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