Genetic gain & Inbreeding

Targeted Allele Frequency Tuning (TAFT) in Friesian horses by exploiting features of the genomic relationship matrix

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Abstract

We present a new selection method that shifts the focus from selecting animals to selecting alleles. This method takes advantage of the behavior of optimal contribution selection when using a genomic relationship matrix (GRM) constructed according to VanRaden (2008) method 1 (VR1). GRMs according to VR1 depend on the choice of centering allele frequencies (CAFs). For example, using AFs observed in selection candidates as CAFs would lead to lower genomic inbreeding estimates than that of their ancestors, because the level of genomic inbreeding estimates is dictated by the average relationships. The average relationship is proportional to the sum of squared deviations of the AFs from the CAFs. Thus, the group of which observed AF are used for CAF, has an average relationship of 0 by design. Our idea is to exploit this feature: we only construct VR1 for loci of interest, set the CAF to the desired frequencies and subsequently select individuals with the lowest "relationship" to other individuals. We call this new approach "TAFT" for Targeted Allele Frequency Tuning. Through simulated toy examples, we explore the behavior of TAFT and compare it to selection with simple indices which do not consider information between animals (off-diagonal elements in GRMs). Both TAFT and selection indices purge the set of alleles in approximately the same number of generations, yet TAFT purges them all simultaneously while selection indices purge them one by one starting with the least frequent allele. TAFT places higher selection pressure on alleles that differ more from the desired frequency. For intermediate desired frequencies (between 0 and 1), selection indices result in slower changes or fail while TAFT easily shifts frequencies to the desired values. We use the Friesian horse breed to showcase usage of TAFT for purging twelve genetic disorders while managing the increase in average kinship and achieving genetic gain on the example trait "withers' height". One of the alleles that should be purged is located in the MHC region, for which in general reducing genetic diversity should be limited as much as possible. Diversity at MHC was managed with haplotypes spanning the entire region. To reflect a practical situation, we considered that only the most promising males were genotyped. Using TAFT, the frequency of genetic disorders was reduced from 35% to close to 0% within 6 generations, while keeping the rate of inbreeding < 0.5% and making 3.7 cm (1.16 genetic SD) genetic gain in withers' height per generation. TAFT was able to keep more diversity in the MHC region, in some scenarios even increase it, while this was not possible with the selection index. In conclusion, TAFT enables to directly manage allele frequencies, and is especially valuable for alleles with intermediate desired frequency.

Keywords: 2026

How to Cite:

Niehoff, T., Steensma, M., Doekes, H., Calus, M., Ducro, B. & Schrauf, M., (2026) “Targeted Allele Frequency Tuning (TAFT) in Friesian horses by exploiting features of the genomic relationship matrix”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2284199. doi: https://doi.org/10.31274/wcgalp.23555

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