The long-term effects of genomic selection

Traditionally, animal breeding was based on the measured performances of animals and their relatives. Recently, the introduction of genomic selection has revolutionised animal breeding. Genomic selection selects animals based on their genome, which is more precise than on pedigree relationships and can double the annual rate of genetic improvement.

Is faster always better? (And is it sustainable?)

Selection to improve the performance of a population also alters the genetic architecture of a trait, such as the genes underlying a trait and their frequencies and effects. Moreover, selection can reduce the genetic variation in a population. Since genetic variation is essential for selection, this can reduce the potential for genetic improvement in the future.

Genomic selection has likely accelerated the change in genetic architecture by strongly selecting on genes with large effects. However, genomic selection largely ignores genes with small effects or with rare variants and therefore increases the risk of losing rare favourable variants. This potentially reduces the genetic variation in a population, which limits the long-term genetic improvement and the potential of populations to adapt to changing environments.

Dr. Yvonne Wientjes, researcher at the Animal Breeding and Genomics group (ABG) investigated the rate of change in the genetic architecture of traits under genomic selection.

Yvonne: “I used stochastic simulations (a simulation model that has one or more random variables as inputs, ed.) to identify and quantify the mechanisms determining the rate of change in genetic architecture under genomic selection. Consequently, I compared this with classical selection methods. In addition, I quantified the change in genetic architecture over several generations under genomic selection in two actual livestock populations (pigs, ed.).”

Yvonne’s research showed that although genomic selection methods can speed up changes in the genetic architecture of traits and result in increased risk of loss of genetic variation, selecting on a broad selection index including many traits can spread the selection pressure across the genome, thereby limiting the negative impact on the potential for animal breeding in the future.