The Almond Tree Genome

Foreword
Preface to the Series
Preface
Contents
Contributors
1 Genome Analysis and Breeding
Abstract
1 History
2 Evolutionary Genomics of Almond and Peach
3 Breeding
4 Rootstock Breeding
5 Biotechnology
5.1 Genomic Resources
5.2 Studies and Markers
5.3 Marker-Assisted Breeding
6 Future Directions
References
2 Origin and Domestication of Wild Bitter Almond. Recent Advancements on Almond Bitterness
Abstract
1 The Origin of Almond
2 Almond Production
3 The Two Old Friends: HCN and Almond
4 Cyanogenic Glucosides
5 Amygdalin, the Bitter Compound in Almond
TheAmygdalinDegradationPathway
6 The Sweet Kernel (Sk) Gene
7 The Sk Marker
8 Future Perspectives
Acknowledgements
Funding
References
3 The Complete Sequence of the Almond Genome
Abstract
1 Introduction
2 The First Chromosome-Scale Almond Genome—The Lauranne Genome
3 The Second Almond Genome Sequenced—The Texas Genome
4 The Third Almond Genome Sequenced—The Nonpareil Genome
5 Future Perspectives
Funding
References
4 Almond miRNA Expression and Horticultural Implications
Abstract
1 Introduction
2 MicroRNA-Mediated Gene Regulation Under Cold Stress in Almond
2.1 Gene Ontology Analysis
2.2 Identification and Verification of Cold-Responsive miRNA Target Genes Using Degradome Sequencing Method
2.3 Pdu-miR168 Under Cold Stress
2.4 Pdu-miR171 Under Cold Stress
2.5 Pdu-miR319 Under Cold Stress
2.6 Pdu-miR398 Under Cold Stress
2.7 Pdu-miR403 Under Cold Stress
2.8 Pdu-miR477a-3p Under Cold Stress
2.9 Pdu-miR7122-3p Under Cold Stress
3 MicroRNA-Mediated Gene Regulation Under Drought Stress in Almond
3.1 Pdu-miR156 Under Drought Stress
3.2 Pdu-miR167 Under Drought Stress
3.3 Pdu-miR408 Under Drought Stress
3.4 Pdu-miR2275 Under Drought Stress
4 Identification of Symbiosis-Related miRNAs Under Salt and Drought Stresses in Almond
5 MicroRNA-Mediated Gene Regulation During Fruit Development
References
5 Epigenetic Regulation in Almond
Abstract
1 Introduction
2 Epigenetic Regulation in Plants
2.1 The Dynamic Plant Genome
2.2 Plants as Epigenetic Machineries
2.3 Epigenetic Machinery in Plants
2.4 Propagation, Reproduction, Reprograming, and Extended Limited Inheritance
3 Epigenetic Mechanisms in Almond
3.1 Transposable Elements as Architects of the Almond Genome and Its Domestication
3.2 Epigenetic Regulation of Dormancy and Flowering
3.3 Dysfunctionalization of the Sf Allele Conferring Gametophytic Self-compatibility in Breeding Germplasm
3.4 The Role of Genome-Wide DNA-(De)methylation in Noninfectious Bud Failure
4 Concluding Remarks and Perspectives
Acknowledgements
References
6 Metabolomic Studies in Almond
Abstract
1 Introduction
2 Target Metabolomic in Different Prunus Spp.
2.1 Metabolomics in Salt-Stress Response in Plum
2.2 Endodormancy and Target Metabolomics in Prunus Spp.
3 Non-target Metabolomics in Almond
3.1 Almond Classification
3.2 Endodormancy in Almond Flower Buds
4 Non-target Metabolomics in Other Prunus Spp.
4.1 Antioxidant Activity in Peach Fruits
4.2 Endodormancy in Sweet Cherry Flower Buds
5 Conclusions and Future Sights
Funding
References
7 Recent Advances on Self-incompatibility in Almond: A Glance at Genomic and Transcriptomic Levels
Abstract
1 Genetic Control of GSI in Almond
1.1 The Almond S-locus
1.2 The S-RNase Gene
1.3 The Almond S-RNase Gene Structure
2 The SFB Gene
2.1 The SLF Gene
2.2 LTRs
2.3 The Molecular Basis of Self-recognition and Rejection in the Almond GSI
2.4 Characterization and Marker Assays for S-RNase Alleles in Almond
2.5 Three-Dimensional (3D) Models of the S-RNase
3 Proteomic and Transcriptomic Analyses of Pistils and Anthers from Self-incompatible and Self-compatible Almonds
4 Practical Aspects of GSI in Almond
5 Self-incompatibility in Almond Production and Breeding
6 Implications of Self-fertility for Almond Production
7 Conclusion and Future Perspectives
References
8 Transcriptional Changes Associated to Flower Bud Dormancy and Flowering in Almond: DNA Sequence Motifs, mRNA Expression, Epigenetic Modifications and Phytohormone Signaling
Abstract
1 Introduction
2 Dormancy and Flowering in Almond Trees
2.1 Paradormancy
2.2 Endodormancy Factors
2.3 Ecodormancy
3 DNA Sequence Motifs Linked to Breaking Dormancy and Flowering Date in Almond Trees
4 mRNA Expression Associated to Flowering in Almond Trees
5 Epigenetic Regulation of Flowering in Almond Trees
6 Phytohormone Signaling of Bud Dormancy and Flowering in Almond Trees
7 Concluding Remarks and Future Prospects in the New Post-genomic Context
Acknowledgements
References
9 Molecular Basis of the Abiotic Stresses in Almond
Abstract
1 Introduction
2 Rootstock Development to Overcome Abiotic Stress
3 Other Important Criteria for Almond Rootstocks
4 Water and Nutrient Uptake
5 Physiological Metabolic and Molecular Response of Abiotic Stresses
5.1 Calcareus Soils Stress
5.2 Waterlogging Stress
5.3 Drought Stress
5.4 Salinity Stress
5.5 Scion Cold Stress
6 Final Outlook
7 Conclusion
References
10 Discovery of Quantitative Trait Loci for Nut and Quality Traits in Almond
Abstract
1 Introduction
2 Brief History of Linkage and QTL Map Construction in Almond
3 Marker-Assisted Breeding in Crops
4 Marker-Assisted Selection (MAS) in Almond
5 Use of Marker Assisted Introgression (MAI) in Almond
6 Molecular Tools in Almond Breeding
7 Marker-Assisted Pyramiding
8 QTL Mapping in Almond
9 Association Mapping (AM) in Almond
10 A Well Characterised Trait in Almond Using QTL Mapping
11 New Approaches and Technologies
11.1 Genomic Selection (GS)
11.2 High-Throughput Sequencing
11.3 High-Throughput Phenotyping (HTP)
12 Conclusion
References
11 Accelerating Almond Breeding in Post-genomic Era
Abstract
1 Introduction
2 Genomic Selection in Almond Breeding
3 Aspects Influencing Genomic Selection in Almond
4 Previous Studies in Prunus and Nuts Species
5 Almond Breeding Cycle Updating
References
12 Prospects and Future Questions
Abstract
References