Whole genome sequencing identified a 16 kilobase deletion on ECA13 associated with distichiasis in Friesian horses

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.

Genomic analysis and prediction of genomic values for distichiasis in Staffordshire bull terriers

BACKGROUND

Distichiasis is a condition characterized by aberrant hairs along the eyelid margins. The symptoms are usually mild but can lead to ulcerations and lesions of the cornea in severe cases. It is the most frequently noted ocular disorder in Norwegian Staffordshire bull terriers (SBT), with a prevalence above 18% in the adult population. A complex inheritance is assumed, but there is sparse knowledge about the genetic background of distichiasis in dogs. We have performed a genome-wide association study of distichiasis in SBT and used genomic data in an attempt to predict genomic values for the disorder.

RESULTS

We identified four genetic regions on CFA1, CFA18, CFA32 and CFA34 using a mixed linear model association analysis and a Bayesian mixed model analysis. Genomic values were predicted using GBLUP and a Bayesian approach, BayesR. The genomic prediction showed that the 1/4 of dogs with predicted values most likely to acquire distichiasis had a 3.9 -4.0 times higher risk of developing distichiasis compared to the quarter (1/4) of dogs least likely to acquire the disease. There was no significant difference between the two methods used.

CONCLUSION

Four genomic regions associated with distichiasis were discovered in the association analysis, suggesting that distichiasis in SBT is a complex trait involving numerous loci. The four associated regions need to be confirmed in an independent sample. We also used all 95 K SNPs for genomic prediction and showed that genomic prediction can be a helpful tool in selective breeding schemes at breed level aiming at reducing the prevalence of distichiasis in SBTs in the future, even if the predictive value of single dogs may be low.

Longitudinal Training and Workload Assessment in Young Friesian Stallions in Relation to Fitness: Part 1

Friesian stallions have to complete a 10-week studbook approval test (70-day test) consisting of dressage and driving training for acceptance as a breeding stallion. Training response of the horses to this approval program was evaluated. External workload (EW) of 16 stallions (3.2 ± 0.4 years old) was registered during the 9 weeks preceding the 70-day test (preparation period) and during 70-day test. Ridden indoor standardized exercise tests (SET), measuring heart rate (HR) and plasma lactate concentration (LA) at walk, trot and canter, were performed in week 1 (SET-I), 6 (SET-II) and 10 (SET-III) of the 70-day test. Linear mixed effect models were used to analyze HR and LA related to SETs and EW related to the phase of the study, using Akaike's information criterion for model reduction. EW was higher in the 70-day test compared to the preparation period, with longer duration of training sessions. Compared to SET-I, horses showed increased HR and LA after canter in SET-II and SET-III, indicating that they were more fatigued. The fact that the fitness of these Friesian stallions decreased during the 70-day test suggests overtraining. To optimize training effects and welfare of these horses, the workload of the training program needs to be adjusted.

Heritability estimates of distichiasis in Staffordshire bull terriers using pedigrees and genome-wide SNP data

BACKGROUND

Distichiasis is the most frequently recorded eye disorder in the Norwegian Staffordshire bull terrier (SBT). The condition is often mild but can, in severe cases, lead to pain and blindness. The current study's main purpose was to estimate the heritability based on pedigree information as well as single nucleotide polymorphisms (SNPs) to evaluate whether it is realistic to reduce the frequency by systematic breeding. The majority of the dogs had only one examination as a young puppy. To evaluate whether this early screening gave a reliable representation of the disease burden in the population, we compared the diagnosis in puppies and adult dogs.

RESULTS

Our material consisted of data from 4177 dogs with an overall prevalence of distichiasis of 8.38% (CI 7.56-9.26). The prevalence in puppies examined around eight weeks of age was significantly lower than in dogs examined after 52 weeks (2.87%, CI 2.29-3.54 versus 18.72%, CI 16.71-20.87). The heritability was estimated in dogs examined after 52 weeks. We used both pedigree (1391 dogs) and genotype (498 dogs) information for the estimates. The pedigree-based heritability was ~ 0.22 (on the underlying scale ~ 0.48), while the genomic-based heritability (on the underlying scale) was ~ 0.47, and ~ 0.37 when excluding close relatives with equal affection status.

CONCLUSIONS

Screening for distichiasis in puppies before eight weeks of age is not sufficient to give an accurate estimate of the prevalence, and an additional examination after one year is recommended. The heritability of distichiasis is medium to high, showing that it should be possible to reduce the prevalence by selective breeding.

Decoding the Equine Genome: Lessons from ENCODE

The horse reference genome assemblies, EquCab2.0 and EquCab3.0, have enabled great advancements in the equine genomics field, from tools to novel discoveries. However, significant gaps of knowledge regarding genome function remain, hindering the study of complex traits in horses. In an effort to address these gaps and with inspiration from the Encyclopedia of DNA Elements (ENCODE) project, the equine Functional Annotation of Animal Genome (FAANG) initiative was proposed to bridge the gap between genome and gene expression, providing further insights into functional regulation within the horse genome. Three years after launching the initiative, the equine FAANG group has generated data from more than 400 experiments using over 50 tissues, targeting a variety of regulatory features of the equine genome. In this review, we examine how valuable lessons learned from the ENCODE project informed our decisions in the equine FAANG project. We report the current state of the equine FAANG project and discuss how FAANG can serve as a template for future expansion of functional annotation in the equine genome and be used as a reference for studies of complex traits in horse. A well-annotated reference functional atlas will also help advance equine genetics in the pan-genome and precision medicine era.