Plant Breeding in the Omics Era

Contents

1. Introduction to Plant Breeding

Plant Breeding and Society

Genetics, Omics and Plant Breeding

Populations

Genetic Diversity

Distances Measures

Grouping Germplasm

Quantitative Variation

Mapping Traits

Genotype-by-Environment Interaction

Phenotyping

Phenomics

References

2. Plant Genetic Resources for Food and Agriculture

Crop Evolution and Plant Species Feeding the World

Genebanks

Gene Pools

Describing Variation and Identifying Redundancy

Germplasm Evaluation

Descriptors

Documentation and Bioinformatics

Geo-documentation to Identify Germplasm

Genebank Sampling and Core Subsets

Genomics of Plant Genetic Resources

Putting Genes into Usable Forms

References

3. Inbred Development

DNA markers for Mapping Quantitative Trait Loci (QTL) and Aided Breeding

Inbreeding and Line Development

Doubled Haploids

Adaptability: Learning for Model Plant Systems

Breeding for Stress-prone Environments and Resource-use Efficiency

Host-plant Resistance Breeding

Participatory and Client-driven Plant Breeding

References

4. Population Improvement

Recurrent Selection and Breeding Populations

Genome-wide Association and Quantitative Trait Variation

Plant Genomics

Genomic Selection and Prediction of Breeding Values

References

5. Heterosis and Inter-Specific Hybridization

Heterotic Groups

Hybrid Vigor

Heterosis in Plant Breeding

Understanding Hybrid Vigor in Model Plants and Crops

Omics Research on Heterosis

Hybrids in Selfing Species

Polyploid Heterosis

Interspecific hybridization

References

6. Mutations and Epigenetics

Induced Mutations and Plant Breeding

Induced Mutations and Genomics-led Plant Breeding

Targeting Induced Local Lesions IN Genomes (TILLING)

Epigenetics

References

7. Genetic Engineering and Transgenic Breeding

Plant Genetic Engineering "Issues"

Transgenic Crops "Risks"

Transgene Flow

Pest Resistance and Impacts on Non-target Organisms

Detecting Genetically Modified Organisms and Other Safety Assessments

Transgenic Agriculture and Co-existence

Plant Genetic Engineering Impacts

Transgenic Agriculture Outlook

New Plant Breeding Techniques

References

8. DNA Sequencing, other Omics and Synthetic Biology

DNA Sequencing

Next Generation Sequencing

Genotyping-by-Sequencing

Other Relevant Omics for Plant Breeding

Breeding Informatics

Case Study: Omics-led Legume Breeding

Pl

References

9. Breeding Self-fertilizing Plants: From Inbred to Hybrid Cultivars

Rice

Domestication

Genetic Enhancement

Genomics

Marker-aided Selection (MAS)

Stress Breeding

Interspecific Hybridization and Participatory Breeding

Hybrid Cultivars

Phenotyping

Genetic Engineering

Wheat

Evolution and Diversity

Germplasm Enhancement

Resynthesizing Wheat

Shuttle Breeding and Mega-environments

Grain Yield Potential

Perennial Wheat

Biotechnology

Ex ante and in silico Breeding

Tomato

References

10. Breeding Open Pollinated, Hybrid and Transgenic Outcrossing Species

Maize

Domestication and Diversity

Germplasm Enhancement

Breeding

Inbred Line Development and Hybrids
About the Author:

Rodomiro Ortiz is Professor of Genetics and Plant Breeding at the Swedish University of Agricultural Sciences (SLU) in Alnarp, Sweden. He worked as geneticist at Universidad Nacional Agraria La Molina (UNALM), Centro Internacional de la Papa (CIP, Lima, Perú), Rutgers University (Chatsworth, New Jersey, USA) and International Institute of Tropical Agriculture (IITA, Ibadan, Nigeria), held a Nordic professorship in plant genetic resources at the Danish Royal Veterinary and Agricultural University (merged now with the University of Copenhagen, Denmark), served as Director at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT, Patancheru, Telangana, India), IITA, and the Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT, El Batán, México), and independent free-lance consultant for international, regional and national organizations engaged in agricultural research-for-development. CGIAR awarded IITA in 1994 the prestigious King Baudouin Award for the multidisciplinary research of the team working in plantain and banana improvement, in which Ortiz was both a hands-on researcher and program leader. His professional expertise includes genetics, genetic resources, germplasm enhancement, plant breeding, agro-biotechnology, biosafety, intellectual property rights, and developing agro-ecosystem and livelihood system approaches aiming sustainable intensification of agriculture in the developing world. His h-index was 44 accord