The Lupin Genome (Compendium of Plant Genomes)

Preface to the Series
Preface to the Volume
	Introduction to the Lupin Genome
	References
Contents
1 Genetic Diversity in Narrow-Leafed Lupin Breeding After the Domestication Bottleneck
	Abstract
	1.1 Introduction
	1.2 Analysis of Genetic Diversity and Population Inbreeding
		1.2.1 Coefficient of Coancestry and Inbreeding Coefficient
		1.2.2 Four Phases of Lupin Breeding Based on Coancestry
		1.2.3 Rate of Population Inbreeding
		1.2.4 Founders and Migrants Contributing to the Pedigree
	1.3 Characteristics of Varieties Released in the Australian Narrow-Leafed Lupin Breeding Program 1967–2016
		1.3.1 Domestication (Pre-1967)
		1.3.2 Phase 1: Foundation (1967–1987)
		1.3.3 Phase 2: First Diversification (1987–1998)
		1.3.4 Phase 3: Exploitation (1998–2007)
		1.3.5 Phase 4: Second Diversification (2007–2016)
		1.3.6 Move to the Private Sector
	1.4 Genetic Progress in Lupin Breeding
		1.4.1 Australia
		1.4.2 Global Genetic Advances
	1.5 Technologies to Improve Long-Term Genetic Gain
	1.6 Conclusions and Recommendations
	Acknowledgements
	References
2 Ecophysiology and Phenology: Genetic Resources for Genetic/Genomic Improvement of Narrow-Leafed Lupin
	Abstract
	2.1 Adaptation and Phenology
	2.2 Germplasm Resources: Phenotypic and Genetic Variation for Flowering Time
		2.2.1 Phenological Variation Found in Wild Germplasm Collections
		2.2.2 Phenotypic and Genetic Variation Found in Fully- and Semi-domesticated Germplasm Resources
	2.3 Conclusions
	References
3 Overview of Genomic Resources Available for Lupins with a Focus on Narrow-Leafed Lupin (Lupinus angustifolius)
	Abstract
	3.1 Introduction
	3.2 BAC Libraries Provided Early Insight Into The Narrow-Leafed Lupin Genome
	3.3 Narrow-Leafed Lupin Genome Sequences Including the Current Reference Genome
	3.4 Insight from the Reference Genome into Plant-Microbe Interactions for Narrow-Leafed Lupin
	3.5 The Lupin Genome Portal
	3.6 What is in the Pipeline?
		3.6.1 Generating a Gold Standard Reference Genome
		3.6.2 Generation of a Narrow-Leafed Lupin Pan-Genome
		3.6.3 Reverse Genetic Resources to Exploit Genomic Advances in Narrow-Leafed Lupin
		3.6.4 A White Lupin (L. albus) Reference Genome
	3.7 Conclusions
	Acknowledgements
	References
4 Cytomolecular Insight Into Lupinus Genomes
	Abstract
	4.1 Lupinus spp. Genome Sizes and Chromosome Numbers
	4.2 Chromosome Markers for Cytogenetic Mapping of Lupinus Species
	4.3 Cytogenomic Map of L. angustifolius as a Basic Tool for Comparative Studies
	4.4 Karyotype Variation and Rearrangements Among Lupins
	4.5 Variation in Chromatin Modifications Within Lupins
	4.6 Conclusion
	References
5 Transcriptome Resources Paving the Way for Lupin Crop Improvement
	Abstract
	5.1 Background
	5.2 The Use of Transcriptomics in Lupins
		5.2.1 Development of Gene-Based Molecular Markers in Narrow-Leafed Lupin
		5.2.2 Development of Gene-Based Molecular Markers in Yellow Lupin
		5.2.3 Using Molecular Markers to Generate Genetic Maps in Lupins
		5.2.4 Use of Transcriptome Data for Annotation of the Narrow-Leafed Lupin Genome
		5.2.5 Identification of Seed Storage Proteins in Lupins
		5.2.6 Cluster Root Formation and Phosphorus Acquisition in White Lupin
		5.2.7 Alkaloid Biosynthesis in Narrow-Leafed Lupin
		5.2.8 Organ Abscission in Yellow Lupin
		5.2.9 SmallRNAs in Narrow-Leafed Lupin
	5.3 Conclusion
	References
6 Molecular Marker Resources Supporting the Australian Lupin Breeding Program
	Abstract
	6.1 Introduction
	6.2 Methods Applied for Development of Molecular Markers
	6.3 Detection Methods
	6.4 Traits Subjected to Molecular Selection
		6.4.1 Pod Shattering
		6.4.2 Alkaloid Content
		6.4.3 Soft Seededness
		6.4.4 Early Flowering
		6.4.5 Anthracnose Resistance
		6.4.6 Phomopsis Stem Blight Resistance
		6.4.7 Lupin Rust Resistance
	6.5 Adoption of Molecular Markers in European Breeding Programs
	6.6 Conclusion
	References
7 Chromosomal Structure, History, and Genomic Synteny Relationships in Lupinus
	Abstract
	7.1 Introduction
		7.1.1 Chromosomal Background and NLL Assembly
		7.1.2 Phylogenetic and Synteny Evidence Indicate a Whole-Genome Triplication in Lupinus
	7.2 Online Resources for Lupin Genetic and Genomic Research
	References
8 How Have Narrow-Leafed Lupin Genomic Resources Enhanced Our Understanding of Lupin Domestication?
	Abstract
	8.1 Background
	8.2 Multiple Lupin Domestications Spanning Time and Space
		8.2.1 Ancient Lupin Domestication
		8.2.2 Modern Lupin Domestication
	8.3 Genetic and Genomic Resources Supporting Domestication Research in Lupin
		8.3.1 Genetic Resources
		8.3.2 Genomic Resources
	8.4 Lupin Domestication Gene Discovery
		8.4.1 Lupinus angustifolius
		8.4.2 Lupinus albus
		8.4.3 Lupinus luteus
		8.4.4 Other Lupin Species
	8.5 Genetic Consequences of Domestication on Genome Diversity
	8.6 Closing Remarks
	References
9 Genomic Applications and Resources to Dissect Flowering Time Control in Narrow-Leafed Lupin
	Abstract
	9.1 Genetic Mapping and Accounting for the Phenotypic Contribution of Flowering Time Loci
		9.1.1 Bi-parental Mapping Populations
		9.1.2 Association Mapping Populations
	9.2 Identifying Candidate Genes for Major Flowering Time Loci and Understanding the Evolution of Genetic Networks for Flowering Time Regulation in Lupinus
		9.2.1 Identification of Candidate and Causal Genes for Flowering Time Loci
			9.2.1.1 Involvement of the FT Gene Family in the Narrow-Leafed Lupin Vernalisation Pathway
	9.3 The Evolution of Flowering Time Genetic Control in Lupinus and the Fabaceae
		9.3.1 A MADS-Box Transcription Factor Clade Key to the Vernalisation Pathway in the Brassicaceae is Absent in Lupinus
			9.3.1.1 Divergence of the Phosphatidyl Ethano lamine-Binding Protein (PEBP) Family Within the Lupinus Genus and from Other Legumes
			9.3.1.2 Representation of the Basic Region/Leucine Zipper (bZIP) Transcription Factors Involved in Floral Integration in Narrow-Leafed Lupin Indicate Earlier Evolution of this Gene Family in the Fabaceae
			9.3.1.3 Homologous Genes Related to Light Detection, Signalling and Response to the Photoperiod Pathway in Narrow-Leafed Lupin
		9.3.2 Future Prospects of Improved Adaptive Genetic Variation Discovery with New and Improved Genetic and Genomic Resources
			9.3.2.1 Genetic Maps, Genome Assemblies and Transcriptome Resources
			9.3.2.2 TILLING and EcoTILLING Populations and Tools
	9.4 Using Genomic Information and Resources to Shape Adaptive Flowering Time Diversity in Domestic Narrow-Leafed Lupins
		9.4.1 Marker-Assisted Selection to Improve Breeding Efficiency
		9.4.2 Future Genome Editing for Rapid Germplasm Improvement
	9.5 Conclusions
	References
10 Genetic and Genomic Resources in White Lupin and the Application of Genomic Selection
	Abstract
	10.1 White Lupin Cultivation and Breeding Targets
	10.2 White Lupin Genetic Resources
	10.3 White Lupin Genomic Resources
	10.4 Potential Adoption of Genomic Selection in White Lupin
	10.5 Case Study of White Lupin Genomic Selection—Materials and Methods
	10.6 Case Study of White Lupin Genomic Selection—Results
	10.7 Perspective and Conclusion
	Acknowledgements
	References
11 Genomics of Yellow Lupin (Lupinus luteus L.)
	Abstract
	11.1 Background
	11.2 Genetic Resources for Yellow Lupin
	11.3 Genomic Resources for Yellow Lupin
	11.4 Using Genomics to Address Constraints on Yellow Lupin Cultivation
	11.5 Conclusions
	References
12 The Repetitive Content in Lupin Genomes
	Abstract
	12.1 Introduction
		12.1.1 Tandem Repeats
		12.1.2 Transposable Elements
		12.1.3 Advancing the Discovery of Repetitive Sequences Using Next-Generation Sequencing Technology
		12.1.4 Lupinus: A System of Interest to Evaluate the Dynamics of the Genomic Repetitive Compartment
	12.2 Exploring Retrotransposons Diversity in Genomes of Lupins and Allied Genistoids
	12.3 NGS-Based Evaluation of the Repetitive Compartment in Lupin Genomes
		12.3.1 Composition of the Repetitive Compartment in Lupin Genomes
		12.3.2 Identification and Distribution of LTR Retrotransposons in the Lupin Genomes
		12.3.3 Phylogenetic Analysis on LTR Retrotransposons RT Domains
		12.3.4 Diversity and Abundance of Tandem Repeats in Lupin Genomes
	12.4 Repetitive Compartment of Lupin Genomes
		12.4.1 The Repetitive Compartment Represents a Significant Fraction of Lupin Genomes
		12.4.2 Gypsy and Copia Retrotransposons Significantly Contribute to Genome Size Variation
		12.4.3 Evolutionary Considerations on the Dynamics of Transposable Elements in Lupins
		12.4.4 Tandem Repeats May also Greatly Contribute to Genome Obesity and Dynamics in Lupins
	12.5 Conclusion and Perspectives
	Acknowledgements
	References
13 Correction to: Genetic Diversity in Narrow-Leafed Lupin Breeding After the Domestication Bottleneck
	Correction to: Chapter 1 in: K. B. Singh et al. (eds.), The Lupin Genome, Compendium of Plant Genomes, https://doi.org/10.1007/978-3-030-21270-4_1