The use of high density genotyping in animal health

The sequencing of genomes, such as that of the cow, has led to the discovery of thousands of single nucleotide polymorphisms (SNPs). By combining this knowledge with new methods that can genotype thousands of SNPs efficiently, it has become possible to carry out genome-wide association studies in domestic animals to map genes for complex traits, including disease resistance, using the linkage disequilibrium between the SNPs and the unknown genes affecting the trait of interest. Although experiments using 10,000 SNPs and 384 animals have found many significant associations, power calculations suggest that we need >50,000 SNPs and >1000 animals to map genes explaining most of the genetic variance for complex traits. Such experiments are now underway and the results will have two applications. Firstly, they will lead to panels of SNPs that can be used to accurately select animals with high breeding value for desired traits leading to a great increase in the rate of genetic improvement. Secondly, they will form the first step in identifying the genes and mutations that cause variation in complex traits. A collaborative approach to achieving this second goal is proposed.