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From 2000 onwards, genomic selection is developed. Phenotypes are collected only on a select number of animals as well as detailed genotypes on those animals. Then, that information is used to estimate the link between the DNA composition of the animals (e.g. 60000 SNPs) and the phenotype. Basic idea is that there are two groups of animals: a select group with detailed phenotypes, also called the reference population, and a large group without those phenotypes, also called the populationyoung selection candidates. All animals of both the reference population and the population are genotyped. In the reference population the associations between markers and phenotype are estimated. Then, those associations are combined with the genotypes of the animals in the population to predict their breeding values.

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The above figure illustrates the concept behind genomic selection. In the reference population many animals are genotyped and their phenotypes recorded. Equations predicting breeding values are developed using this data, and these prediction equations can be applied to a population of young selection candidates using their genotypes alone.

Genomic selection is very useful when phenotypes are very difficult or expensive to measure. Think about certain health related traits where you don’t want to make the animal ill to be able to measure the phenotype. Or traits that do require expensive equipment, such as a CT scan. Genomic selection also makes it possible to select animals based on an estimated breeding value before they have reached the age to produce a phenotype themselves. This allows for (very) early selection, and thus can have economic benefits, as well as faster genetic gain because animals can be used as parents earlier in their life. Disadvantage of genomic selection is that the reference population needs to be of sufficient size to be able to estimate accurate associations between genotype and phenotype. It also needs to be updated (=new animals need to be added) at a regular basis because the estimated associations between the SNP and the genes determining the phenotype may be lost due to recombination and/or mutation.