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Table of contents
Chapter 1 Introduction
Chapter 2 Background
2.1 Characteristics of dairy cattle breeding
2.2 Pedigree-based selection methods
2.2.1 Best linear unbiased prediction
2.2.2 Implementation in our study
2.3 Genetic background of quantitative traits and genetic markers
2.3.1 Quantitative trait loci
2.3.2 Genetic markers
2.3.2.1. Microsatellite
2.3.2.2. Single nucleotide polymorphism
2.3.3 Haplotype
2.3.4 Imputation and phase reconstruction
2.4 Genomic evaluation
2.4.1 Marker-assisted BLUP
2.4.2 Genomic-BLUP
2.4.3 Bayesian methods
2.4.4 Genomic evaluation methods with haplotype markers
2.5 French routine genomic evaluation of dairy cattle
2.6 Consequences of genomic selection
2.6.1 Advantages of genomic selection
2.6.2 Drawbacks of genomic evaluation
2.7 Assessment of genomic evaluation studies
2.7.1 Principles of validation in genomic evaluation studies
2.7.2 Measured parameters
2.8 Analyzed breeds and traits
2.9 Single-breed and multi-breed genomic evaluation
2.9.1 Review of the recent multi-breed genomic evaluation studies
2.10 Problem statement and motivation
Chapter 3 Haplotype construction for genomic evaluation purposes .
3.1 The Montbéliarde dataset
3.2 Haplotypic BayesC-π results
3.3 Influence of allele frequency on genomic evaluation
3.3.1 Introduction
3.3.2 Alternative haplotype construction methods for genomic evaluation
3.3.3 Discussion
3.4 Genomic evaluation with HD data
3.5 Inclusion of linkage disequilibrium information
3.5.1 Introduction
3.5.2 Combining LD and allele frequency information to improve selection accuracy
3.5.3 Discussion
Chapter 4 Genomic evaluation in regional breeds
4.1 Datasets
4.1.1 Genotyping and imputation
4.2 LD-pattern in the regional breeds
4.3 Genomic evaluation with 50K data
4.3.1 Introduction
4.3.2 Single-breed and multi-breed genomic evaluation with 50K data
4.3.3 BayesC results
4.3.4 Discussion
4.4 Genomic evaluation with high-density data
4.4.1 Introduction
4.4.2 Materials and methods
4.4.3 Results
4.4.4 Conclusions
4.5 Genomic evaluation with causative mutations
4.5.1 Introduction
4.5.2 Materials and Methods
4.5.3 Results and discussion
4.5.4 Conclusions
Chapter 5 General discussion
5.1 Introduction
5.2 Biodiversity
5.3 Effects of the slower genetic progress
5.4 Perspectives for the regional breeds
5.5 Genomic evaluation in the regional breeds
5.6 Financial considerations
5.7 Genomic evaluation with haplotypes
5.8 Future perspectives
Chapter 6 Concluding remarks
References
