The Citrus Genome (Compendium of Plant Genomes)

Preface to the Series
Preface
Contents
1 The Citrus Genome: Past, Present and Future
	Abstract
	Acknowledgements
	References
2 Citrus Origin, Diffusion, and Economic Importance
	Abstract
	2.1 On the Origin Center of Citrus
	2.2 Inference from Citrus Domestication History
	2.3 Inference from the Distribution of Extant Wild Citrus
	2.4 Inference from Genomic Data
	2.5 On the Origins of Some Important Citrus Species
		2.5.1 Sweet Orange
		2.5.2 Clementine
		2.5.3 Citron
		2.5.4 Pummelo
		2.5.5 Grapefruit
		2.5.6 Mandarins
	2.6 Citrus Economic Importance
		2.6.1 Major Citrus Production Areas
	2.7 Main Commercial Citrus Groups and Producing Countries
		2.7.1 Sweet Oranges
		2.7.2 Mandarins
		2.7.3 Grapefruit
		2.7.4 Lemons and Limes
	References
3 Genetic Resources of Citrus and Related Genera
	Abstract
	3.1 Introduction
	3.2 Present Status of the Citrus Genetic Resources Around the World
	3.3 Significance of Citrus Genetic Resources for Breeding
	3.4 Major Challenges for Citrus Genetic Resources
	3.5 Present Activity and Future Challenges
	Acknowledgements
	References
4 Conventional Breeding of Cultivated Citrus Varieties
	Abstract
	4.1 Aspects of Citrus Biology Related to Breeding
	4.2 Origin of Cultivated Citrus Varieties
	4.3 Breeding Methods
		4.3.1 Hybridization
		4.3.2 Mutagenesis
		4.3.3 Clonal Selection
	4.4 Important Breeding and Selection for Important Traits
		4.4.1 Peel Color
		4.4.2 Fruit Size and Shape
		4.4.3 Ease of Peeling
		4.4.4 Seedlessness
		4.4.5 Fruit Flavor
		4.4.6 Blood Mandarins
		4.4.7 Furanocoumarins
		4.4.8 Yield and Alternate Bearing
		4.4.9 Harvesting Season
		4.4.10 Pest and Disease Resistance
		4.4.11 Long Shelf Life
	4.5 Conclusions
	Acknowledgements
	References
5 Citrus Rootstock Breeding and Selection
	Abstract
	5.1 Introduction
	5.2 Dominant Rootstocks
		5.2.1 Sour Orange
		5.2.2 Citranges
		5.2.3 Citrumelos
		5.2.4 Trifoliate Orange
		5.2.5 Cleopatra Mandarin
		5.2.6 Alemow or Macrophylla
		5.2.7 Volkamer Lemon
		5.2.8 Emerging Rootstocks (What Looks Good Today from Recent and Ongoing Trials)
	5.3 Abiotic Factors
		5.3.1 Calcareous Soils
		5.3.2 Salinity
		5.3.3 Drought
		5.3.4 Flooding
		5.3.5 Boron Toxicity
	5.4 Biotic Factors
		5.4.1 CTV
		5.4.2 Nematodes
		5.4.3 Blight
		5.4.4 The Diaprepes/Phytophthora (DP) Complex
		5.4.5 HLB (High Throughput Screening Method)
	5.5 Tree Size Control
	5.6 Field Evaluation
		5.6.1 Yield and Yield Efficiency
		5.6.2 Alternate Bearing Index (ABI)
		5.6.3 Fruit Drop
		5.6.4 Fruit Quality Variables
	Acknowledgements
	References
6 Ploidy Manipulation for Citrus Breeding, Genetics, and Genomics
	Abstract
	6.1 Introduction
	6.2 Natural Mechanisms of Polyploidization and Their Implications on the Genetic Diversity of Polyploid Populations
		6.2.1 Chromosome Doubling in Apomictic Lines
		6.2.2 Unreduced Gametes
		6.2.3 Tetraploid Meiosis
	6.3 Biotechnology and Ploidy Manipulation
		6.3.1 Gametic Embryogenesis
		6.3.2 Chromosome Doubling by Chemical Treatments
		6.3.3 Somatic Hybridization
		6.3.4 Cytogenetic and Molecular Tools for Polyploid Genome Studies
	6.4 Haploids and Polyploids as Biological Resources for Phenotypic, Genetic, and Genomic Studies
		6.4.1 Haploids for Genome Sequencing and Haplotyping
		6.4.2 Centromere Mapping from Unreduced Gametes
		6.4.3 Marker–Trait Association Study: The Alternaria alternata Recessive Resistance Gene
		6.4.4 Phenome and Gene Expression in Polyploids
		6.4.5 Polyploidy and Adaptation
	6.5 Ploidy Manipulation for Breeding
		6.5.1 New Developments on Citrus Polyploidy Breeding in China
		6.5.2 Ploidy Manipulation for Cultivar Development at the University of Florida’s Citrus Research and Education Center (Lake Alfred, FL, USA)
		6.5.3 New Developments on Citrus Polyploidy Breeding in the Mediterranean
	References
7 Markers, Maps, and Marker-Assisted Selection
	Abstract
	7.1 Introduction
	7.2 DNA Marker Development
		7.2.1 Background
		7.2.2 RFLP Markers
		7.2.3 PCR-Based Markers
		7.2.4 Application of Genome Information for DNA Marker Development
			7.2.4.1 SSR Marker Development
			7.2.4.2 SNP Markers
			7.2.4.3 CAPS and Other Markers
	7.3 Molecular Markers for Genetic Analysis
		7.3.1 RAPD Marker Analysis
		7.3.2 ISSR and SRAP Marker Analysis
		7.3.3 AFLP Analysis
		7.3.4 SSR and InDel Marker Analysis
		7.3.5 SNP and CAPS Marker Analysis
	7.4 Linkage Map Construction and QTL Mapping
		7.4.1 Linkage Map Construction, a Brief Introduction
		7.4.2 Developed Linkage Maps in Citrus
		7.4.3 High-Throughput Genotyping
		7.4.4 QTL Mapping for Particular Traits
	7.5 Marker-Assisted Selection (MAS)
		7.5.1 Target Traits for MAS
		7.5.2 Available DNA Markers for MAS
		7.5.3 Practical Procedures of MAS in Citrus Breeding
			7.5.3.1 MAS for Polyembryonic Seedlings
			7.5.3.2 Fast and Low-Cost Genotyping
		7.5.4 Quality Control of Genotype Data
		7.5.5 Current Constraints on MAS
	7.6 Future Perspectives
	Acknowledgements
	References
8 Citrus Genomes: From Sequence Variations to Epigenetic Modifications
	Abstract
	8.1 Introduction
	8.2 Genome Assembly
	8.3 Genome Annotation and Databases
	8.4 Transposon Elements in Citrus Genome
	8.5 Citrus Cytogenomics
	8.6 Citrus Unique Genes by Comparative Genomics
	8.7 SNP Marker in Citrus Genome
	8.8 Citrus Population Genomics
		8.8.1 Bulk Segregant Analysis (BSA) Sequencing
		8.8.2 Genome-Wide/Region-Based Association Analyses
		8.8.3 Comparative Population Analyses
	8.9 Transcriptome Analyses
	8.10 MicroRNAs
	8.11 Epigenome
	8.12 Prospects in Genomic Studies of Citrus
	Acknowledgements
	References
9 Citrus Reproductive Biology from Flowering to Fruiting
	Abstract
	9.1 Genetic Regulation of Flowering Induction in Citrus
	9.2 Flower and Gametophytes Development
	9.3 Self-Incompatibility System in Citrus
	9.4 Seed Development and Nucellar Embryony
	References
10 Genomics of Citrus Fruit Ripening
	Abstract
	10.1 Introduction
	10.2 Environmental and Hormonal Cues Regulating Fruit Maturation
	10.3 Acid and Sugar Metabolism; Key Components of Fruit Quality
	10.4 Citrus Fruits as a Source of Carotenoids, Anthocyanins and Vitamin C
	10.5 Transcription Factors and Ripening-Related Mutants, and Epigenetics
	References
11 Pigments in Citrus Fruit: Mutants, Compounds, Genes, and Beyond
	Abstract
	11.1 Introduction
	11.2 Pigmented Mutants
	11.3 Pigment Compounds
	11.4 Biosynthesis Genes
	11.5 Postharvest Altercations
	11.6 Potential Health Benefits
	11.7 Conclusion
	References
12 Essential Oils in Citrus
	Abstract
	12.1 Introduction
	12.2 An Historical Overview
	12.3 Chemical Composition
	12.4 Main Citrus Essential Oils
	12.5 Uses
	12.6 Future Perspective and Strategies
	12.7 Conclusions
	References
13 Abiotic Stress Resistance
	Abstract
	13.1 Drought Stress
	13.2 Salinity
	13.3 Low Temperature
	13.4 Heat and Flooding
	13.5 Heavy Metals
	13.6 Combined Abiotic Stress
	13.7 Concluding Remarks
	References
14 Biotechnological Approaches for the Resistance to Citrus Diseases
	Abstract
	14.1 Agrobacterium-Mediated Transgenic Expression
	14.2 CTV-Mediated Expression
	14.3 CRISPR Technology in Citrus Disease Management
	References
15 Genetic Basis of Resistance to Citrus Canker Disease
	Abstract
	15.1 Introduction
		15.1.1 The Disease Groups
		15.1.2 The Pathogen
		15.1.3 The Host Range and the Disease Symptoms
		15.1.4 The Disease Cycle
		15.1.5 The Control of the Disease
	15.2 Evaluation of Citrus Genotypes for Resistance to Canker Disease
	15.3 Pathogenesis of Xcc
		15.3.1 The Pathogen Genome
		15.3.2 Xcc Infection Process
		15.3.3 Xcc Pathogenicity
		15.3.4 Citrus Disease Susceptibility Genes
	15.4 Resistance Mechanism
		15.4.1 Overview of Plant Resistance to Bacterial Pathogen
		15.4.2 Brief Introduction to the Plant Innate Immune System
			15.4.2.1 PAMP-Triggered Immunity (PTI)
			15.4.2.2 Effector-Triggered Immunity (ETI)
		15.4.3 Citrus-Xcc Interaction
			15.4.3.1 PAMPs Derived from the Factors Related to Biofilm Formation
			15.4.3.2 Citrus PRR FLS2—Xcc PAMP Flagellin Interaction
			15.4.3.3 Systemic Defence Response Against Xcc Induced by Rhizobacteria
		15.4.4 Resistance Genes
	15.5 Breeding for Resistant Citrus Genotypes
		15.5.1 Transfer of Antimicrobial Peptides in Citrus Genome to Enhance Resistance to Xcc
		15.5.2 Genetic Transformation of Exotic Genes in Citrus Genome to Enhance Resistance to Xcc
		15.5.3 Regeneration of Resistant Genotypes by Modifying Susceptible Gene CsLob1
		15.5.4 Breeding for Genotypes Resistant to Xcc by Cell Culture
	15.6 Conclusion
	References
16 Molecular Mechanisms for Resistance to Biotic Stresses
	Abstract
	16.1 Plant Diseases that Pose a Threat to Citrus Industry
	16.2 Plant Resistance
		16.2.1 Plant Innate Immunity—PRRs and PTI
		16.2.2 Plant Innate Immunity—NLRs and ETI
		16.2.3 Plant Innate Immunity—Effectors Recognition ‘Ligand and Guard/Decoy Models’
		16.2.4 Plant Innate Immunity—Effectors Recognition ‘the Integrated Decoy Model’
		16.2.5 Plant Innate Immunity—Citrus spp NLRsomes
	16.3 Disease Case Studies
		16.3.1 Phythophthora Diseases
		16.3.2 Alternaria Brown Spot of Tangerines
		16.3.3 Citrus Tristeza
	References