Genomic selection has revolutionized animal breeding and accelerated genetic gains in breeding programs. However, the introduction of genomic selection in some cosmopolitan breeds has also been associated with increased inbreeding rates, raising concerns about the potential effects of genomic selection on genetic diversity in smaller or local breeds.
Researchers from Wageningen University & Research, Animal Breeding and Genomics (WUR-ABG), in collaboration with colleagues from research institutions in Norway (NMBU) and France (INRAE and Institut de l'Elevage), investigated the impact of genomic selection on genetic diversity in 5 local cattle breeds from 3 European countries: Meuse Rhine Yssel from the Netherlands, Norwegian Red from Norway, and Abondance, Tarentaise and Vosgienne from France. They investigated changes in population demographic structure, as well as trends and rates of kinship and inbreeding, using both pedigree- and genomic-based measures.
"While genomic selection has become standard practice in common popular cattle breeds, local breeds have only recently started to implement it," says Renzo Bonifazi, researcher at WUR-ABG and first author of the study. "With the implementation of genomic selection, there are also concerns that the higher selection intensity and reduced generation intervals brought by it may lead to increased mating of related individuals, especially in small populations, potentially leading to reduced genetic diversity, higher levels of inbreeding depression, and a greater prevalence of harmful recessive mutations. It is therefore essential to investigate and monitor the possible impact of implementing genomic selection on the genetic diversity of local cattle breeds, as these breeds may present unique features in their management strategies and breeding programs compared with more popular ones."
The researchers, using data provided by the breeds' organizations from existing databases, conducted data analysis which showed that implementing genomic selection reduced sires' generation intervals, decreased the number of calves that later became sires, and led to a more balanced contribution of the top 10 sires. Changes in genetic diversity after the introduction of genomic selection were not consistent across breeds. Renzo: "We observed that rates of kinship, pedigree inbreeding and genomic inbreeding increased in Meuse Rhine Yssel and Tarentaise, but decreased in Norwegian Red, Abondance and Vosgienne. Moreover, the timing of the changes in genetic diversity did not always correspond to the introduction of genomic selection, which means that it is likely that there are other genetic management factors influencing inbreeding and kinship rates in these breeds."
"Our study suggests that increases in inbreeding rates may occur after the introduction of genomic selection, although they may not be directly due to genomic selection per se but rather reflect population management strategies, which strongly influence kinship and inbreeding in the long term, such as the implementation of optimal contribution selection methods in the Norwegian Red breed or the "cold sire system" in the Meuse Rhine Yssel breed. Therefore, after the implementation of genomic selection it is essential to monitor changes in both genetic diversity and population demographic structure and adapt the breed management accordingly when necessary."
This project has received funding from the European Union's Horizon 2020 Programme for Research and Innovation under grant agreement no. 101000226. This project is part of EuroFAANG.
