiotic stresses; traits fostered by human intervention. When the hurdles to ef?cient cultivation, breeding and selection are considered, the quality and qu- tity of rosaceous plant products derived from traditional breeding techniques is little short of amazing.

This book reviews various aspects of papaya genomics, including existing genetic and genomic resources, recent progress on structural and functional genomics, and their applications in papaya improvement.

A few members of the Gossypium (cotton) genus are cultivated for the production of elongated single-celled fibers valued worldwide at about $20 billion annually at the farm gate, and which sustain one of the world’s largest industries (textiles) with an annual worldwide economic impact of about $500 billion.

This book offers comprehensive coverage of the advances in genetics and genomics research on rice. It presents special topics pertaining to the rice genome, including the documentation of tools and resources for functional analysis of the rice genome.

This book is the first comprehensive volume on the genetics and genomics of pineapple and provides an overview of the current state of pineapple research.

Linum (flax) is a genus of about 200 species in the flowering plant family Linaceae. The genus includes common flax, which is one of the best fibers to produce linen, the seeds to produce linseed oil and has health-related properties of flax in human and animal nutrition.This book describes the genetics and genomics of Linum including the development of extensive experimental resources (e.g. whole genome sequence, efficient transformation methods, insertional mutant collections, large germplasm collections, resequenced genomes) that have led much progress and its economic importance. The methods and use of Linum to address a wide range of applications (e.g. disease resistance, cell wall composition, abiotic stress tolerance, floral development, natural diversity) is also discussed.

The genus includes common flax, which is one of the best fibers to produce linen, the seeds to produce linseed oil and has health-related properties of flax in human and animal nutrition.This book describes the genetics and genomics of Linum including the development of extensive experimental resources (e.g.

Grasses dominate many natural ecosystems and produce the bulk calories consumed by humans either directly in the form of grains or indirectly through forage/grain fed animals. In addition, grasses grown as biomass crops are poised to become a significant source of renewable energy. Despite their economic and environmental importance, research into the unique aspects of grass biology has been hampered by the lack of a truly tractable experimental model system. Over that past decade, the small, annual grass Brachypodium distachyon has emerged as a viable model system for the grasses. This book describes the development of extensive experimental resources (e.g. whole genome sequence, efficient transformation methods, insertional mutant collections, large germplasm collections, recombinant inbred lines, resequenced genomes) that have led many laboratories around the world to adopt B. distachyon as a model system. The use of B. distachyon to address awide range of biological topics (e.g. disease resistance, cell wall composition, abiotic stress tolerance, root growth and development, floral development, natural diversity) is also discussed.

Setaria viridis and S.italica make up a model grass system to investigate C4 photosynthesis, cell wall biosynthesis, responses to drought, herbicide, and other environmental stressors, genome dynamics, developmental genetics and morphology, and interactions with microorganisms.

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.

This book provides an overview of the current state of knowledge of the genetics and genomics of the agriculturally important Cucurbitaceae plant family, which includes crops such as watermelon, melon, cucumber, summer and winter squashes, pumpkins, and gourds.

Setaria viridis and S.italica make up a model grass system to investigate C4 photosynthesis, cell wall biosynthesis, responses to drought, herbicide, and other environmental stressors, genome dynamics, developmental genetics and morphology, and interactions with microorganisms.