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The consequences of selection on allele frequency change in pigs

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January 20, 2025

Researchers from Animal Breeding and Genomics (ABG) of Wageningen University & Research, together with researchers from breeding company Hendrix Genetics, have investigated the changes on the genome in two commercial pig populations under intense selection.

In animal breeding, the best animals are selected to produce the next generation, which will generally increase the performance of the population. As a result of this selection, the genome of the animals can change over time. More insights in those changes can help to make selection more efficient and sustainable.

Aim of the study

The aim of the study was to investigate the changes on the genome in two pig populations under selection to provide more insights in the long-term effects of selection. Understanding those changes is important to ensure that enough genetic variation is maintained for genetic gain and a healthy population in the future. In this research, data from two purebred pig populations was used. Both
populations served as a dam line in a commercial breeding program, and have been under intense selection for both production and reproduction traits for
many generations. In the past, selection was based on pedigree data, while genomic data was also used to identify the best animals in recent generations. Over the investigated time frame, clear genetic progress was achieved.

Allele frequency change

The researchers tracked the allele frequencies of many markers during seven generations of selection. Clear changes in allele frequencies were observed over the different generations in some regions on the genome. Those large changes were, however, not larger than could be expected in a population without selection. This means that those changes were not necessarily a result of the selection process, but could also be a result of random processes such as genetic drift. Nonetheless, the impact of selection was visible in the average change in allele frequency, which was slightly higher in the investigated populations under selection than could be expected in a population without selection.

Surprisingly, the observed changes in allele frequencies over one generation were unrelated to the results of genome-wide-association studies (GWAS) that aimed to find regions with a large effect on important traits under selection. This means that even in populations with strong selection, random processes have a large impact on allele frequency change. “We expect that this is a result of selecting the animals on a combination of multiple production and reproduction traits, which resulted in spreading the selection pressure across the genome,” says Yvonne Wientjes, first author of the study. “Moreover, many regions on the genome were found to affect multiple traits in an antagonistic way. This means that to increase the performance of one trait, you want to increase the frequency of the allele that you want to reduce in frequency in order to the increase the performance of another trait. Those antagonistic interactions can also substantially reduce the selection pressure on particular regions on the genome.”

Implications

All in all, the observation that the selection pressure was spread across the genome in the studied pig populations is good news. “Strong selection pressure on a specific region can result in strong allele frequency changes in that region, but can also strongly change the allele frequency of linked regions in the unfavorable direction,” says Wientjes. “This can result in loosing favorable alleles from the population and, thereby, limit long-term genetic variation and gain.”

The publication ‘Changes in allele frequencies and genetic architecture due to selection in two pig populations’ is part of the project ‘(R)evolution of traits? Quantifying the genetic change in traits over generations as a result of Genomic Selection’ (with project number 16774) of the research program Veni which is (partly) financed by the Dutch Research Council (NWO).