{"product_id":"plant-genomics-isbn-9781394211555","title":"Plant Genomics","description":"\u003cp\u003e\u003cb\u003eIntroduction to the range of molecular techniques to investigate unique facets of plant growth, development, and responses to the environment\u003c\/b\u003e \u003c\/p\u003e\u003cp\u003e\u003ci\u003ePlant Genomics\u003c\/i\u003e introduces the complex relationship between the genome, microbiome, genes, and epigenetics of plants, as well as the range of molecular techniques applicable to investigating the unique facets of plant growth, development, and response to the environment. State-of-the-art science in the field is discussed, as well as future outlooks on what the next decade is likely to bring. \u003c\/p\u003e\u003cp\u003eThis book includes new techniques for modifying the plant genome and their impact on modifying plants to combat the impact of biotic and abiotic stresses, including those associated with climate change, new technologies including long and short read sequencing and proximity ligation and the combination of these technologies for assembling sequence data into chromosomes, a new chapter on the sequences of the chloroplast and mitochondrial genomes, and a dedicated chapter to epigenetics and the importance in gene regulation. \u003c\/p\u003e\u003cp\u003eWritten by a highly qualified author with significant published research contributions to the field, \u003ci\u003ePlant Genomics\u003c\/i\u003e includes information on: \u003c\/p\u003e\u003cul\u003e\n\u003cli\u003eStructure and information content of the chloroplast and mitochondrial genomes and their use in phylogeny\u003c\/li\u003e\n\u003cli\u003eUse of transcriptomes from various tissues to identify expressed sequences and their identification as genes\u003c\/li\u003e\n\u003cli\u003eFunction of small regulatory RNAs and long non-coding RNAs and involvement of small RNAs in the control of gene expression\u003c\/li\u003e\n\u003cli\u003eEpigenetic silencing of transposable elements and their release by stress and cross-generational contribution of epigenetic variation \u003c\/li\u003e\n\u003cli\u003eUse of the pan-genome to assemble a comprehensive germplasm for a particular crop species\u003c\/li\u003e\n\u003c\/ul\u003e \u003cp\u003e\u003ci\u003ePlant Genomics\u003c\/i\u003e is an ideal textbook for undergraduate courses on plant biology, particularly those focusing on molecular descriptions, and a helpful auxiliary text to plant biology laboratory courses. It will also be of interest to students in plant molecular biology, agricultural and food sciences, and plant, food, and crop bioengineering. \u003c\/p\u003e\u003cp\u003eAbout the Author xiii\u003c\/p\u003e \u003cp\u003ePreface xv\u003c\/p\u003e \u003cp\u003eAcknowledgments xvii\u003c\/p\u003e \u003cp\u003eAbout the Companion Website xix\u003c\/p\u003e \u003cp\u003eIntroduction xxi\u003c\/p\u003e \u003cp\u003e\u003cb\u003e1 The Structure of Plant Genomes 1\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eIntroduction 1\u003c\/p\u003e \u003cp\u003eDNA Variation— Quantity 1\u003c\/p\u003e \u003cp\u003eChromosome Variation 4\u003c\/p\u003e \u003cp\u003eChromosome Structures 7\u003c\/p\u003e \u003cp\u003eTelomeres 7\u003c\/p\u003e \u003cp\u003eCentromeres 8\u003c\/p\u003e \u003cp\u003eThe Nucleolus Organizer Region 9\u003c\/p\u003e \u003cp\u003eHeterochromatin 9\u003c\/p\u003e \u003cp\u003eOrigin of DNA Variation 10\u003c\/p\u003e \u003cp\u003eOrganization and Representation of the Various Classes of Sequences 10\u003c\/p\u003e \u003cp\u003eLow- Copy Sequences 11\u003c\/p\u003e \u003cp\u003eDispersed Repetitive Sequences 12\u003c\/p\u003e \u003cp\u003eTandemly Repeated Sequences 15\u003c\/p\u003e \u003cp\u003eSummary of the Organization of the Maize Genome 17\u003c\/p\u003e \u003cp\u003eProcesses that Affect Genome Size 17\u003c\/p\u003e \u003cp\u003eConsequences of Multiple Genomes 20\u003c\/p\u003e \u003cp\u003ePangenome Concept 23\u003c\/p\u003e \u003cp\u003eExtrachromosomal Circular DNA 25\u003c\/p\u003e \u003cp\u003eIntraspecific Genome Size Variation 25\u003c\/p\u003e \u003cp\u003eSummary 26\u003c\/p\u003e \u003cp\u003eReferences 27\u003c\/p\u003e \u003cp\u003e\u003cb\u003e2 Basic Toolbox 31\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eThe Fundamental Basis of Most Genomic Technologies 31\u003c\/p\u003e \u003cp\u003eGenome Fractionation 32\u003c\/p\u003e \u003cp\u003eSequencing Genomes 33\u003c\/p\u003e \u003cp\u003eNext- Generation Sequencing (NGS) Technologies 34\u003c\/p\u003e \u003cp\u003eThird- Generation Sequencing (Long- Read Sequencing) - Single- Molecule Sequencing 36\u003c\/p\u003e \u003cp\u003eTwo of the Third- Generation Sequencing Technologies 36\u003c\/p\u003e \u003cp\u003eSimultaneous Identification of Sequence and Methylation— Epigenetics 38\u003c\/p\u003e \u003cp\u003eAlternative Methylation Profiling 38\u003c\/p\u003e \u003cp\u003eOxford Nanopore Technologies 39\u003c\/p\u003e \u003cp\u003eAssembling Telomere- to- Telomere Genome Assemblies 39\u003c\/p\u003e \u003cp\u003eProximity- Based Ligation 39\u003c\/p\u003e \u003cp\u003eOptical Mapping 40\u003c\/p\u003e \u003cp\u003eSummary of Genomic Sequencing 40\u003c\/p\u003e \u003cp\u003eThe Transcriptome 40\u003c\/p\u003e \u003cp\u003eRNA Library Preparation 42\u003c\/p\u003e \u003cp\u003eSingle- Cell Sequencing 43\u003c\/p\u003e \u003cp\u003eWhole Transcriptome Sequencing (Total RNA- seq) 43\u003c\/p\u003e \u003cp\u003ePoly(A) Selection RNA- seq 43\u003c\/p\u003e \u003cp\u003eRibosome Profiling (Ribo- seq) 43\u003c\/p\u003e \u003cp\u003eStrand- Specific RNA- seq 44\u003c\/p\u003e \u003cp\u003eSmall RNA- seq 44\u003c\/p\u003e \u003cp\u003eSpatial Transcriptomics 44\u003c\/p\u003e \u003cp\u003ePseudouridine (Ψ) Sequencing 44\u003c\/p\u003e \u003cp\u003eQuantitative PCR 44\u003c\/p\u003e \u003cp\u003eDigital Droplet PCR (ddPCR) 45\u003c\/p\u003e \u003cp\u003eMicroarrays 45\u003c\/p\u003e \u003cp\u003eProteomics 46\u003c\/p\u003e \u003cp\u003eExtraction of the Proteome 47\u003c\/p\u003e \u003cp\u003eProtein Separation 48\u003c\/p\u003e \u003cp\u003eReferences 51\u003c\/p\u003e \u003cp\u003e\u003cb\u003e3 Sequencing and Assembly Strategies for Large Complex Genomes 53\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eAssembling Genomes in the Cloning and Sanger Sequencing Era 54\u003c\/p\u003e \u003cp\u003eSteps for Genome Assembly from High- Throughput DNA Sequence Data 54\u003c\/p\u003e \u003cp\u003eIntegration of Short Reads from Shotgun Sequencing 56\u003c\/p\u003e \u003cp\u003eThird- Generation Sequencing Technologies 56\u003c\/p\u003e \u003cp\u003eHybrid Assemblies 56\u003c\/p\u003e \u003cp\u003eStitching Scaffolds Together 56\u003c\/p\u003e \u003cp\u003eAdvanced Bioinformatics Tools 57\u003c\/p\u003e \u003cp\u003eA Genome Assembly for a Polyploid Plant of Genome Size ~1 Gb as a Tetraploid with a Total Chromosome Count of 44 Using PacBio HiFi Reads 58\u003c\/p\u003e \u003cp\u003eDNA Isolation 58\u003c\/p\u003e \u003cp\u003eData Assembly and Analysis 58\u003c\/p\u003e \u003cp\u003eEstimation of Genome Size and Heterozygosity 59\u003c\/p\u003e \u003cp\u003eDe Novo Genome Assembly and Evaluation 59\u003c\/p\u003e \u003cp\u003eComparison of the Genome Assemblies with a Close Relative 59\u003c\/p\u003e \u003cp\u003eTelomere- to- Telomere Assembly 67\u003c\/p\u003e \u003cp\u003eRNA Assembly 67\u003c\/p\u003e \u003cp\u003eSummary 73\u003c\/p\u003e \u003cp\u003eReferences 73\u003c\/p\u003e \u003cp\u003e\u003cb\u003e4 The Organelle Genomes 75\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eChloroplasts 75\u003c\/p\u003e \u003cp\u003eChloroplast Genome Size and Structure 76\u003c\/p\u003e \u003cp\u003eSequencing the Chloroplast Genome 76\u003c\/p\u003e \u003cp\u003eChloroplast Genes 76\u003c\/p\u003e \u003cp\u003eVariation in the Chloroplast Genomes Within and Between Species 76\u003c\/p\u003e \u003cp\u003eUse in Phylogenetics 84\u003c\/p\u003e \u003cp\u003eMitochondrial Genome Size and Structure 84\u003c\/p\u003e \u003cp\u003eVariation in the Mitogenome 86\u003c\/p\u003e \u003cp\u003eTransfer of DNA Between the Nucleus Chloroplast and Mitochondrion 88\u003c\/p\u003e \u003cp\u003eHeteroplasmy 90\u003c\/p\u003e \u003cp\u003eAnterograde and Retrograde Signaling 92\u003c\/p\u003e \u003cp\u003eRetrograde Signaling and RNA Metabolism in Plants 94\u003c\/p\u003e \u003cp\u003eReferences 96\u003c\/p\u003e \u003cp\u003e\u003cb\u003e5 Gene Discovery Paradigms 99\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eIntroduction 99\u003c\/p\u003e \u003cp\u003eGenome Annotation 101\u003c\/p\u003e \u003cp\u003eIdentification of Genes by Mutagenesis 107\u003c\/p\u003e \u003cp\u003eInsertional Mutagenesis with T- DNA 109\u003c\/p\u003e \u003cp\u003eTargeting- Induced Local Lesions in Genomes (Tilling) 110\u003c\/p\u003e \u003cp\u003eGene Editing 111\u003c\/p\u003e \u003cp\u003eSummary 112\u003c\/p\u003e \u003cp\u003eReferences 112\u003c\/p\u003e \u003cp\u003e\u003cb\u003e6 Control of Gene Expression 115\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003e\u003cb\u003eIntroduction 115\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eSpecific Promoter Sequences Are Required for Regulated Gene Expression 117\u003c\/p\u003e \u003cp\u003eThe Effect of Enhancer Elements on Gene Expression 119\u003c\/p\u003e \u003cp\u003ePosttranscriptional Effects of mRNA Signals 120\u003c\/p\u003e \u003cp\u003eRole of 5′ Sequences in Gene Expression 122\u003c\/p\u003e \u003cp\u003eRole of 3′ Sequences in Gene Expression 122\u003c\/p\u003e \u003cp\u003eRole of Introns in Gene Expression 122\u003c\/p\u003e \u003cp\u003eConserved Sequences in Eukaryotic Promoters 124\u003cbr\u003e Trans- Acting Factors Control Gene Expression 125\u003c\/p\u003e \u003cp\u003emRNA Stability 125\u003c\/p\u003e \u003cp\u003eChemically\/Physically Regulated Gene Expression in Plants 127\u003c\/p\u003e \u003cp\u003eEffects of Chromatin Structure 128\u003c\/p\u003e \u003cp\u003eTranslational Control 133\u003c\/p\u003e \u003cp\u003eSummary 137\u003c\/p\u003e \u003cp\u003eReferences 140\u003c\/p\u003e \u003cp\u003eContents ix\u003c\/p\u003e \u003cp\u003e\u003cb\u003e7 Epigenetics 145\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eIntroduction 145\u003c\/p\u003e \u003cp\u003eDNA Methylation 147\u003c\/p\u003e \u003cp\u003eHistone Modifications 148\u003c\/p\u003e \u003cp\u003eEpigenetic Silencing of Transposable Elements 149\u003c\/p\u003e \u003cp\u003eUnstable Inheritance of Epialleles 150\u003c\/p\u003e \u003cp\u003eSummary 151\u003c\/p\u003e \u003cp\u003eReferences 153\u003c\/p\u003e \u003cp\u003e\u003cb\u003e8 Functional Genomics 155\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eIntroduction 155\u003c\/p\u003e \u003cp\u003eTranscriptome Profile 157\u003c\/p\u003e \u003cp\u003eProtein– Protein Interactions 157\u003c\/p\u003e \u003cp\u003eYeast Two- Hybrid Systems 158\u003c\/p\u003e \u003cp\u003eProtein Tags and Transgenics 158\u003c\/p\u003e \u003cp\u003eMetabolomics 161\u003c\/p\u003e \u003cp\u003eSingle- Cell – Omics 163\u003c\/p\u003e \u003cp\u003eConclusions 164\u003c\/p\u003e \u003cp\u003eReferences 164\u003c\/p\u003e \u003cp\u003e\u003cb\u003e9 The Microbiome 167\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eIntroduction 167\u003c\/p\u003e \u003cp\u003eThe Rhizosphere 168\u003c\/p\u003e \u003cp\u003eBacterial Communities 169\u003c\/p\u003e \u003cp\u003eWhat Influences the Composition of the Bacterial Microbiome in the Rhizosphere? 170\u003c\/p\u003e \u003cp\u003ePhyllosphere 170\u003c\/p\u003e \u003cp\u003eEndosphere 174\u003c\/p\u003e \u003cp\u003ePlant Growth- Promoting Rhizobacteria 175\u003c\/p\u003e \u003cp\u003eRhizobia and Mycorrhizae 176\u003c\/p\u003e \u003cp\u003eImportance and Use of the Microbiome 179\u003c\/p\u003e \u003cp\u003eReferences 182\u003c\/p\u003e \u003cp\u003e\u003cb\u003e10 Interactions with the External Environment 185\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eIntroduction 185\u003c\/p\u003e \u003cp\u003eAbiotic Stresses 186\u003c\/p\u003e \u003cp\u003eBiotic Interactions 190\u003c\/p\u003e \u003cp\u003eDisease Resistance 191\u003c\/p\u003e \u003cp\u003ePest Resistance 198\u003c\/p\u003e \u003cp\u003eBiotechnological Opportunities 198\u003c\/p\u003e \u003cp\u003eReferences 199\u003c\/p\u003e \u003cp\u003e\u003cb\u003e11 Complex Character Manipulation— Plant Breeding 201\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eIntroduction 201\u003c\/p\u003e \u003cp\u003eConventional Breeding Methods 202\u003c\/p\u003e \u003cp\u003eMarker- Assisted Selection 204\u003c\/p\u003e \u003cp\u003eQuantitative Trait Loci 208\u003c\/p\u003e \u003cp\u003eGenomic Selection 214\u003c\/p\u003e \u003cp\u003eHigh- Throughput Phenotyping 215\u003c\/p\u003e \u003cp\u003eSpeed Breeding 215\u003c\/p\u003e \u003cp\u003ePangenomics as a Source of Useful Alleles 215\u003c\/p\u003e \u003cp\u003eConcluding Integration 218\u003c\/p\u003e \u003cp\u003eReferences 220\u003c\/p\u003e \u003cp\u003e\u003cb\u003e12 Genetic Manipulation of the Plant Genome 223\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eIntroduction 223\u003c\/p\u003e \u003cp\u003eAgrobacterium-Mediated Plant Transformation: Biology and Applications 225\u003c\/p\u003e \u003cp\u003eBypassing the Bottleneck of Tissue Culture 228\u003c\/p\u003e \u003cp\u003eTransformation Through Direct Delivery of DNA 228\u003c\/p\u003e \u003cp\u003eBiolistic Transformation 228\u003c\/p\u003e \u003cp\u003eElectroporation 229\u003c\/p\u003e \u003cp\u003eNanotechnology Strategies 229\u003c\/p\u003e \u003cp\u003eCarbon Nanotubes 229\u003c\/p\u003e \u003cp\u003eMagnetofection 229\u003c\/p\u003e \u003cp\u003eDNA Origami 232\u003c\/p\u003e \u003cp\u003eGene Editing 233\u003c\/p\u003e \u003cp\u003eSummary and Outlook 235\u003c\/p\u003e \u003cp\u003eReferences 237\u003c\/p\u003e \u003cp\u003eContents xi\u003c\/p\u003e \u003cp\u003e\u003cb\u003e13 Bioethical Concerns and the Future of Plant Genomics 239\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eDevelopment of Biotechnologically Modified Plants 240\u003c\/p\u003e \u003cp\u003eThe Global Landscape for Regulation of GM Plants 241\u003c\/p\u003e \u003cp\u003eThe Regulatory Environment in the United States 247\u003c\/p\u003e \u003cp\u003eEuropean Union (EU) Responses to Genetically Modified (GM) Plants 248\u003c\/p\u003e \u003cp\u003eCase Studies 250\u003c\/p\u003e \u003cp\u003eBT Brinjal 250\u003c\/p\u003e \u003cp\u003eGolden Rice 251\u003c\/p\u003e \u003cp\u003eReferences 253\u003c\/p\u003e \u003cp\u003eIndex 255\u003c\/p\u003e  \u003cp\u003e\u003cb\u003eChristopher A. Cullis\u003c\/b\u003e is the Francis Hobart Herrick Professor of Biology at Case Western Reserve University, an AAAS Fellow, and a Life Fellow of the Ohio Academy of Sciences. In addition to directing an MS in Biotechnology Entrepreneurship program from 2002 to 2023, he was instrumental in setting up the Society for International Bioenterprise Education and Research (SIBER) and incorporating it as a 503C3. He has published on the genomics of more than 20 plant species.   \u003c\/p\u003e\u003cp\u003e\u003cb\u003eIntroduction to the range of molecular techniques to investigate unique facets of plant growth, development, and responses to the environment\u003c\/b\u003e \u003c\/p\u003e\u003cp\u003e\u003ci\u003ePlant Genomics\u003c\/i\u003e introduces the complex relationship between the genome, microbiome, genes, and epigenetics of plants, as well as the range of molecular techniques applicable to investigating the unique facets of plant growth, development, and response to the environment. State-of-the-art science in the field is discussed, as well as future outlooks on what the next decade is likely to bring. \u003c\/p\u003e\u003cp\u003eThis book includes new techniques for modifying the plant genome and their impact on modifying plants to combat the impact of biotic and abiotic stresses, including those associated with climate change, new technologies including long and short read sequencing and proximity ligation and the combination of these technologies for assembling sequence data into chromosomes, a new chapter on the sequences of the chloroplast and mitochondrial genomes, and a dedicated chapter to epigenetics and the importance in gene regulation. \u003c\/p\u003e\u003cp\u003eWritten by a highly qualified author with significant published research contributions to the field, \u003ci\u003ePlant Genomics\u003c\/i\u003e includes information on: \u003c\/p\u003e\u003cul\u003e\n\u003cli\u003eStructure and information content of the chloroplast and mitochondrial genomes and their use in phylogeny\u003c\/li\u003e\n\u003cli\u003eUse of transcriptomes from various tissues to identify expressed sequences and their identification as genes\u003c\/li\u003e\n\u003cli\u003eFunction of small regulatory RNAs and long non-coding RNAs and involvement of small RNAs in the control of gene expression\u003c\/li\u003e\n\u003cli\u003eEpigenetic silencing of transposable elements and their release by stress and cross-generational contribution of epigenetic variation \u003c\/li\u003e\n\u003cli\u003eUse of the pan-genome to assemble a comprehensive germplasm for a particular crop species\u003c\/li\u003e\n\u003c\/ul\u003e \u003cp\u003e\u003ci\u003ePlant Genomics\u003c\/i\u003e is an ideal textbook for undergraduate courses on plant biology, particularly those focusing on molecular descriptions, and a helpful auxiliary text to plant biology laboratory courses. It will also be of interest to students in plant molecular biology, agricultural and food sciences, and plant, food, and crop bioengineering.\u003c\/p\u003e","brand":"Wiley","offers":[{"title":"Default Title","offer_id":47989798207717,"sku":"NP9781394211555","price":75.5,"currency_code":"USD","in_stock":false}],"thumbnail_url":"\/\/cdn.shopify.com\/s\/files\/1\/1842\/7735\/files\/9781394211555.jpg?v=1761785509","url":"https:\/\/k12savings.com\/es\/products\/plant-genomics-isbn-9781394211555","provider":"K12savings","version":"1.0","type":"link"}