The Seabuckthorn Genome

Preface to the Series
Foreword
Preface
Contents
Contributors
Abbreviations
1 Biosystematics and Botanical Descriptions of Seabuckthorn (Hippophae Sp.) in India
Abstract
1.1 Introduction
1.2 Taxonomic History and Current Status of the Genus Hippophae L.
1.2.1 Current Biosystematics of Hippophae Sp.
1.2.1.1 Hippophae rhamnoides
1.2.1.2 Hippophae salicifolia
1.2.1.3 Hippophae tibetana
1.3 Variations in Seabuckthorn Morphology
1.3.1 Hippophae rhamnoides
1.3.1.1 Habitat
1.3.1.2 General Morphology
1.4 Morphotypes Distinguishing Features
1.5 Genetic Variability Assessment
1.5.1 Hippophae salicifolia
1.5.2 Morphological Variations
1.5.2.1 Variability of Fruits Physical Characteristics
1.5.2.2 Variation in Chemical Properties of Fruits
1.5.2.3 Variation in Seed, Pomace, and Juice Content of Hippophae salicifolia Fruits
1.6 Conclusion
References
2 Genetic Diversity, Evolution, and Biogeography of Seabuckthorn
Abstract
2.1 Introduction: Why to Study Intraspecific Genetic Diversity?
2.1.1 Protection and Conservation of Genetic and Biodiversity
2.1.2 Association Between Genetic Diversity and Fitness of Populations
2.1.3 Factors Shaping Intraspecific Genetic Diversity in Plants
2.1.3.1 Genetic Diversity at Equilibrium
2.1.3.2 Historical Processes
2.1.3.3 Adaptive Processes
2.1.3.4 Genetics of Populations and Biological Characteristics of Plants
2.2 Taxonomy, Systematics, and Evolution of Elaeagnaceae and Hippophae
2.2.1 Taxonomy and Systematics of Hippophae
2.2.2 Phylogeny and Biogeography
2.2.2.1 Molecular Phylogenies and Biogeography of Elaeagnaceae
2.2.2.2 Molecular Phylogenies and Biogeography of Hippophae
2.2.3 Phylogeography of Different Species of Hippophae
2.2.3.1 Western Subspecies of H. rhamnoides
2.2.3.2 Eastern Subspecies of H. rhamnoides
2.2.3.3 H. rhamnoides subsp. mongolica
2.2.3.4 H. gyantsensis
2.2.3.5 H. neurocarpa
2.2.3.6 H. tibetana
2.2.3.7 Directions of Further Phylogeographic Studies in Hippophae
2.3 Genetic Diversity
2.3.1 Genetic Diversity in Populations of Different Species
2.3.1.1 Molecular Markers and Variation in Samples of Loci and Plants
2.3.1.2 Western Subspecies of H. rhamnoides
2.3.1.3 Eastern Subspecies of H. rhamnoides
2.3.1.4 Eastern Species of Hippophae
2.3.1.5 High Genetic Diversity Within Populations Based on Microsatellite Markers
2.3.2 Genetic Differentiation Between Populations of Different Species
2.3.2.1 Partitioning of Genetic Diversity Within the Genus
2.3.2.2 Genetic Differentiation in Western Subspecies of H. rhamnoides
2.3.2.3 Genetic Differentiation in Eastern Subspecies of H. rhamnoides
2.3.2.4 Genetic Differentiation in Other Species of Hippophae
2.3.2.5 Genetic Differentiation Between Populations Across Different Studies and Molecular Markers
2.4 Interspecific Hybridization in the Genus
2.4.1 Evolutionary Recent Hybridization
2.4.2 Evolutionary Ancient Hybridization
2.4.3 New Hybrid Taxa Indicated by Molecular Analyses
2.4.4 Hybrid Zones Across the Range of Hippophae
2.5 Assessment of Gene Bank Collections
2.5.1 Why Assessment of Gene Bank Collections is Necessary?
2.5.2 Assessment of Cultivars Developed from Siberian and Western Subspecies of H. rhamnoides
2.5.3 Assessment of Cultivars Developed in Chinese Breeding Programs
2.5.4 Assessment of Cultivars Developed in Other Breeding Programs
2.5.5 General Overview of Assessment of Cultivars
2.6 Preservation of Genetic Diversity in Hippophae
2.7 Prospects of Studies on Genetic Diversity in Hippophae
2.8 Conclusions
Acknowledgements
References
3 Current Status of Chromosome-Based Gender Determination in Seabuckthorn
Abstract
3.1 Introduction
3.2 Cytogenetics of Hippophae rhamnoides: A Riddle
3.3 Gender Determination Mechanisms: Where Hippophae Stands?
3.3.1 Status of Sex Chromosomes
3.3.2 Sexual System and Gender Determination in Hippophae rhamnoides
3.4 Gender-Specific Markers and Clue of Gender Determination
3.5 Hormonal and Environmental Control of Gender Determination
3.6 X: Autosome Ratio and Epigenetics of Gender Determination
3.7 Conclusions and Future Perspective
References
4 Analytical Techniques for the Biochemical Profiling in Seabuckthorn
Abstract
4.1 Introduction
4.2 Targeted Analysis of Seabuckthorn Constituents
4.2.1 Chromatographic Methods
4.2.1.1 Liquid Chromatography
4.2.1.2 Gas Chromatography
4.2.2 Capillary Electrophoresis
4.2.3 Elemental and Isotopic Fingerprint
4.3 Non-targeted Metabolomics for Seabuckthorn Authentication
4.3.1 Vibrational Spectroscopy (IR and Raman)
4.3.2 NMR Spectroscopy
4.4 Conclusions and Perspectives
Acknowledgements
References
5 Effect of Processing and Storage on Seabuckthorn Products
Abstract
5.1 Introduction
5.2 Processing of Seabuckthorn Berries—Chemical Changes, Processing and Storage
5.2.1 Pre-processing of Berries
5.2.2 Juice Production
5.2.3 Jam Production
5.3 Processing of Seabuckthorn Oil—Chemical Changes, Processing and Storage
5.3.1 Processing of Seeds and Berries Before Oil Extraction
5.3.2 Fatty Acids Profile and Processing of Seabuckthorn Oil
5.3.3 Oxidative Stability of Seabuckthorn Oil
5.4 Products Fortified with Seabuckthorn
5.4.1 Yoghurts
5.4.2 Drinks
5.5 Extraction of Seabuckthorn Compounds and Their Preservation
5.5.1 Ultrasound-Assisted Extraction
5.5.2 Microwave-Assisted Extraction (MAE)
5.5.3 Subcritical Water Extraction
5.5.4 Supercritical Carbon Dioxide Extraction
5.6 Conclusions and Future Remarks
References
6 Metabolomic Diversity of Seabuckthorn Collections from Different Geographical Regions
Abstract
6.1 Introduction
6.2 Major Compounds of Seabuckthorn Associated with Health Benefits
6.3 Effect of Limiting Climatic Factors Prevailing at Different Geographical Regions on Metabolites
6.3.1 Primary Metabolites
6.3.1.1 Sugars
6.3.1.2 Organic Acids
6.3.1.3 Fatty Acids
6.3.2 Secondary Metabolites
6.3.2.1 Phenolic Compounds
6.3.2.2 Flavonoids
6.3.2.3 Ascorbic Acid
6.3.2.4 Sugar Alcohols
6.4 Environmental Variation in Different Groups of Compounds
6.5 Role of Different Metabolites in the Sensory Attributes of Seabuckthorn
6.5.1 Sourness and Sweetness
6.5.2 Astringency
6.5.3 Bitterness
6.6 Analytical Techniques Used to Identify Metabolites
6.7 Application of Spectroscopic Techniques in Combination with Chemometrics
6.8 Importance of Metabolomic Diversity
6.9 Conclusions and Future Perspective
Acknowledgements
References
7 Deciphering the Proteomes and Nanotechnological Potential of an Unexplored Plant Seabuckthorn
Abstract
7.1 Introduction
7.2 Gel-Based and Gel-Free Proteomics
7.3 Application of Proteomics in Resolving the Proteomes of Different Seabuckthorn Tissues
7.3.1 Seedling Proteome
7.3.2 Leaf Proteome
7.3.3 Berry Proteome
7.4 Post-translational Modification Proteomes
7.4.1 Phosphoproteome
7.4.2 Glycoproteome
7.5 Nanotechnological Potential of Seabuckthorn Extracts
7.6 Conclusion
Acknowledgements
References
8 Biotechnological Approaches for Seabuckthorn Improvement
Abstract
8.1 Introduction
8.2 Classical Improvement Efforts in Seabuckthorn
8.3 Genomic Landscape: Gene Resources and Repetitive DNA
8.3.1 Repetitive DNA in Seabuckthorn Genome
8.3.2 Plastid Genome
8.4 Biotechnology Assisted Crop Improvement
8.4.1 Biotechnology for Authentication of Genetic Material in Seabuckthorn
8.4.2 Biotechnology for Sex Discrimination at Early Stage
8.4.3 Metabolomic Environment of Seabuckthorn
8.4.4 Micropropagation and Somatic Embryogenesis
8.4.4.1 Micropropagation
8.4.4.2 Callus Induction
8.4.4.3 Somatic Embryogenesis
8.4.4.4 Genetic Transformation of Seabuckthorn
8.5 Conclusion and Future Prospects
References
9 Repertoire of Molecular Markers and Their Applications in Seabuckthorn
Abstract
9.1 Introduction
9.2 Taxonomy of the Genus Hippophae
9.3 Genetic Diversity and Phylogenetic Relationships
9.4 Sex Determination in Seabuckthorn
9.5 Mapping Studies in Seabuckthorn
9.6 Future Opportunities for Seabuckthorn Improvement
9.7 Conclusion
References
10 Identification of Hippophae Species Using DNA Barcoding
Abstract
10.1 Introduction
10.2 Identification of Hippophae Species Using DNA Barcoding-Based Identification of Hippophae Species
10.2.1 Barcoding Marker Selection
10.2.2 Materials
10.2.2.1 DNA Extraction, Amplification, Sequencing, and Analysis
10.2.3 Inter- and Intra-specific Variation
10.2.4 Analysis of Barcoding Gaps
10.2.5 Analysis of Phylogenetic Neighbor‑Joining Trees
10.3 In-Depth Discrimination Between Hippophae Species and Validation of Bar-HRM in Commercial Seabuckthorn Products
10.3.1 Materials
10.3.1.1 DNA Extraction, Amplification, Sequencing, and Analysis
10.3.2 Validation of Bar-HRM for Identification and Discrimination of Specimen Plants
10.3.3 Validation of Bar-HRM for Species Identification and Discrimination of Bulk Hippophae Products
10.3.4 Examination of a Non-conforming Sample
10.3.4.1 Identification of Adulterating Material
10.4 Conclusions
References
11 Transcriptome Sequencing and Analysis of Seabuckthorn (Hippophae Sp.)
Abstract
11.1 Introduction
11.2 Transcriptome Sequencing and Bioinformatics Analysis
11.3 Complete Transcriptome Profiling of Seabuckthorn: Challenges and Breakthrough
11.3.1 Transcriptome Analysis for Fatty Acid Composition in Seabuckthorn Mature Seeds
11.3.2 De Novo Assembly of Seabuckthorn Transcriptome
11.4 Seabuckthorn Transcriptome Analysis for Different Prospects
11.4.1 DeepSAGE-Based Transcriptome Analysis in Seabuckthorn Under Cold and Freeze Stress
11.4.2 De Novo Transcriptome Analysis of Male and Female Seabuckthorn
11.4.3 Seabuckthorn Transcriptome Analysis Under Drought Stress
11.4.4 Transcriptome Analysis in Response to Carbon Dioxide (CO2) Elevation in Seabuckthorn
11.4.5 RNA-Seq-Based Fatty Acids Analysis in Seabuckthorn Berry Pulp
11.5 Perspectives of Second- and Third-Generation Sequencing Technology and Seabuckthorn
11.6 Conclusion
References
12 Mining of Microsatellites and Transcription Factors in Seabuckthorn (Hippophae Sp.) Transcriptomes
Abstract
12.1 Introduction
12.2 Microsatellites
12.3 Transcription Factors (TFs)
12.4 Next-Generation Sequencing (NGS) Technology
12.5 Applications of NGS in Seabuckthorn
12.6 Comparative Transcriptome Analysis in Seabuckthorn: Hippophae rhamnoides Versus Hippophae salicifolia
12.6.1 Transcriptome Analysis in Hippophae rhamnoides L.
12.6.2 Transcriptome Analysis in Hippophae salicifolia
12.7 Comparative Analysis of Microsatellite Abundance in Hippophae rhamnoides L. and Hippophae salicifolia
12.7.1 Occurrence of Microsatellites in Transcriptome Assembly of Hippophae rhamnoides L.
12.7.1.1 Sequence Resource
12.7.1.2 Microsatellite Mining in Seabuckthorn Transcriptome
12.7.1.3 Microsatellite Dynamics in Seabuckthorn H. rhamnoides Transcriptome
12.7.1.4 Functional Assessment of Microsatellite Positive Unigenes
12.7.1.5 Microsatellites Position Within the Genes
12.7.1.6 Codon Usage of Tri-Nucleotide Repeats
12.7.2 Occurrence of Microsatellites in Transcriptome Assembly of Hippophae salicifolia
12.7.2.1 Sequence Resource
12.7.2.2 Microsatellite Mining in H. salicifolia Transcriptome
12.7.2.3 Functional Assessment of Microsatellite Carrying Unigenes
12.7.2.4 Position of Microsatellite Within the Genes
12.7.2.5 Codon Usage of Tri-Nucleotide Repeats
12.7.3 Microsatellite-Based Molecular Markers
12.7.4 Gender-Based Occurrence of Microsatellites in Hippophae salicifolia Transcriptomes
12.8 Comparative Occurrence of Transcription Factors in the Transcriptome of Hippophae rhamnoides and Hippophae salicifolia
12.8.1 Transcription Factors in Hippophae rhamnoides Transcriptome Assembly
12.8.2 Transcription Factors in Hippophae salicifolia Transcriptome Assembly
12.8.3 Gender-Specific Distribution of Transcription Factors in the Hippophae salicifolia Transcriptome
12.9 Conclusion
References
13 Frankia—The Endo-Micro-Symbiont of Hippophae Sp.
Abstract
13.1 Introduction
13.2 The Symbiotic Nitrogen Fixers
13.2.1 The Actinorhizal Symbiosis
13.2.1.1 What is Frankia?
13.2.1.2 Morphology of Frankia in Actinorhizal Root Nodules
13.2.1.3 Morphology of Frankia in Culture
13.2.1.4 Nodule Formation
13.2.1.5 Molecular Biology of Frankia
13.2.1.6 Whole-Genome Sequencing of Frankia
13.2.1.7 Bioinformatics of Frankia
13.2.1.8 Studies on Entrapment of Frankia in Alginate Beads and Its Application
13.3 Studies on Frankia Associated with Seabuckthorn
13.3.1 The Endophyte Within Nodules of Hippophae Sp.
13.3.2 Isolation of Endophyte from Root Nodules of Hippophae Sp.
13.3.3 Infectivity Potential of Hippophae Frankia
13.3.4 Nitrogenase Activity of Hippophae Frankia
13.3.5 Diversity of Hippophae Frankia
13.4 Conclusions and Future Directions
References
14 Medicinal and Nutraceutical Properties of Seabuckthorn
Abstract
14.1 Introduction
14.2 Traditional Uses
14.3 Phytochemical Components: Leaves, Fruits, Seeds, Pulp, and Oil
14.4 Medicinal Activity
14.4.1 Antioxidant
14.4.2 Immunomodulatory Activity
14.4.3 Anti-stress and Adaptogenic Activity/Protective Effects Against High-Altitude Stress
14.4.4 Anti-cancer Activity
14.4.5 Antibacterial and Antiviral Activity
14.4.6 Antidiabetic Activity
14.4.7 Ameliorate Obesity and Obesity-Associated Lipid Metabolism
14.4.8 Hepatotoxicity and Liver Fibrosis
14.4.9 Beneficial Effects Against Heavy Metal Toxicity
14.5 Clinical Studies/Human Data Available
14.6 Nutraceutical Applications of Seabuckthorn
14.7 Food Applications
14.8 Safety and Toxicity Studies
14.9 Conclusion and Future Directions
References
15 Molecular and Cellular Mechanisms of the Anti-oxidative Activity of Seabuckthorn (Hippophae rhamnoides L.)
Abstract
15.1 Introduction
15.2 Anti-oxidative Effects of Seabuckthorn Extracts
15.2.1 Leaf Extracts
15.2.2 Berry Extracts
15.2.3 Oil Extracts
15.3 Anti-oxidative Effects of the Main Components in Seabuckthorn
15.3.1 Polyphenols
15.3.2 Flavonoids
15.3.3 Polysaccharides
15.3.4 Others
15.4 Mechanisms Underlying the Anti-oxidative Effects of Seabuckthorn
15.4.1 Up-Regulation of the Nrf-2/ARE Anti-oxidative System
15.4.2 Cross-Talk with the Anti-inflammation Signaling Pathway
15.4.3 Cross-Talk with the Metabolic Pathway
15.4.4 Modulation of the Microbiota
15.4.5 Others
15.5 Conclusion and Perspective
Acknowledgements
References
16 Knowing More About Seabuckthorn (Hippophae rhamnoides)— A Promising Source of Safe and Effective Medical Radiation Countermeasure
Abstract
16.1 Introduction
16.2 Radiation Countermeasures and Radioprotective Potential of Hippophae rhamnoides
16.3 Understanding the Plant Rhizosphere and Root Characteristics
16.3.1 Physico-chemical Characteristics of Soil
16.4 Root Histology, Isolation of Microorganisms from Nodules and Rhizosphere
16.5 Discussion and Conclusion
Acknowledgements
References
17 Methods in Seabuckthorn Breeding
Abstract
17.1 Introduction
17.2 Genetic Diversity and Breeding Scope
17.2.1 Genetic Diversity
17.2.2 Breeding Scope
17.3 Breeding Strategies
17.3.1 Mass Selection
17.3.2 Hybridization
17.3.3 Induced Mutations
17.3.4 Biotechnological Approach
17.4 Breeding Objectives
17.4.1 Fruit Yield
17.4.2 Fruit Size
17.4.3 Thornlessness
17.4.4 Berry Harvesting
17.4.5 Oil Content
17.4.6 Sweet Berry Forms
17.4.7 Resistance to Insect-Pest and Diseases
17.4.8 Early Fruiting
17.4.9 Winter Hardiness
17.4.10 Pollen Characteristics
17.4.11 Ornamental Value
17.5 Breeding Efforts in Different Countries
17.5.1 Russia
17.5.2 China
17.5.3 Germany
17.5.4 Canada
17.5.5 USA
17.5.6 Sweden
17.5.7 Finland
17.5.8 India
17.5.9 Czechoslovakia
17.6 Elite Cultivars
17.7 Conclusion and Prospects
References
18 Global Distribution of Seabuckthorn (Hippophae Sp.) Resources and Their Utilization
Abstract
18.1 Introduction
18.2 Global Distribution
18.2.1 Climatic Adaptation
18.2.2 Geographical Distribution
18.2.3 Himalayas
18.2.4 China
18.2.5 Russia
18.2.6 Central Asia
18.2.7 Europe
18.2.8 North and South America
18.3 Utilization of Seabuckthorn
18.3.1 Health Food
18.3.2 Skincare
18.3.3 Health Protection
18.3.4 Fodder and Feed
18.3.5 Fuelwood
18.3.6 Environmental Conservation
18.4 Global Market
18.5 Conclusion
References