Plant Breeding in the Omics Era

<p>Contents</p><p> </p><p>1. Introduction to Plant Breeding</p><p> </p><p>Plant Breeding and Society</p><p>Genetics, Omics and Plant Breeding</p><p>Populations</p><p>Genetic Diversity</p><p>Distances Measures</p><p>Grouping Germplasm</p><p>Quantitative Variation</p><p>Mapping Traits</p><p>Genotype-by-Environment Interaction</p><p>Phenotyping</p><p>Phenomics</p><p>References</p><p> </p><p> </p><p>2. Plant Genetic Resources for Food and Agriculture</p><p> </p><p>Crop Evolution and Plant Species Feeding the World</p><p>Genebanks</p><p>Gene Pools</p><p>Describing Variation and Identifying Redundancy</p><p>Germplasm Evaluation</p><p>Descriptors</p><p>Documentation and Bioinformatics</p><p>Geo-documentation to Identify Germplasm</p><p>Genebank Sampling and Core Subsets</p><p>Genomics of Plant Genetic Resources</p><p>Putting Genes into Usable Forms</p><p>References</p><p> </p><p> </p><p>3. Inbred Development</p><p> </p><p>DNA markers for Mapping Quantitative Trait Loci (QTL) and Aided Breeding</p><p>Inbreeding and Line Development</p><p>Doubled Haploids</p><p>Adaptability: Learning for Model Plant Systems</p><p>Breeding for Stress-prone Environments and Resource-use Efficiency</p><p>Host-plant Resistance Breeding</p><p>Participatory and Client-driven Plant Breeding</p><p>References</p><p> </p><p> </p><p>4. Population Improvement</p><p> </p><p>Recurrent Selection and Breeding Populations</p><p>Genome-wide Association and Quantitative Trait Variation</p><p>Plant Genomics</p> and Marker-assisted Selection<p></p><p>Genomic Selection and Prediction of Breeding Values</p><p>References</p><p> </p><p> </p><p>5. Heterosis and Inter-Specific Hybridization</p><p> </p><p>Heterotic Groups</p><p>Hybrid Vigor</p><p>Heterosis in Plant Breeding</p><p>Understanding Hybrid Vigor in Model Plants and Crops</p><p>Omics Research on Heterosis</p><p>Hybrids in Selfing Species</p><p>Polyploid Heterosis</p><p>Interspecific hybridization</p><p>References</p><p> </p><p> </p><p>6. Mutations and Epigenetics</p><p> </p><p>Induced Mutations and Plant Breeding</p><p>Induced Mutations and Genomics-led Plant Breeding</p><p>Targeting Induced Local Lesions IN Genomes (TILLING)</p><p>Epigenetics</p><p>References</p><p> </p><p> </p><p>7. Genetic Engineering and Transgenic Breeding</p><p> </p><p>Plant Genetic Engineering “Issues”</p><p>Transgenic Crops “Risks”</p><p>Transgene Flow</p><p>Pest Resistance and Impacts on Non-target Organisms</p><p>Detecting Genetically Modified Organisms and Other Safety Assessments</p><p>Transgenic Agriculture and Co-existence</p><p>Plant Genetic Engineering Impacts</p><p>Transgenic Agriculture Outlook</p><p>New Plant Breeding Techniques</p><p>References</p><p> </p><p> </p><p>8. DNA Sequencing, other Omics and Synthetic Biology</p><p> </p><p>DNA Sequencing</p><p>Next Generation Sequencing</p><p>Genotyping-by-Sequencing</p><p>Other Relevant Omics for Plant Breeding</p><p>Breeding Informatics</p><p>Case Study: Omics-led Legume Breeding</p><p>Pl</p>ant Synthetic Biology: Another Tool for Plant Breeding?<p></p><p>References</p><p> </p><p> </p><p>9. Breeding Self-fertilizing Plants: From Inbred to Hybrid Cultivars</p><p> </p><p>            Rice</p><p>Domestication</p><p>Genetic Enhancement</p><p>Genomics</p><p>Marker-aided Selection (MAS)</p><p>Stress Breeding</p><p>Interspecific Hybridization and Participatory Breeding</p><p>Hybrid Cultivars</p><p>Phenotyping</p><p>Genetic Engineering</p><p> </p><p>            Wheat</p><p>Evolution and Diversity</p><p>Germplasm Enhancement</p><p>Resynthesizing Wheat</p><p>Shuttle Breeding and Mega-environments</p><p>Grain Yield Potential</p><p>Perennial Wheat</p><p>Biotechnology</p><p>Ex ante and in silico Breeding</p><p>Tomato</p><p>References</p><p> </p><p> </p><p>10. Breeding Open Pollinated, Hybrid and Transgenic Outcrossing Species</p><p> </p><p>Maize</p><p>Domestication and Diversity</p><p>Germplasm Enhancement</p><p>Breeding</p><p>Inbred Line Development and Hybrids</p><p>Doubled Haploids</p><p>Genomics-led Improvement for Enhancing Genetic Gains</p><p>Developing Stress-resilient Germplasm</p><p>Nutritious Maize</p><p>Prediction of Breeding Values</p><p>Genetic Engineering</p><p>Cotton</p><p>Cassava</p><p>Case Study: Cassava Breeding in sub-Saharan Africa</p><p>References</p><p> </p><p> </p><p>11. Polyploidy and Plant Breeding</p><p> </p><p>Potato</p><p>Origin, Diversity and Taxonomy</p><p>Ploidy Manipulations</p><p>Genetic Resources and Breeding</p><p>True Potato Seed</p><p>Genomics</p><p>Genetic Engineering</p><p>Banana/Plantain</p><p>References</p><p> </p><p> </p><p>12.  Seeds, Clones and Perennials</p><p> </p><p>Seed Development: Learning from a Model Plant System</p><p>Inbred and Open Pollinated Seed Cultivars</p><p>Hybrid Seed</p><p>Rapid Multiplication of Healthy and Improved Planting Material of Vegetatively Propagated Crops</p><p>Seed Health</p><p>Apomixis: Procreation without Recreation</p><p>Perennial Crops</p><p>References</p><p> </p><p> </p><p>13.  Diversity, Intellectual Property and Plant Variety Protection</p><p> </p><p>Plant Genetic Resources</p><p>The Question of Derivatives</p><p>Multinational Private and Public Seed Sectors</p><p>Managing Agro-biotechnology Intellectual Property Rights</p><p>References</p>