Molecular genetics is the study of molecules important for biological inheritance. Advances in molecular genetics allow more accurate identification and selection of superior animals, diagnosis and treatment of inherited disorders, and a clearer understanding of biological processes that dictate inherited traits. Traditionally, animal breeders have made genetic progress by using phenotypic information on available animals for selection of breeding stock. Breeding goals may involve a combination of traits, and mass selection for these traits can be difficult. Experimental and statistical methods have been developed that separate environmental from genetic effects to better define quantitative traits and to identify chromosomal positions of loci affecting those traits (called quantitative trait loci, or QTL). The ultimate goal is to identify DNA sequence variations having effects on important phenotypes, understand the biology of pheno-typic differences, and develop schemes that use this information to direct breeding decisions using marker-assisted selection. The mid-1990s saw the first genetic linkage maps for chicken, cattle, and swine and the concept of incorporating marker-assisted selection for production traits and disease resistance in livestock species. Development of detailed comparative maps has facilitated application of information from the human genome to accelerate the discovery of genes (or chromosomal regions) involved in phenotypic differences. Since that time, several instances of causal genetic variations or mutations in livestock that alter phenotype have been identified at the molecular level.

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