Oil Crop Genomics

Foreword
Preface
Contents
About the Editors
Contributors
Part I: Genomes of Oil-Bearing Crops
	Chapter 1: Soybean Genome
		1.1 Introduction
		1.2 Soybean Taxonomy and Morphology
			1.2.1 Soybean Morphology
				1.2.1.1 The Plant
				1.2.1.2 Roots
				1.2.1.3 Stem
				1.2.1.4 Leaves
				1.2.1.5 Flowers
				1.2.1.6 Fruit
				1.2.1.7 Seeds
		1.3 Soybean Cytogenetics
		1.4 Soybean Genome
			1.4.1 Soybean Genome Assembly
			1.4.2 The Sequence of Soybean’s Chloroplast and Mitochondria Genome
			1.4.3 Website Links
		1.5 Soybean Genetic Resources (Germplasm)
			1.5.1 A List of Some Germplasm Resources for Soybeans
		1.6 Economic Importance of Soybean
		References
	Chapter 2: Overview and Application of Soybean Genomics Study
		2.1 Introduction
		2.2 Available Soybean Genomic Information
			2.2.1 Cultivated Soybean Genome
			2.2.2 Wild Soybean Genome
			2.2.3 Pan-Genome of Soybean
		2.3 Functional Genomics
			2.3.1 Transcriptomics
			2.3.2 Proteomics
			2.3.3 Epigenomics
		2.4 Methods for Molecular Breeding and Functional Analysis
			2.4.1 Genome Editing
			2.4.2 Genome-Wide Association Analysis
			2.4.3 Genomic Selection
		2.5 Conclusion and Perspectives
		References
	Chapter 3: Genetics and Genomics of Cottonseed Oil
		3.1 Introduction
		3.2 Genetic Improvement of Oil Content
		3.3 Genetic Mapping and Quantitative Trait Loci
		3.4 Genome-Wide Association Study
		3.5 Transcriptome Analysis and Candidate Genes
		3.6 Genetic Transformation
		3.7 Gossypol
		3.8 Summary
		References
	Chapter 4: Olive-Tree Genome Sequencing: Towards a Better Understanding of Oil Biosynthesis
		4.1 Introduction
		4.2 Content of Olive Oil
		4.3 Olive-Oil Biosynthesis
		4.4 Genome Sequencing and Analyses
			4.4.1 Genome Sequencing and Assembly
			4.4.2 Genome Annotation
			4.4.3 Olive-Genome Evolution
			4.4.4 Role of Key Genes in Oil Biosynthesis
			4.4.5 Analyses of Repetitive Sequences
			4.4.6 Analyses of miRNA
		4.5 Future Perspectives
		References
	Chapter 5: Translational Genomics of Cucurbit Oil Seeds
		5.1 Introduction
		5.2 Genomic Resources for Cucurbitaceae
		5.3 Cucurbita
			5.3.1 Major Nutritional Components of Cucurbita Seeds
				5.3.1.1 Seed Oil and Fatty Acid Composition
				5.3.1.2 Seed Protein
				5.3.1.3 Antioxidants and Minerals
			5.3.2 Biology and Genetics of the Hull-Less Seed Trait
			5.3.3 Considerations for Cucurbita Seed Pumpkin Breeding
				5.3.3.1 Seed Yield and Yield Components
				5.3.3.2 Enhancement of Cucurbita Seed Nutritive Value
			5.3.4 Opportunities for Marker-Assisted Selection in Cucurbita Seed Pumpkin
		5.4 Citrullus
			5.4.1 Seed Coat Types
			5.4.2 Seed Oil Percentage (SOP)
			5.4.3 Kernel Percentage (KP)
			5.4.4 Seed Size (SS)
			5.4.5 Fatty Acid Composition
			5.4.6 Seed Coat Color
		5.5 Conclusion
		References
	Chapter 6: Genome Sequence of Oil Palm
		6.1 Introduction
		6.2 Oil Palm Genome Sequence
			6.2.1 Oil Palm Databases
			6.2.2 Molecular Markers in Oil Palm
			6.2.3 Identification of Oil Palm Genes
			6.2.4 Genetic Diversity
		6.3 Conclusion
		References
	Chapter 7: Argane Genetics and Genomics
		7.1 Introduction
		7.2 Argane Genetics
		7.3 The Argania spinosa Genome
		7.4 Argania spinosa Metabolomics
		7.5 Perspectives and Prospective Impact of the Argania Genomics
		7.6 Conclusion
		References
	Chapter 8: On “The Most Useful” Oleaginous Seeds: Linum usitatissimum L., A Genomic View with Emphasis on Important Flax Seed Storage Compounds
		8.1 Introduction
		8.2 A Short History of Flax and Its Usages
		8.3 Phylogeny of Linaceae Family
		8.4 The Flax Genome
		8.5 Genomics Considerations About Flax
			8.5.1 Flaxseed α-Linolenic Acid (ALA)
			8.5.2 Flaxseed Storage Proteins
			8.5.3 Flaxseed Lignan SDG
		8.6 Conclusions
		References
Part II: Oil Crop Genomics
	Chapter 9: Coconut Genomics
		9.1 Introduction
		9.2 Botany and Genetics of Coconut
			9.2.1 Genetic Resources of Coconut
			9.2.2 Origin and Domestication of Coconut
		9.3 DNA-Based Molecular Marker Studies
			9.3.1 Genetic Variation and Diversity Studies
				9.3.1.1 Use of Simple Sequence Repeat (SSR) Markers in Diversity Analysis
			9.3.2 Linkage Mapping and QTL Identification and Association Studies
		9.4 Genomics
			9.4.1 Unraveling the Coconut DNA for Candidate Genes
				9.4.1.1 Somatic Embryogenesis
				9.4.1.2 Endosperm Development and Oil Biosynthesis
				9.4.1.3 Database and Genomic Resources Available for Coconut Functional Studies
			9.4.2 Transcriptomics
			9.4.3 Sequencing of the Coconut Genome: Genome Size Estimation to Whole-Genome Sequencing
				9.4.3.1 Estimation of Coconut Nuclear DNA Content
				9.4.3.2 Whole-Genome Sequencing
		9.5 Coconut Organelle Genomics
			9.5.1 Coconut Chloroplast Genome
			9.5.2 Coconut Mitochondrial Genome
		9.6 Genetic Transformation
		9.7 Conclusion
		References
	Chapter 10: Complete Chloroplast Genome Sequences of Coconut cv. Kopyor Green Dwarf and Comparative Genome Analysis to Oil Palm, Date Palm, Sago Palm, and Miniature Sugar Palm
		10.1 Introduction
		10.2 Chloroplast Genome in Genetic Studies
		10.3 DNA Sequencing Technology for Chloroplast Genome Study
		10.4 Kopyor Coconut Chloroplast Genome Annotation
		10.5 Codon Usage Analysis in Kopyor Coconut Chloroplast Genome
		10.6 Quantity and Distribution of SNPs and InDels in Kopyor Coconut Chloroplast Genome
		10.7 Expansion and Contraction of IR Regions of Kopyor Coconut Chloroplast Genome
		10.8 Cross-Species Comparative Chloroplast Genome Analysis
		10.9 Cross-Species Comparative Quantity and Distribution of Chloroplast Microsatellites
		10.10 Cross-Species Comparative Phylogenetic Analysis Based on Chloroplast Genome
		10.11 Conclusion
		References
	Chapter 11: Genomics, Phenomics, and Next Breeding Tools for Genetic Improvement of Safflower (Carthamus tinctorius L.)
		11.1 Introduction
		11.2 Name
		11.3 Phenomics of Safflower
		11.4 Chemical Compositions of Essential Oil in Safflower
		11.5 Chemical Compositions of Fatty Acids in Safflower
		11.6 Origin and Diffusion
		11.7 Safflower Similarity Centers
		11.8 Weed and Wild Relatives of Carthamus tinctorius L. (Carthamus spp.)
		11.9 Safflower Genetic Resources and the Idea of Core Collection
		11.10 Trade in Safflower
		11.11 Safflower Breeding Activities in the World
			11.11.1 Biotic and Abiotic Factors
			11.11.2 Classical Breeding
			11.11.3 Mutation Breeding
			11.11.4 Biotechnological Tools
				11.11.4.1 Tissue Culture
				11.11.4.2 Genomics of Safflower
					QTL Mapping
					Association Mapping
					Genomic Selection
				11.11.4.3 Functional Genomics
					Transgenic Breeding
					Genome Editing
			11.11.5 Speed Breeding
		11.12 Conclusion
		References
	Chapter 12: Genomics of Mustard Crops
		12.1 Introduction
		12.2 History and Distribution of Mustard Crops
		12.3 Origin of Mustard Crop
		12.4 An Overview of Genetics
		12.5 Utilization and Oil Content
		12.6 History of Genetic Improvement in Mustard
		12.7 Basic Genomics of Mustard Crop
		12.8 Genome Identification and Variation-Causing Tools
		12.9 Different Studies Used for the Improvement of Sequencing and Gene Structure
		12.10 Which Genes Cope with Environmental Stresses
		12.11 Genomics and Radiation
		12.12 Conclusion
		References
	Chapter 13: Integrated Omics Analysis of Benzylisoquinoline Alkaloid (BIA) Metabolism in Opium Poppy (Papaver somniferum L.)
		13.1 General Characteristics of Papaver somniferum L.
		13.2 Benzylisoquinoline Alkaloids (BIA) and Opium Poppy
		13.3 Biosynthesis of the Major Alkaloids in Opium Poppy
			13.3.1 (S)-Norcoclaurine to (S)-Reticuline
			13.3.2 Papaverine Biosynthesis
			13.3.3 Protoberberine, Protopine, and Benzophenanthridine Biosynthesis
			13.3.4 Noscapine Biosynthesis
			13.3.5 Morphine Biosynthesis
		13.4 Methyl Jasmonate Treatment of Opium Poppy
		13.5 Approaches to Study Specialized Metabolisms in Opium Poppy
			13.5.1 Genomics
			13.5.2 Transcriptomics
			13.5.3 Proteomics
			13.5.4 Metabolomics
		13.6 Integrative Omics–Based Studies to Unravel Complex Biological Interactions in Opium Poppy
		13.7 Transcriptional Regulation in Opium Poppy
		13.8 Metabolic Engineering in Opium Poppy
		13.9 Conclusion
		References
	Chapter 14: Transcriptome Analysis in Jatropha During Abiotic Stress Response
		14.1 Introduction
			14.1.1 Abiotic Stresses Affecting Jatropha
				14.1.1.1 Drought
				14.1.1.2 Salinity
				14.1.1.3 Cold
				14.1.1.4 Waterlogging
				14.1.1.5 Nutrient Deficiency
		14.2 Transcriptome Analysis Approaches in Jatropha
			14.2.1 Transcriptome Profiling
				14.2.1.1 Drought
				14.2.1.2 Salinity
				14.2.1.3 Cold
				14.2.1.4 Waterlogging
				14.2.1.5 Nutrient Deficiency
			14.2.2 Genome-Wide Identification and Functional Analysis of Gene Families
		14.3 Application of Jatropha Transcriptomics
			14.3.1 Functional Analysis of Stress-Responsive Genes
			14.3.2 Generation of Transgenic Plants
		14.4 Conclusion
		References
Part III: Oil Crop Biotechnology
	Chapter 15: Oilseed Crops as the Alternate Source of Omega Fatty Acids: A Paradigm Shift
		15.1 Introduction
		15.2 Oilseeds: Novel Sources of Omega Fatty Acids
		15.3 Omega Fatty Acid Composition of Oilseeds
		15.4 Synthesis of Series of Omega Fatty Acids
		15.5 Genetic Regulation of Omega Fatty Acid Concentration in Oilseeds
		15.6 Extraction of Omega Fatty Acids from Oil Seeds
		15.7 Encapsulation of Omega Fatty Acids from Oil Seeds
		15.8 Commercial Applications of Omega Fatty Acids from Oil Seeds
		15.9 Therapeutic Effects of Omega Fatty Acids from Oilseeds
		15.10 Conclusions
		References
	Chapter 16: Genetic Manipulation for Developing Desired Engineered Oil Crops
		16.1 Introduction
		16.2 Methods to Obtain Transgenic Oil Crops
		16.3 Techniques to Analyze or Characterize Putative Transgenic Oil Crops
			16.3.1 Phenotypic Assays
			16.3.2 Polymerase Chain Reaction
			16.3.3 Southern and Western Blot Hybridization
			16.3.4 Next-Generation Sequencing Technologies
			16.3.5 Progeny Analysis/Backcross Breeding
			16.3.6 Bioassay
		16.4 Modification of Oil Crops for Agricultural Traits
			16.4.1 Soybean (Glycine max L.)
			16.4.2 Palm (Elaeis guineensis)
			16.4.3 Peanuts (Arachis hypogaea)
		16.5 Genetic Engineering for Development of Insect Resistance in Oil Crops
		16.6 Genetic Engineering for Development of Disease Resistance in Oil Crops
			16.6.1 Virus Resistance
			16.6.2 Fungal Resistance
			16.6.3 Bacterial Resistance
		16.7 Development of Herbicide-Resistant Oil Crops
		16.8 Development of Plants Resistant to Various Abiotic Stresses
			16.8.1 Drought Tolerance
			16.8.2 Heat Resistance
			16.8.3 Salinity Tolerance
		16.9 Improvement in Nutritional Quality and Oil Production
		16.10 Conclusion
		References
	Chapter 17: CRISPR Applications in Crops
		17.1 Introduction
		17.2 Mechanism of CRISPR/Cas9
		17.3 Genome Editing in Plants
		17.4 CRISPR Construct Delivery Methods for Plant Cells
			17.4.1 Agrobacterium-Mediated T-DNA Delivery
			17.4.2 Protoplast Transfection
			17.4.3 Particle Bombardment
		17.5 Agricultural Applications of CRISPR/Cas9
			17.5.1 CRISPR/Cas9 on Yield Improvement
			17.5.2 CRISPR/Cas9 to Improve Disease Resistance
			17.5.3 CRISPR/Cas9 to Increase Drought Tolerance
			17.5.4 CRISPR/Cas9 to Improve Resistance Against Pests
		17.6 Conclusion
		References
	Chapter 18: Applications of CRISPR/Cas9 in Oil Crops to Improve Oil Composition
		18.1 Introduction
		18.2 CRISPRed Oil Crops
			18.2.1 Soybean
			18.2.2 Rapeseed
			18.2.3 Cotton
			18.2.4 Melon
			18.2.5 Oil Palm
			18.2.6 Linseed (Flax)
			18.2.7 Coconut
			18.2.8 Mustard
			18.2.9 Opium Poppy
			18.2.10 Jatropha
			18.2.11 Camelina
		18.3 Future Perspective
		References
	Chapter 19: Economics of Oil Plants: Demand, Supply, and International Trade
		19.1 Introduction
		19.2 Green Revolution and Oil Crops
		19.3 Demand of Oil Crops
			19.3.1 Population and Urbanization
			19.3.2 Income
			19.3.3 Prices
			19.3.4 Health and Nutrition
		19.4 Profitability Analysis of Oil Crops
		19.5 Role of Oil Crops in Poverty Alleviation
		19.6 Oil Crops in Global Trade
		19.7 Conclusion
		References
	Chapter 20: Production and Trade of Oil Crops, and Their Contribution to the World Economy
		20.1 Introduction
		20.2 Latest Trends in Oilseed Production
		20.3 Cultivation and Use of Oilseed Crops
		20.4 Oilseed Crops
			20.4.1 Soybeans
			20.4.2 Rapeseed
			20.4.3 Cotton
			20.4.4 Palms
			20.4.5 Sunflower
			20.4.6 Peanut
			20.4.7 Coconut
			20.4.8 Olive
		20.5 Conclusion and Future Perspective
		References
Index