The DNA provides a blueprint of life containing the instruction, together with the environment, that determine the phenotype. In livestock breeding, we are in an era of genomic selection (selecting animals based on their DNA). All the genomic data now generated within commercial livestock populations is a true goldmine to find both harmful and positive mutations in the DNA. In this thesis I delved into the genome (the entire genetic code) of livestock populations and found various mutations that cause embryonic, fetal, or postnatal mortality. Some lethal mutations are maintained in the population because of a positive effect in carrier animals (animals that carry one copy of the mutation). We also describe mutations that affect important phenotypes in breeding populations (e.g. growth in pigs). With the tools generated we can now more accurately predict the impact of mutations, which will be applied to improve livestock breeds in the future.