The Saffron Genome

Preface to the Series
Contents
Contributors
Abbreviations
Introduction
1 Crocus Sativus Saffron: A 360-Degree Overview
	Abstract
	1.1 Introduction
	1.2 Origin and History of Saffron
	1.3 Dissemination, Production and Economic Value
	1.4 Physio-Morphological Traits
	1.5 Cytogenetics and Penological Stages of Saffron
	1.6 Climatic Adaption
	1.7 Agronomical Practices
		1.7.1 Major Planting Parameters
		1.7.2 Corm Characteristics: Size, Weight and Storage
		1.7.3 Fertilizers and Biostimulants
		1.7.4 Crop Rotation and Intercropping
		1.7.5 Irrigation
		1.7.6 Harvesting of Flowers
		1.7.7 Post-Harvest Treatment
	1.8 Phytochemistry of Saffron
	1.9 Saffron Adulteration
	1.10 Biotechnological Interventions
		1.10.1 Tissue Culture (in Vitro Culturing)
		1.10.2 Role of Genome Editing in Saffron
	1.11 Saffron’omics’
		1.11.1 Genomics
		1.11.2 Transcriptomics
		1.11.3 Microbiome
		1.11.4 Metabolomics
		1.11.5 Proteomics
	1.12 Conclusion and Future Research Recommendations
	Ethics Declarations
	References
Omics Studies on Saffron
2 Reference Genome of Saffron “The Golden Condiment”
	Abstract
	2.1 Introduction
	2.2 Saffron, Crocus sativus L.
	2.3 Crocus sativus, Triploidy and Sterility
	2.4 Available Genomic Resources of Saffron
		2.4.1 Genetic Diversity
		2.4.2 Saffron Transcriptomics
		2.4.3 Saffron Genome
			2.4.3.1 Repetitive Region in Crocus Sativus Genome and SSR Marker Prediction
			2.4.3.2 Gene Prediction and Annotation
			2.4.3.3 Transcription Factors
			2.4.3.4 Orthology Analysis
			2.4.3.5 Metabolic Pathway Analysis
	2.5 Conclusion
	References
3 SaffronOMICS: Novel Approaches Toward Putting Saffron Data at Work
	Abstract
	3.1 Introduction
	3.2 How OMICS-Based Approaches Benefit Saffron Trade
	3.3 OMICS Approaches in Saffron
	3.4 Genomics of Saffron and Allied Species
	3.5 Transcriptomics
	3.6 Metabolomics
	3.7 Proteomics
	3.8 History of Saffron Cultivation and Domestication
	3.9 Saffron Genome Structure and Essential Key Points to Decode the Genome of Red Gold
	3.10 Decode the Genome of Red Gold
	3.11 Conclusions
	References
4 Bioinformatics for Saffron-Omics and Crop Improvement
	Abstract
	4.1 Introduction
	4.2 Why Is Bioinformatics Important?
	4.3 Bioinformatics for Saffron-Omics
		4.3.1 Saffron Flowering and Stigma Development
		4.3.2 Saffron Corm Rot
		4.3.3 Molecular Modelling
	4.4 Bioinformatics Resources for Crop Improvement and Omics Studies
		4.4.1 SAM and BCF Tools
		4.4.2 MEGA
		4.4.3 Trinity
		4.4.4 SMART 9
		4.4.5 MPI Bioinformatics Toolkit
		4.4.6 BiGGEsTS
		4.4.7 PlantGDB
		4.4.8 KEGG
		4.4.9 TrichOME
		4.4.10 PlantTFcat
		4.4.11 PlnTFDB
		4.4.12 Ensembl Plants
		4.4.13 WEGO
		4.4.14 edgeR
		4.4.15 Bowtie
		4.4.16 KaPPA-View
		4.4.17 Transcriptogramer
		4.4.18 Cufflinks
		4.4.19 Paintomics
		4.4.20 PIECE
		4.4.21 MISA-Web
		4.4.22 Prodigal
		4.4.23 GeneMarkS-T
		4.4.24 MaxQuant
		4.4.25 Perseus
		4.4.26 GenAlex
		4.4.27 DnaSP
		4.4.28 TransDecoder
		4.4.29 RepeatMasker Package
		4.4.30 GenoType and GenoDive
		4.4.31 PsRNATarget
		4.4.32 DESeq2 Package
	4.5 Future Perspective
	Acknowledgements
	References
5 Genetic Mapping and Molecular Markers in Saffron
	Abstract
	5.1 Introduction
	5.2 An Overview of Breeding in Saffron and Wild Allies
	5.3 Molecular Markers in Saffron and Its Wild Allies
	5.4 Approaches Towards Saffron Breeding
	References
Microbiomics
6 Soil Classification, Nutrient Management and Land Cover of Saffron Growing Areas of Kashmir Valley
	Abstract
	6.1 Introduction
	6.2 Location and Climatic Description
	6.3 Methodology of Soil Classification and Nutrient Management
	6.4 Site and Morphological Characteristics
	6.5 Physico-chemical Properties and Particle Size Distribution
	6.6 Mineralogical Make Up of These Soils
	6.7 Soil Classification
	6.8 Nutrient Management for Sustainable Saffron Production
	6.9 Land Use–Land Cover and Contours of Saffron Growing Area
	References
7 Cultromic and Metabarcodic Insights into Saffron-Microbiome Associations
	Abstract
	7.1 Introduction
	7.2 Microbial Cultivation-Based, Culturomic Approach
		7.2.1 Culturable Rhizosphere, Cormosphere and Bulk Soil Microbiome
			7.2.1.1 Isolation and Characterization of Pathogens by Culturomics
			7.2.1.2 Isolation and Characterization of Bacterial Diversity and PGPB by Culturomics
			7.2.1.3 Isolation and Characterization of Endophytes by Culturomics
	7.3 Cultivation-Independent Metabarcoding Approach for Microbiome Studies
		7.3.1 Microbiome Across Saffron Niches During Different Growth Stages
		7.3.2 Microbiome Across Different Geographical Location
	7.4 Conclusions
	References
8 Saffron, Bacteria and Mycorrhiza
	Abstract
	8.1 Introduction
		8.1.1 Sustainable and Organic Agriculture
		8.1.2 Bio-Fertilizers
		8.1.3 Types of Soil Bacteria and the Role of Reinforcing Them
		8.1.4 ACC Deaminase
		8.1.5 Enzymes and Biochemical Properties
		8.1.6 Mycorrhiza Fungi
		8.1.7 Positive Effects of Bio-Fertilizers on Saffron
	8.2 Conclusion
	References
9 Diversity and Bioprospection of the Fungal Endophytic Microbiome of Crocus sativus L. (Saffron)
	Abstract
	9.1 Introduction
	9.2 Decline in Saffron Productivity: Causes and Concerns
	9.3 Plant Endophyte Interactions: A Way Forward for Sustainable Agriculture
	9.4 Plant–Microbe Association in C. sativus
	9.5 Fungal Endophytic Microbiome of C. sativus
	9.6 Bioactive Potential of Fungal Endophytes of C. sativus
	9.7 Conclusion
	References
10 Epidemiology and Management of Corm Rot of Saffron
	Abstract
	10.1 Epidemiology of Corm Rot Complex
	10.2 Management
	References
11 Pathogenicity and Genetic Diversity of Microbes in Crocus Sativus L. and Various Strategies Combating Diseases
	Abstract
	11.1 Introduction
	11.2 Phytochemistry and Therapeutic Uses
	11.3 Diversity and Cultivation
	11.4 Pathogenicity and Genetic Diversity of Microbes
	11.5 Plant Defense Response
	11.6 Strategies to Combat the Diseases of Crocus Sativus
	11.7 Conclusion and Prospects
	Author Contributions
	References
In-vitro Micropropagation in Saffron
12 Tissue Culture Techniques for Saffron Improvement
	Abstract
	12.1 Introduction
	12.2 In Vitro Micropropagation of Crocus Species
	12.3 Tissue Culture Techniques and Workflow
		12.3.1 Explants and Surface Sterilization
		12.3.2 Tissue Culture Media
		12.3.3 Tissue Culture Approaches in Saffron
			12.3.3.1 Organogenesis
				Indirect Organogenesis and Callugenesis
				Direct Organogenesis
				Stigma-Like Structure and Callus Culture Towards Apocarotenoids Production
			12.3.3.2 Somatic Embryogenesis
			12.3.3.3 Gene Transformation and Genetic Improvement in Saffron
	12.4 Conclusion
	References
13 Saffron Production Under Controlled Conditions
	Abstract
	13.1 Introduction
	13.2 In Vitro Culture
		13.2.1 Disinfection
		13.2.2 Somatic Embryogenesis
		13.2.3 In Vitro Corm Acclimatization
		13.2.4 Interspecific Hybridization
		13.2.5 Production of Saffron Metabolites in Vitro
	13.3 Saffron Production Under Control Condition Ex Vitro (Greenhouse)
		13.3.1 Cultivation Methods
		13.3.2 Nutrition Management
		13.3.3 Water Availability
		13.3.4 Drought and Salt Stress Under Greenhouse Culture
		13.3.6 CO2 and Saffron Production
		13.3.7 Technology Progress and Mechanization of Saffron Production
	13.4 Conclusion
	References
Saffron Metabolomics
14 Saffron: Metabolomics and Quality Point of View
	Abstract
	14.1 Chemical Compounds in Saffron
	14.2 Color in Saffron
	14.3 Flavor in Saffron
	14.4 Aromatic Compounds in Saffron
	14.5 Medicinal and Therapeutic Properties of Saffron
	14.6 Extraction of Compounds from Saffron Stigma 
	14.7 Traditional Methods
	14.8 New Methods and Approaches
		14.8.1 Ultrasonic Extraction
		14.8.2 Steam Distillation
		14.8.3 Emulsion Liquid Membrane
		14.8.4 Supercritical Fluid Extraction
		14.8.5 Solid Phase Extraction (SPE)
		14.8.6 Crystallization
		14.8.7 Two-Phase Water System
		14.8.8 Cold Trap
		14.8.9 Chromatography
	14.9 Conclusion
	References
15 Saffron in Phytotherapy: Pharmacological Properties and Medicinal Uses
	Abstract
	15.1 Saffron Through History
	15.2 Saffron Phytochemistry
	15.3 Pharmacokinetics of Saffron Active Components
	15.4 Therapeutic Applications of Saffron
		15.4.1 Neuroprotective Activity
			15.4.1.1 Depression
			15.4.1.2 Alzheimer’s Disease
			15.4.1.3 Schizophrenia
			15.4.1.4 Antioxidant Activity
			15.4.1.5 Anti-Inflammatory Activity
			15.4.1.6 Antibacterial Effect
			15.4.1.7 Toxicity
	15.5 Conclusion
	References
Saffron Market, Trade and Production
16 Economic Aspects of Saffron in the World
	Abstract
	16.1 Introduction
	16.2 Introducing of Saffron
	16.3 Socio-economic Aspects of Saffron Production
	16.4 Saffron Production Around the World
	16.5 Trade
		16.5.1 Export of Saffron
		16.5.2 Import of Saffron
	16.6 Price of Saffron
	16.7 Economic Performance of Saffron
		16.7.1 Return on Investment (ROI)
		16.7.2 Ratio of Return to Cost (RRC)
	16.8 Uses of Saffron
		16.8.1 Food Industry
		16.8.2 Medicine
		16.8.3 Textile Dye
		16.8.4 Perfume
	16.9 Marketing
	16.10 Saffron Processing
	16.11 Saffron Value Chain
	16.12 Future Research
	References
17 Marketing Prospects for Saffron in Domestic Market: The Case of Moroccan PDO “Saffron of Taliouine”
	Abstract
	17.1 Introduction
	17.2 Methodological Framework
		17.2.1 Strategic Analysis of Moroccan Saffron Sector
		17.2.2 Factorial and Cluster Analysis
		17.2.3 Willing to Pay for the PDO “Saffron of Talouine”
	17.3 The Empirical Application
	17.4 Results
		17.4.1 Strategic Analysis of the Moroccan Saffron Sector
		17.4.2 Reduction by Factor Analysis
		17.4.3 Cluster Analysis
		17.4.4 Willing to Pay Model
	17.5 Conclusion
	References