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.

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.

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. 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 Saccharinae clade of the Poaceae (grass) family of flowering plants includes several important crops with a rich history of contributions to humanity and the promise of still-greater contributions, as a result of some of the highest biomass productivity levels known, resilience to drought and other environmental challenges that are likely to increase, amenability to production systems that may mitigate or even reverse losses of ecological capital such as topsoil erosion, and the recent blossoming of sorghum as a botanical and genomic model for the clade.  In Genomics of the Saccharinae, advances of the past decade and earlier are summarized and synthesized to elucidate the current state of knowledge of the structure, function, and evolution of the Sorghum, Saccharum, and Miscanthus genera, and progress in the application of this knowledge to crop improvement.  As a backdrop, it is important to understand the naturally occurring diversity in each genus, its organization and distribution, and its evolutionary history. Genomic tools and methods for Saccharinae biology and improvement have improved dramatically in the past few years – a detailed summary of these tools and their applications is a central element of this book.  Application of genomic tools to priorities in crop improvement, including understanding and manipulating plant growth and development, composition, and defense, as well as increasing the quality and productivity of seed/grain, sugar, biomass, and other value-added products under a range of conditions and inputs, are addressed. In particular, as the first native African crop to emerge as a genomic model, sorghum offers an excellent case study of challenges and opportunities in linking new advances in biosciences to solving some of Africa’s major agricultural problems. Several members of the clade, exemplified by Sorghum halepense (Johnsongrass) offer insights into weediness and invasion biology. The firstsequence for a member of the clade, sorghum, as well as progress and challenges toward sequencing of additional members and the new opportunities that this will create, are also explored. Indeed, the very complexities that have hindered study of some clade members also offer intriguing opportunities to gain insight into fundamental questions such as roles of polyploidy in agricultural productivity and post-polyploidy evolution.

The Genetics and Genomics of the Brassicaceae provides a review of this important family (commonly termed the mustard family, or Cruciferae). The family contains several cultivated species, including radish, rocket, watercress, wasabi and horseradish, in addition to the vegetable and oil crops of the Brassica genus. There are numerous further species with great potential for exploitation in 21st century agriculture, particularly as sources of bioactive chemicals. These opportunities are reviewed, in the context of the Brassicaceae in agriculture. More detailed descriptions are provided of the genetics of the cultivated Brassica crops, including both the species producing most of the brassica vegetable crops (B. rapa and B. oleracea) and the principal species producing oilseed crops (B. napus and B. juncea). The Brassicaceae also include important “model” plant species. Most prominent is Arabidopsis thaliana, the first plant species to have its genome sequenced. Natural genetic variation is reviewed for A. thaliana, as are the genetics of the closely related A. lyrata and of the genus Capsella. Self incompatibility is widespread in the Brassicaceae, and this subject is reviewed. Interest arising from both the commercial value of crop species of the Brassicaceae and the importance of Arabidopsis thaliana as a model species, has led to the development of numerous resources to support research. These are reviewed, including germplasm and genomic library resources, and resources for reverse genetics, metabolomics, bioinformatics and transformation. Molecular studies of the genomes of species of the Brassicaceae revealed extensive genome duplication, indicative of multiple polyploidy events during evolution. In some species, such as Brassica napus, there is evidence of multiple rounds of polyploidy during its relatively recent evolution, thus the Brassicaceae represent an excellent model system for the study of the impacts of polyploidy and thesubsequent process of diploidisation, whereby the genome stabilises. Sequence-level characterization of the genomes of Arabidopsis thaliana and Brassica rapa are presented, along with summaries of comparative studies conducted at both linkage map and sequence level, and analysis of the structural and functional evolution of resynthesised polyploids, along with a description of the phylogeny and karyotype evolution of the Brassicaceae. Finally, some perspectives of the editors are presented. 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.

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 wheatgenome 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 and22,000 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 barleygenomes 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.

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.

The Genetics and Genomics of the Brassicaceae provides a review of this important family (commonly termed the mustard family, or Cruciferae). The family contains several cultivated species, including radish, rocket, watercress, wasabi and horseradish, in addition to the vegetable and oil crops of the Brassica genus. There are numerous further species with great potential for exploitation in 21st century agriculture, particularly as sources of bioactive chemicals. These opportunities are reviewed, in the context of the Brassicaceae in agriculture. More detailed descriptions are provided of the genetics of the cultivated Brassica crops, including both the species producing most of the brassica vegetable crops (B. rapa and B. oleracea) and the principal species producing oilseed crops (B. napus and B. juncea). The Brassicaceae also include important “model” plant species. Most prominent is Arabidopsis thaliana, the first plant species to have its genome sequenced. Natural genetic variation is reviewed for A. thaliana, as are the genetics of the closely related A. lyrata and of the genus Capsella. Self incompatibility is widespread in the Brassicaceae, and this subject is reviewed. Interest arising from both the commercial value of crop species of the Brassicaceae and the importance of Arabidopsis thaliana as a model species, has led to the development of numerous resources to support research. These are reviewed, including germplasm and genomic library resources, and resources for reverse genetics, metabolomics, bioinformatics and transformation. Molecular studies of the genomes of species of the Brassicaceae revealed extensive genome duplication, indicative of multiple polyploidy events during evolution. In some species, such as Brassica napus, there is evidence of multiple rounds of polyploidy during its relatively recent evolution, thus the Brassicaceae represent an excellent model system for the study of the impacts of polyploidy and thesubsequent process of diploidisation, whereby the genome stabilises. Sequence-level characterization of the genomes of Arabidopsis thaliana and Brassica rapa are presented, along with summaries of comparative studies conducted at both linkage map and sequence level, and analysis of the structural and functional evolution of resynthesised polyploids, along with a description of the phylogeny and karyotype evolution of the Brassicaceae. Finally, some perspectives of the editors are presented. 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 provides a comprehensive coverage of the advances in genetics and genomics research on rice. The chapters feature the latest developments in rice research and cover such topics as the tools and resources for the functional analysis of rice genes, the identification of useful genes for rice improvement, the present understanding of rice development and biological processes, and the application of this present understanding towards rice improvement. The volume also features a perspective on synthesis and prospects, laying the groundwork for future advances in rice genetics and genomics.Written by authorities in the field, Genetics and Genomics of Rice will serve as an invaluable reference for rice researchers for years to come.

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. Organized into four sections, the volume explores the origin and domestication of papaya, classic genetics and breeding, recent progress on molecular genetics, and current and future applications of genomic resources for papaya improvement.Bolstered by contributions from authorities in the field, Genetics and Genomics of Papaya is a valuable resource that provides the most up to date information for papaya researchers and plant biologists.

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.

The Saccharinae clade of the Poaceae (grass) family of flowering plants includes several important crops with a rich history of contributions to humanity and the promise of still-greater contributions, as a result of some of the highest biomass productivity levels known, resilience to drought and other environmental challenges that are likely to increase, amenability to production systems that may mitigate or even reverse losses of ecological capital such as topsoil erosion, and the recent blossoming of sorghum as a botanical and genomic model for the clade.  In Genomics of the Saccharinae, advances of the past decade and earlier are summarized and synthesized to elucidate the current state of knowledge of the structure, function, and evolution of the Sorghum, Saccharum, and Miscanthus genera, and progress in the application of this knowledge to crop improvement.  As a backdrop, it is important to understand the naturally occurring diversity in each genus, its organization and distribution, and its evolutionary history. Genomic tools and methods for Saccharinae biology and improvement have improved dramatically in the past few years – a detailed summary of these tools and their applications is a central element of this book.  Application of genomic tools to priorities in crop improvement, including understanding and manipulating plant growth and development, composition, and defense, as well as increasing the quality and productivity of seed/grain, sugar, biomass, and other value-added products under a range of conditions and inputs, are addressed. In particular, as the first native African crop to emerge as a genomic model, sorghum offers an excellent case study of challenges and opportunities in linking new advances in biosciences to solving some of Africa’s major agricultural problems. Several members of the clade, exemplified by Sorghum halepense (Johnsongrass) offer insights into weediness and invasion biology. The firstsequence for a member of the clade, sorghum, as well as progress and challenges toward sequencing of additional members and the new opportunities that this will create, are also explored. Indeed, the very complexities that have hindered study of some clade members also offer intriguing opportunities to gain insight into fundamental questions such as roles of polyploidy in agricultural productivity and post-polyploidy evolution.

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. Organized into four sections, the volume explores the origin and domestication of papaya, classic genetics and breeding, recent progress on molecular genetics, and current and future applications of genomic resources for papaya improvement.Bolstered by contributions from authorities in the field, Genetics and Genomics of Papaya is a valuable resource that provides the most up to date information for papaya researchers and plant biologists.

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.

This book provides a comprehensive coverage of the advances in genetics and genomics research on rice. The chapters feature the latest developments in rice research and cover such topics as the tools and resources for the functional analysis of rice genes, the identification of useful genes for rice improvement, the present understanding of rice development and biological processes, and the application of this present understanding towards rice improvement. The volume also features a perspective on synthesis and prospects, laying the groundwork for future advances in rice genetics and genomics.Written by authorities in the field, Genetics and Genomics of Rice will serve as an invaluable reference for rice researchers for years to come.

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. Pineapple [Ananas comosus (L.) Merr.] is the second most important tropical fruit after banana in term of international trade. Its features are advantageous for genomic research: it has a small genome of 527 Mb which is diploid and vegetatively propagated; it is monocot, closely related to the grass family that includes major cereal crops, wheat, rice, corn, sorghum, and millet; and it serves as an out group for genetic and genomic research in grasses. In addition to exploring the evolution and improvement of pineapple, this work examines the pineapple genome with respect to genome structure and organization, comparative analyses with other angiosperm genomes, transcription factors, disease resistance, and circadian clock regulation of CAM related genes. With chapters covering  botanical, genetic, genomic, and applied aspects ofpineapple, this text also encourages the application of genomic technologies and suggests future prospects.

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.

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.

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. Setaria viridis (green foxtail) is one of the world’s most widespread weeds, and its small size, native variation, rapidly burgeoning genetic and genomic resources, and transformability are making it the system of choice for both basic research and its translation into crop improvement. Its domesticated variant, S. italica (foxtail millet), is a drought-hardy cereal grown in China, India and Africa, and new breeding techniques show great potential for improving yields and nutrition for drought-prone regions. This book brings together for the first time evolutionary, genomic, genetic, and morphological analyses, together with protocols for growing and transforming Setaria, and approaches to high throughput genotyping and candidate gene analysis. Authors include major Setaria researchers from both the USA and overseas.

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. The diversity of angiosperm trees in morphology, anatomy, physiology and biochemistry has been described and cataloged by various scientific disciplines, but the molecular, genetic, and evolutionary mechanisms underlying this diversity have only recently been explored. Excitingly, advances in genomic and sequencing technologies are ushering a new era of research broadly termed comparative genomics, which simultaneously exploits and describes the evolutionary origins and genetic regulation of traits of interest. Within tree genomics, this research is already underway, as the number of complete genome sequences available for angiosperm trees is increasing at an impressive pace and the number of species for which RNAseq data are available is rapidly expanding. Because they are extensively covered by other literature and are rapidly changing, technical and computational approaches—such as the latest sequencing technologies—are not a main focus of this book. Instead, this comprehensive volume provides a valuable, broader view of tree genomics whose relevance will outlive the particulars of current-day technical approaches.The first section of the book discusses background on the evolution and diversification of angiosperm trees, as well as offers description of the salient features and diversity of the unique physiology and wood anatomy of angiosperm trees. The second section explores the two most advanced model angiosperm tree species (poplars and eucalypts) as well as species that are soon to emerge as new models. The third section describes the structural features and evolutionary histories of angiosperm tree genomes, followed by a fourth section focusing on the genomics of traits ofbiological, ecological, and economic interest. In summary, this book is a timely and well-referenced foundational resource for the forest tree community looking to embrace comparative approaches for the study of angiosperm trees.

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.  Recent years have resulted in tremendous increases in our knowledge of these species due to large scale genomic and transcriptomic studies and production of draft genomes for the four major species, Citrullus lanatus, Cucumis melo, Cucumis sativus, and Cucurbita spp.  This text examines genetic resources and structural and functional genomics for each species group and across species groups. In addition, it explores genomic-informed understanding and commonalities in cucurbit biology with respect to vegetative growth, floral development and sex expression, fruit growth and development, and important fruit quality traits.

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. Setaria viridis (green foxtail) is one of the world’s most widespread weeds, and its small size, native variation, rapidly burgeoning genetic and genomic resources, and transformability are making it the system of choice for both basic research and its translation into crop improvement. Its domesticated variant, S. italica (foxtail millet), is a drought-hardy cereal grown in China, India and Africa, and new breeding techniques show great potential for improving yields and nutrition for drought-prone regions. This book brings together for the first time evolutionary, genomic, genetic, and morphological analyses, together with protocols for growing and transforming Setaria, and approaches to high throughput genotyping and candidate gene analysis. Authors include major Setaria researchers from both the USA and overseas.