Evaluation of breeding strategies to reduce the inbreeding rate in the Friesian horse population: Looking back and moving forward.

In the past, small population sizes and unequal ancestor contributions have resulted in high inbreeding rates (ΔF) in the Friesian horse. Two decades ago, the studbook implemented a mating quota and started publishing individual kinships and reduced ΔF below 1% per generation. However, since then, the breeding population size has decreased and this raises the question whether current breeding strategies are sufficient to keep ΔF below desired rates. The aim of this study was to (1) reflect on past inbreeding trends and their main determinants, using pedigree analysis and (2) evaluate the effectiveness of the current and additional breeding strategies using stochastic simulations. We estimated the current ΔF (2013-2022) at 0.72% per generation. While the total contribution of the top 10 sires to the number of offspring per year has decreased from 75% in 1980 to 35% in 2022, this was mainly due to an increased number of approved studbook sires, and not due to more equalized contributions among sires. Of the simulated breeding strategies, selecting only breeding stallions with a below average mean kinship (i.e., "mean kinship selection") was most effective to decrease ΔF (from 0.66% to 0.33%). Increasing the number of breeding sires only had an effect when also a mating quota was applied. However, its effect remained limited. For example, a ~1.5 fold increase, combined with a mating quota of 80 offspring per sire per year, reduced ΔF from 0.55% to 0.51%. When increasing the number of breeding mares, a practically unfeasible large increase was needed for a meaningful reduction in ΔF (e.g. twice as many mares were needed to reduce ΔF from 0.66% to 0.56%). Stratified mating quotas, a novel approach in which we assigned each sire a mating quota (of 60, 80, 100 or 120 offspring per year) based on its mean kinship to recently born foals, resulted in a lower ΔF (0.43%) than a general mating quota of 90 offspring per sire per year (0.55%). Overall, while the current ΔF is below 1%, we recommend to implement additional strategies to further reduce ΔF below 0.5% in the Friesian horse population. For this breed and similar populations, we recommend to focus on breeding strategies based on kinship levels to effectively reduce ΔF.