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Table of contents
Chapter 1. General Introduction
1.1 Large-scale sequencing and genotyping
1.2 Genetic Markers
1.3 Homozygous Haplotype Deficiency (HHD)
1.4 Genotype Imputation
1.5 Genome-wide association study (GWAS)
1.6 Genomic Prediction
1.7 Aim and objectives of this PhD study
1.8 References
Chapter 2. A missense mutation (p.Tyr452Cys) in the CAD gene compromises reproductive success in French Normande cattle
2.1 Abstract
2.2 Introduction
2.3 Methods
2.4 Results and Discussion
2.5 Conclusion
2.6 References
Chapter 3. Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle
3.1 Abstract
3.2 Introduction
3.3 Materials and methods
3.4 Results and discussion
3.5 Conclusions
3.6 References
Chapter 4. Joint imputation of whole-genome sequence variants and large chromosomal deletions in cattle
4.1 Abstract
4.2 Introduction
4.3 Methods
4.4 Results and discussion
4.5 Conclusion
4.6 References
Chapter 5. Genome-wide association study with imputed whole-genome sequence variants including large deletions for female fertility in three Nordic dairy breeds
5.1 Abstract
5.2 Introduction
5.3 Methods
5.4 Results and Discussion
5.5 Conclusion
5.6 References
Chapter 6. Genomic prediction for female fertility using imputed whole-genome sequence variants including large chromosomal deletions
6.1 Abstract
6.2 Introduction
6.3 Methods
6.4 Results and Discussion
6.5 Conclusion
6.6 References
Chapter 7. General Discussion
7.1 Recessive Lethals
7.2 Use of Whole-Genome Sequence Variants
7.3 Genomic Prediction
7.4 Evolutionary Conservation as a Tool for Identifying Lethal Genes
7.5 Conclusions
7.6 Perspectives
7.7 References
