Plant Genomics 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.
This 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.
Written by a highly qualified author with significant published research contributions to the field, Plant Genomics includes information on: - Structure and information content of the chloroplast and mitochondrial genomes and their use in phylogeny- Use of transcriptomes from various tissues to identify expressed sequences and their identification as genes- Function of small regulatory RNAs and long non-coding RNAs and involvement of small RNAs in the control of gene expression- Epigenetic silencing of transposable elements and their release by stress and cross-generational contribution of epigenetic variation - Use of the pan-genome to assemble a comprehensive germplasm for a particular crop species
Plant Genomics 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.
Table of Contents
About the Author xiii
Preface xv
Acknowledgments xvii
About the Companion Website xix
Introduction xxi
1 The Structure of Plant Genomes 1
Introduction 1
DNA Variation - Quantity 1
Chromosome Variation 4
Chromosome Structures 7
Telomeres 7
Centromeres 8
The Nucleolus Organizer Region 9
Heterochromatin 9
Origin of DNA Variation 10
Organization and Representation of the Various Classes of Sequences 10
Low- Copy Sequences 11
Dispersed Repetitive Sequences 12
Tandemly Repeated Sequences 15
Summary of the Organization of the Maize Genome 17
Processes that Affect Genome Size 17
Consequences of Multiple Genomes 20
Pangenome Concept 23
Extrachromosomal Circular DNA 25
Intraspecific Genome Size Variation 25
Summary 26
References 27
2 Basic Toolbox 31
The Fundamental Basis of Most Genomic Technologies 31
Genome Fractionation 32
Sequencing Genomes 33
Next- Generation Sequencing (NGS) Technologies 34
Third- Generation Sequencing (Long- Read Sequencing) - Single- Molecule Sequencing 36
Two of the Third- Generation Sequencing Technologies 36
Simultaneous Identification of Sequence and Methylation - Epigenetics 38
Alternative Methylation Profiling 38
Oxford Nanopore Technologies 39
Assembling Telomere- to- Telomere Genome Assemblies 39
Proximity- Based Ligation 39
Optical Mapping 40
Summary of Genomic Sequencing 40
The Transcriptome 40
RNA Library Preparation 42
Single- Cell Sequencing 43
Whole Transcriptome Sequencing (Total RNA- seq) 43
Poly(A) Selection RNA- seq 43
Ribosome Profiling (Ribo- seq) 43
Strand- Specific RNA- seq 44
Small RNA- seq 44
Spatial Transcriptomics 44
Pseudouridine (Ψ) Sequencing 44
Quantitative PCR 44
Digital Droplet PCR (ddPCR) 45
Microarrays 45
Proteomics 46
Extraction of the Proteome 47
Protein Separation 48
References 51
3 Sequencing and Assembly Strategies for Large Complex Genomes 53
Assembling Genomes in the Cloning and Sanger Sequencing Era 54
Steps for Genome Assembly from High- Throughput DNA Sequence Data 54
Integration of Short Reads from Shotgun Sequencing 56
Third- Generation Sequencing Technologies 56
Hybrid Assemblies 56
Stitching Scaffolds Together 56
Advanced Bioinformatics Tools 57
A 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
DNA Isolation 58
Data Assembly and Analysis 58
Estimation of Genome Size and Heterozygosity 59
De Novo Genome Assembly and Evaluation 59
Comparison of the Genome Assemblies with a Close Relative 59
Telomere- to- Telomere Assembly 67
RNA Assembly 67
Summary 73
References 73
4 The Organelle Genomes 75
Chloroplasts 75
Chloroplast Genome Size and Structure 76
Sequencing the Chloroplast Genome 76
Chloroplast Genes 76
Variation in the Chloroplast Genomes Within and Between Species 76
Use in Phylogenetics 84
Mitochondrial Genome Size and Structure 84
Variation in the Mitogenome 86
Transfer of DNA Between the Nucleus Chloroplast and Mitochondrion 88
Heteroplasmy 90
Anterograde and Retrograde Signaling 92
Retrograde Signaling and RNA Metabolism in Plants 94
References 96
5 Gene Discovery Paradigms 99
Introduction 99
Genome Annotation 101
Identification of Genes by Mutagenesis 107
Insertional Mutagenesis with T- DNA 109
Targeting- Induced Local Lesions in Genomes (Tilling) 110
Gene Editing 111
Summary 112
References 112
6 Control of Gene Expression 115
Introduction 115
Specific Promoter Sequences Are Required for Regulated Gene Expression 117
The Effect of Enhancer Elements on Gene Expression 119
Posttranscriptional Effects of mRNA Signals 120
Role of 5′ Sequences in Gene Expression 122
Role of 3′ Sequences in Gene Expression 122
Role of Introns in Gene Expression 122
Conserved Sequences in Eukaryotic Promoters 124
Trans- Acting Factors Control Gene Expression 125
mRNA Stability 125
Chemically/Physically Regulated Gene Expression in Plants 127
Effects of Chromatin Structure 128
Translational Control 133
Summary 137
References 140
Contents ix
7 Epigenetics 145
Introduction 145
DNA Methylation 147
Histone Modifications 148
Epigenetic Silencing of Transposable Elements 149
Unstable Inheritance of Epialleles 150
Summary 151
References 153
8 Functional Genomics 155
Introduction 155
Transcriptome Profile 157
Protein- Protein Interactions 157
Yeast Two- Hybrid Systems 158
Protein Tags and Transgenics 158
Metabolomics 161
Single- Cell - Omics 163
Conclusions 164
References 164
9 The Microbiome 167
Introduction 167
The Rhizosphere 168
Bacterial Communities 169
What Influences the Composition of the Bacterial Microbiome in the Rhizosphere? 170
Phyllosphere 170
Endosphere 174
Plant Growth- Promoting Rhizobacteria 175
Rhizobia and Mycorrhizae 176
Importance and Use of the Microbiome 179
References 182
10 Interactions with the External Environment 185
Introduction 185
Abiotic Stresses 186
Biotic Interactions 190
Disease Resistance 191
Pest Resistance 198
Biotechnological Opportunities 198
References 199
11 Complex Character Manipulation - Plant Breeding 201
Introduction 201
Conventional Breeding Methods 202
Marker- Assisted Selection 204
Quantitative Trait Loci 208
Genomic Selection 214
High- Throughput Phenotyping 215
Speed Breeding 215
Pangenomics as a Source of Useful Alleles 215
Concluding Integration 218
References 220
12 Genetic Manipulation of the Plant Genome 223
Introduction 223
Agrobacterium-Mediated Plant Transformation: Biology and Applications 225
Bypassing the Bottleneck of Tissue Culture 228
Transformation Through Direct Delivery of DNA 228
Biolistic Transformation 228
Electroporation 229
Nanotechnology Strategies 229
Carbon Nanotubes 229
Magnetofection 229
DNA Origami 232
Gene Editing 233
Summary and Outlook 235
References 237
Contents xi
13 Bioethical Concerns and the Future of Plant Genomics 239
Development of Biotechnologically Modified Plants 240
The Global Landscape for Regulation of GM Plants 241
The Regulatory Environment in the United States 247
European Union (EU) Responses to Genetically Modified (GM) Plants 248
Case Studies 250
BT Brinjal 250
Golden Rice 251
References 253
Index 255
