Plenaries

Genomic Selection à¢â‚¬â€œ the next 25 years

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Abstract

Genomic selection has now been implemented in almost all livestock species, with millions of animals genotyped for this purpose. In the nearly two decades since the first application genomic selection has more than doubled genetic gain for traits including milk production and fertility in dairy cattle and generation intervals have decreased substantially in a number of species. This paper speculates on advances in genomic selection that may occur in the next 25 years. Genomic selection is increasingly combined with reproductive technologies which reduce generation intervals and intensify selection, particularly on the dam side (IVF). The next step in reproductive technology that decrease generation time is likely to be in-vitro meiosis. If many generations of genomic selection are conducted in the test tube, genomic prediction accuracy based on current SNP arrays may decay substantially, due to recombination between array SNP and causative mutations. To investigate if using whole genome sequence data, which potentially includes mutations affecting the target trait, results in better persistence of accuracy over many generations of selection that may be possible with invitro meiosis, we used 1000 bull genomes data as a starting point for simulations. Chromosome one data, including 1.09 million SNPs genotyped in 1350 Holstein, Jersey and Red cattle was used as a starting point for the simulations. 1000 of the SNPs were randomly selected to be QTL, with effects sampled from a multivariate normal distribution. Random error were added to true breeding values such that h2 of the simulated phenotype was 0.3. Fifty bulls and 1000 dams were selected each generation. In early generations, there was little difference in genetic gain from selection in GEBV using 50K SNP, HD SNP, or between BayesR and GBLUP. However by generation 20, substantial differences were evident in genetic gain, with the use of whole genome sequence clearly resulting in more gain than from SNP arrays. Genetic gains may be further increased by increasing recombination. In crops, the use of CRISPR/CAS9 to generate targeted recombination is now a reality. When recombination rates were increased 10 fold, at linkage disequilibrium block boundaries, gains were increased by up to 20%.Finally, the implementation of genomic selection has been associated with an increase in inbreeding, particularly in dairy cattle, and this is likely to accelerate as advanced reproductive technologies are adopted. It has been demonstrated that genetic diversity can be maintained when genomic selection using optimum contribution selection, provided the correct inbreeding metric is used. Maintaining genetic diversity will be critical to ensure animals bred with the accelerated schemes described above due not suffer from reduced fitness, and livestock populations have sufficient diversity to respond to selection for traits such as heat tolerance that will become increasingly important in the future.

Keywords: 2026

How to Cite:

Hayes, B., Villiers, K., Meuwissen, T. & Goddard, M., (2026) “Genomic Selection à¢â‚¬â€œ the next 25 years”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286160. doi: https://doi.org/10.31274/wcgalp.23865

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