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.

Identification and characterisation of de novo germline structural variants in two commercial pig lines using trio-based whole genome sequencing.

BACKGROUND: De novo mutations arising in the germline are a source of genetic variation and their discovery broadens our understanding of genetic disorders and evolutionary patterns. Although the number of de novo single nucleotide variants (dnSNVs) has been studied in a number of species, relatively little is known about the occurrence of de novo structural variants (dnSVs). In this study, we investigated 37 deeply sequenced pig trios from two commercial lines to identify dnSVs present in the offspring. The identified dnSVs were characterised by identifying their parent of origin, their functional annotations and characterizing sequence homology at the breakpoints. RESULTS: We identified four swine germline dnSVs, all located in intronic regions of protein-coding genes. Our conservative, first estimate of the swine germline dnSV rate is 0.108 (95% CI 0.038-0.255) per generation (one dnSV per nine offspring), detected using short-read sequencing. Two detected dnSVs are clusters of mutations. Mutation cluster 1 contains a de novo duplication, a dnSNV and a de novo deletion. Mutation cluster 2 contains a de novo deletion and three de novo duplications, of which one is inverted. Mutation cluster 2 is 25 kb in size, whereas mutation cluster 1 (197 bp) and the other two individual dnSVs (64 and 573 bp) are smaller. Only mutation cluster 2 could be phased and is located on the paternal haplotype. Mutation cluster 2 originates from both micro-homology as well as non-homology mutation mechanisms, where mutation cluster 1 and the other two dnSVs are caused by mutation mechanisms lacking sequence homology. The 64 bp deletion and mutation cluster 1 were validated through PCR. Lastly, the 64 bp deletion and the 573 bp duplication were validated in sequenced offspring of probands with three generations of sequence data. CONCLUSIONS: Our estimate of 0.108 dnSVs per generation in the swine germline is conservative, due to our small sample size and restricted possibilities of dnSV detection from short-read sequencing. The current study highlights the complexity of dnSVs and shows the potential of breeding programs for pigs and livestock species in general, to provide a suitable population structure for identification and characterisation of dnSVs.