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Summary: The present study focuses on the Belgian Milk Sheep in Flanders (Belgium) and compares its genetic diversity and relationship with the Flemish Sheep, the Friesian Milk Sheep, the French Lacaune dairy sheep and other Northern European breeds. For this study, 94 Belgian Milk Sheep, 23 Flemish Sheep and 22 Friesian Milk Sheep were genotyped with the OvineSNP50 array. In addition, 29 unregistered animals phenotypically similar to Belgian Milk Sheep were genotyped using the 15K ISGC chip. Both Belgian and Friesian Milk Sheep as well as the East Friesian Sheep were found to be less diverse than the other seven breeds included in this study. Genomic inbreeding coefficients based on runs of homozygosity (ROH) were estimated at 14.5, 12.4 and 10.2% for Belgian Milk Sheep, Flemish Sheep and Friesian Milk Sheep respectively. Out of 29 unregistered Belgian Milk Sheep, 28 mapped in the registered Belgian Milk Sheep population. Ancestry analysis, PCA and FST calculations showed that Belgian Milk Sheep are more related to Friesian Milk Sheep than to Flemish Sheep, which was contrary to the breeders' expectations. Consequently, breeders may prefer to crossbreed Belgian Milk Sheep with Friesian sheep populations (Friesian Milk Sheep or East Friesian Sheep) in order to increase diversity. This research underlines the usefulness of SNP chip genotyping and ROH analyses for monitoring genetic diversity and studying genetic links in small livestock populations, profiting from internationally available genotypes. As assessment of genetic diversity is vital for long‐term breed survival, these results will aid flockbooks to preserve genetic diversity. [ABSTRACT FROM AUTHOR]

Summary: The Piétrain pig originates from the Belgian village Piétrain some time between 1920 and 1950. Owing to its superior conformation, the Piétrain has spread worldwide since the 1960s. As initial population sizes were limited and close inbreeding was commonplace, the breed's genetic diversity has been questioned. Therefore, this study examines Piétrain breed substructure, diversity and selection signatures using SNP data in comparison with Duroc, Landrace and Large White populations. Principal component analysis indicated three subpopulations, and FST analysis showed that US Piétrains differ most from European Piétrains. Average inbreeding based on runs of homozygosity (ROH) segments larger than 4 Mb ranged between 16.7 and 20.9%. The highest chromosomal inbreeding levels were found on SSC8 (42.7%). ROH islands were found on SSC8, SSC15 and SSC18 in all Piétrain populations, but numerous population‐specific ROH islands were also detected. Moreover, a large ROH island on SSC8 (34–126 Mb) appears nearly fixed in all Piétrain populations, with a unique genotype. Chromosomal ROH patterns were similar between Piétrain populations. This study shows that Piétrain populations are genetically diverging, with at least three genetically distinct populations worldwide. Increasing genetic diversity in local Piétrain populations by introgression from other Piétrain populations seems to be only limited. Moreover, a unique 90 Mb region on SSC8 appeared largely fixed in the Piétrain breed, indicating that fixation was already present before the 1960s. We believe that strong selection and inbreeding during breed formation fixed these genomic regions in Piétrains. Finally, we hypothesize that independent coat color selection may have led to large ROH pattern similarities on SSC8 between unrelated pig breeds. [ABSTRACT FROM AUTHOR]

Dairy cow fertility is a complex trait that depends on the cow's physiological status, the farm's environmental and management conditions, and their interactions. Already the slightest improvement in fertility can positively impact a farm's profitability and sustainability. In research, milk progesterone (P4) has often been used as an accurate and feasible way to identify a dairy cow's reproduction status. Moreover, in Europe and Canada, it has been used to improve fertility management on commercial farms as it allows to accurately identify reproduction issues, pregnancy and the optimal insemination window. An on-farm P4 device (OPD) automatically samples, measures and monitors the milk P4 concentration of individual cows. To this end, the P4 data is smoothed to be robust for measurement errors and outliers, and fixed thresholds are used to estimate the time of luteolysis preceding ovulation, thereby generating a luteolysis alert (LA). By smoothing the P4 data, the OPD introduces a time lag on the LA. Variation in this time lag is not considered in the estimation of the optimal insemination window that is advised to the farmer. Ignoring this variation might decrease the accuracy of the optimal insemination window and, therefore, decreases the likelihood of conception. We hypothesize that considering the length of the time lag and adapting the advice accordingly improves the conception rate. This observational retrospective study uses an extensive data set from 17 commercial dairy farms that are equipped with an OPD. We estimated the time lag on the alerts and evaluated their relationship with the interval from LA to insemination for successful (n = 3721) and unsuccessful inseminations (n = 3896) separately. Results showed that the probability of conception increases when a longer LA time lag is compensated with a shorter interval from LA to insemination and vice versa. In addition, for successful inseminations, we found a clear negative relation between the time lag and the interval from LA to insemination and the interval was significantly shorter when the time lag of the LA was longer. This negative relation between time lag and interval from LA to insemination was less pronounced for unsuccessful inseminations. Additionally, we evaluated the conception rates for inseminations that are performed too early, in time or too late with respect to the optimal insemination window advised by the OPD, in function of their associated time lags. We found that, for inseminations that were preceded by a short time lag (<8 h), the conception rate was 17.5 percentage points higher when cows were inseminated later than advised. Likewise, when inseminations were preceded by a long time lag (≥24 h), we found that the conception rate was 13 percentage points higher when cows were inseminated earlier than advised. Our results suggest that farmers using an OPD could potentially increase their conception success by compensating the variable time lag on the LA by adapting the interval from alert to insemination accordingly. This could be used to develop reproductive management strategies to improve reproductive performance on those farms, which can positively impact their sustainability., (The Authors. Published by Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

Background: Psoroptic mange, caused by Psoroptes ovis mites, is affecting Belgian Blue cattle's welfare and production potential. The Belgian Blue cattle-known for its high degree of muscling, low feed conversion ratio and high beef quality-is highly susceptible for this disease., Results: In this study, we phenotyped 1975 Belgian Blue cattle from more than 100 different groups on commercial beef farms for their psoroptic mange susceptibility. Substantial individual differences were observed within these management groups, with lesion extent differences up to ± 15%. Animal models showed that estimated heritabilities were low for lesion extent and severe lesion extent (0.07 and 0.09, respectively) and 0.12 for the number of mites. A genome wide association study for mange susceptibility revealed signals on BTA6, BTA11, BTA15 and BTA24. In these regions, candidate genes GBA3, RAG2, and TRAF6 were identified., Conclusions: Despite the challenges in phenotyping for psoroptic mange due to the timing of screening, the continuous evolution of lesions and different management conditions, we successfully conducted a study on the genetic susceptibility to psoroptic mange in Belgian Blue cattle. Our results clearly indicate that psoroptic mange is under polygenic control and the underlying candidate genes should be studied more thoroughly. This is the first study providing candidate genes for this complex disease. These results are already valuable for Belgian Blue breeding, however, further research is needed to unravel the architecture of this disease and to identify causal mutations., (© 2024. The Author(s).)

Background: Previous research showed that deviations in longitudinal data are heritable and can be used as a proxy for pigs' general resilience. However, only a few studies investigated the relationship between these resilience traits and other traits related to resilience and welfare. Therefore, this study investigated the relationship between resilience traits derived from deviations in longitudinal data and traits related to animal resilience, health and welfare, such as tail and ear biting wounds, lameness and mortality., Results: In our experiment, 1919 finishing pigs with known pedigree (133 Piétrain sires and 266 crossbred dams) were weighed every 2 weeks and scored for physical abnormalities, such as lameness and ear and tail biting wounds (17,066 records). Resilience was assessed via deviations in body weight, deviations in weighing order and deviations in observed activity during weighing. The association between these resilience traits and physical abnormality traits was investigated and genetic parameters were estimated. Deviations in body weight had moderate heritability estimates (h 2  = 25.2 to 36.3%), whereas deviations in weighing order (h 2  = 4.2%) and deviations in activity during weighing (h 2  = 12.0%) had low heritability estimates. Moreover, deviations in body weight were positively associated and genetically correlated with tail biting wounds (r g  = 0.22 to 0.30), lameness (r g  = 0.15 to 0.31) and mortality (r g  = 0.19 to 0.33). These results indicate that events of tail biting, lameness and mortality are associated with deviations in pigs' body weight evolution. This relationship was not found for deviations in weighing order and activity during weighing. Furthermore, individual body weight deviations were positively correlated with uniformity at the pen level, providing evidence that breeding for these resilience traits might increase both pigs' resilience and within-family uniformity., Conclusions: In summary, our findings show that breeding for resilience traits based on deviations in longitudinal weight data can decrease pigs' tail biting wounds, lameness and mortality while improving uniformity at the pen level. These findings are valuable for pig breeders, as they offer evidence that these resilience traits are an indication of animals' general health, welfare and resilience. Moreover, these results will stimulate the quantification of resilience via longitudinal body weights in other species., (© 2024. The Author(s).)

The main goal of the Belgian Warmblood horse studbook (BWP) is to breed successful competition horses, with emphasis on show jumping. However, competition results are only available later in life and competition traits are lowly heritable. Hence, the use of phenotypes that record performance-related traits at an early life stage could help increase genetic progress. In this study, we evaluated the potential of eleven linear scored early life jumping traits assessed during jumping in freedom (2-5 years old) or under the saddle (4-6 years old) as proxies for later success in show jumping competitions. To this end, we estimated their heritabilities and genetic correlations with the competition trait, adjusted fence height, by using 2170 free jumping records, 1588 jumping under saddle records, 674,527 show jumping competition records and almost 81,000 informative horses in the pedigree. As participation of young horses in these contests is on a voluntary basis, a pre-selection most probably exists. To verify this hypothesis, we investigated the association between participation to young horse contests and participation to show jumping competitions later on (called here start status phenotype). We also estimated heritabilities for "start status in free jumping contest", "start status in jumping under saddle contest" and "start status in free jumping or jumping under saddle contest" by fitting threshold models. Furthermore, we calculated genetic correlations between these traits and adjusted fence height and calculated the correlations between EBVs for start status in young horse contests and EBVs for success in competitions. Estimated heritabilities of early life jumping traits ranged between 0.05 and 0.30. Their genetic correlations with adjusted fence height were moderate to high (r g  = 0.37-0.63). Relatively more horses that participated in young horse contests competed later on compared to horses that did not participate in young horse contests (p-value < 0.001). They were also significantly more successful in show jumping competitions. Furthermore, start status in young horse contests was moderately heritable in BWP horses (h 2  = 0.56-0.65) and moderately to highly correlated with later success in competitions (r g  = 0.30-0.77). Hence, we showed that ELJ traits are good proxies for later success in competitions and that a pre-selection of horses occurs in young horse contests. It is suggested to stimulate participation to young horse contests to achieve a more representative sample of the population. Early life jumping traits can therefore optimize the genetic progress for show jumping performance., (© 2023 The Authors. Journal of Animal Breeding and Genetics published by John Wiley & Sons Ltd.)

Screening for genetic diversity in livestock species breeds is of utmost importance, especially for local, small populations that are at the risk of extinction. Luckily, recent developments in technology increase access to genotyping, also for numerically small breeds. One of these new technologies is the IMAGE001 single nucleotide polymorphism genotyping array that includes markers for 6 different species (cow, pig, sheep, chicken, horse and goat). For our current study, we studied the Turkey-headed Malines chicken, a local chicken breed in Belgium, for the first time. A total of 110 animals were genotyped, together with 29 samples from 4 supposedly related breeds. The genotypes were used to assess the genetic diversity of this local breed. Our analysis revealed an average inbreeding coefficient of 0.20 through runs of homozygosity analysis, and effective population size estimation based on linkage disequilibrium indicated a low genetic diversity (N e  = 34). Moreover, a principal component analysis and a genetic differentiation study (F ST ) were performed using these marker data to position the Turkey-headed Malines relative to the 4 other indigenous Belgian chicken breeds. Finally, we discussed the practical implications of the overlap between the IMAGE001 array and other existing chicken genotyping arrays. This study is the first use of the novel IMAGE001 array to evaluate a local chicken breed, and demonstrates it as a viable option for genomic characterization a breed. Moreover, with this research, we are able to provide a good basis for further evaluation of the Belgian chicken heritage., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: Increasing resilience is a priority in modern pig breeding. Recent research shows that general resilience can be quantified via variability in longitudinal data. The collection of such longitudinal data on weight, feed intake and feeding behaviour in pigs has been facilitated by the development of technologies such as automated feeding stations. The goal of this study was to investigate resilience traits, which were estimated as deviations from longitudinal weight, feed intake and feeding behaviour data during the finishing phase. A dataset with 324,207 records between the age of 95 and 155 days on 5,939 Piétrain pigs with known pedigree and genomic information was used. We provided guidelines for a rigid quality control of longitudinal body weight data, as we found that outliers can significantly affect results. Gompertz growth curve analysis, linear modelling and trajectory analyses were used for quantifying resilience traits., Results: To our knowledge, this is the first study comparing resilience traits from longitudinal body weight, feed intake and feeding behaviour data in pigs. We demonstrated that the resilience traits are lowly to moderately heritable for deviations in body weight (h 2  = 2.9%-20.2%), in feed intake (9.4%-23.3%) and in feeding behaviour (16.2%-28.3%). Additionally, these traits have good predictive abilities in cross-validation analyses. Deviations in individual body weight and feed intake trajectories are highly correlated (r g  = 0.78) with low to moderate favourable genetic correlations with feed conversion ratio (r g  = 0.39-0.49). Lastly, we showed that some resilience traits, such as the natural logarithm of variances of observed versus predicted body weights (lnvar weight ), are more robust to lower observation frequencies and are repeatable over three different time periods of the finishing phase., Conclusions: Our results will help future studies investigating resilience traits and resilience-related traits. Moreover, our study provides first results on standardization of quality control and efficient data sampling from automated feeding station data. Our findings will be valuable for breeding organizations as they offer evidence that pigs' general resilience can be selected on with good accuracy. Moreover, this methodology might be extended to other species to quantify resilience based on longitudinal data., (© 2023. The Author(s).)

Background: Show jumping is one of the most popular disciplines in the horse sector, which makes success in show jumping competitions an important breeding goal for many studbooks. Therefore, the genetic evaluation of show jumping performance is of major interest and this is the case for two Belgian Warmblood studbooks: the Belgian Warmblood horse and Zangersheide. In this study, first an improved phenotype for show jumping performance was developed, i.e. adjusted fence height based on a new non-arbitrary method to scale ranking and competition level, which are two major components of success in competitions. Second, we assessed the importance of including a rider effect in genetic models for show jumping performance, this effect being under debate in sport horse breeding. Third, genetic models based on elementary performances and one model based on a summarized performance were compared in terms of model fit, heritabilities and the stability of estimated breeding values to define the most suitable one for the genetic evaluation of show jumping performance., Results: In this study, more than 600,000 Belgian competition records and almost 81,000 horses were used. Genetic evaluations were developed based on elementary performances (Blom-transformed ranking and adjusted fence height) and on a summarized performance (highest level achieved). Estimated heritabilities of Blom-transformed ranking, adjusted fence height and highest level achieved were 0.09, 0.12 and 0.39, respectively. Including a rider effect improved the models for genetic evaluations. Estimated genetic correlations between the studied models were moderate to high (r g  = 0.60-0.99). With the best fit model, the accuracy of the estimated breeding value (EBV) for adjusted fence height reached 0.70 for a larger number of stallions and for stallions that tended to be younger., Conclusions: We recommend breeders to implement this new phenotype 'adjusted fence height' in breeding programs. It is moderately to highly correlated with Blom-transformed ranking and highest level achieved, a proxy for lifetime success, and is available for selection candidates from an early age onwards., (© 2023. The Author(s).)

Animals used in research often have to be euthanised, especially when tissue sampling is essential. Recently, a euthanasia method, utilizing an inhalant anaesthetic 'nitrogen gas in foam' in an anoxia box (ANOXIA TM ), has gained considerable interest as it claimed to be more animal-friendly. However, it is not clear whether the use of this euthanasia method has an influence on RNA measurements. Moreover, there are no studies on the interaction effect of different euthanasia methods on the tissue sample storage conditions. The current study compared RNA measurements from two euthanasia methods (ANOXIA TM vs. T-61 ® injection) and two storage conditions (RNA later ™ vs. snap freezing) in 12 male piglets. The nitrogen anoxia method had a significantly higher RNA yield ( p < 0.01) compared to the T-61 ® method. However, no effect of the euthanasia methods on the A260/230 ratio and RIN value was observed. Tissues stored in RNA later ™ had significantly higher RIN values ( p < 0.001) compared to snap frozen samples. The present study could not find a significant difference between the two euthanasia methods in piglets, with regard to RNA quality measurements. Hence, the nitrogen anoxia technique (ANOXIA TM ) might be considered as a suitable alternative to T-61 ® for euthanasia of piglets used in research.

Pig breeding is changing rapidly due to technological progress and socio-ecological factors. New precision livestock farming technologies such as computer vision systems are crucial for automated phenotyping on a large scale for novel traits, as pigs' robustness and behavior are gaining importance in breeding goals. However, individual identification, data processing and the availability of adequate (open source) software currently pose the main hurdles. The overall goal of this study was to expand pig weighing with automated measurements of body dimensions and activity levels using an automated video-analytic system: DeepLabCut. Furthermore, these data were coupled with pedigree information to estimate genetic parameters for breeding programs. We analyzed 7428 recordings over the fattening period of 1556 finishing pigs (Piétrain sire x crossbred dam) with two-week intervals between recordings on the same pig. We were able to accurately estimate relevant body parts with an average tracking error of 3.3 cm. Body metrics extracted from video images were highly heritable (61-74%) and significantly genetically correlated with average daily gain (r g  = 0.81-0.92). Activity traits were low to moderately heritable (22-35%) and showed low genetic correlations with production traits and physical abnormalities. We demonstrated a simple and cost-efficient method to extract body dimension parameters and activity traits. These traits were estimated to be heritable, and hence, can be selected on. These findings are valuable for (pig) breeding organizations, as they offer a method to automatically phenotype new production and behavioral traits on an individual level., (© 2022. The Author(s).)

Genetic diversity is increasingly important for researchers and society. Small and local populations deserve more attention especially, as they may harbor important characteristics. Moreover, small populations are at greater risk and their genetic management is often more challenging. Likewise, European red cattle populations are threatened, as they are outcompeted by more specialized cattle breeds. In this study, we investigate the genetic diversity of two local Belgian red cattle breeds: Belgian Red and Belgian White Red cattle. A total of 270 animals were genotyped via medium density SNP arrays. Genetic diversity was assessed using runs of homozygosity screening, effective population size estimation and F st analyses. Genomic inbreeding coefficients based on runs of homozygosity were estimated at 7.0% for Belgian Red and 6.1% for Belgian White Red cattle, and both populations had a low effective population size (68 and 86, respectively). PCA, F st and admixture analyses revealed the relationship to 52 other international breeds, where they were closest related to some Belgian, French, Scandinavian and Dutch breeds. Moreover, F st analyses revealed for Belgian Red cattle a signature of selection on BTA6, adjacent to the KIT gene. This study gains important knowledge on the genetic diversity of these two small local red cattle breeds, and will aid in their (genetic) management.

The use of antimicrobials in animal production is under public debate, mainly due to the risk of transfer of resistance to pathogenic bacteria in humans. Therefore, measures have been taken during the last few decades to reduce antibiotic usage in animals, for instance, by national monitoring programmes and by improving animal health management. Although some initiatives exist in molecular genetic selection, quantitative genetic selection of animals towards decreased antibiotic usage is an underexplored area to reduce antibiotic usage. However, this strategy could yield cumulative effects. In this study, we derived new phenotypes from on-farm parenteral antibiotic records from commercially grown crossbred finishing pigs used in the progeny test of Piétrain terminal sires to investigate the heritability of antibiotics usage. Parenteral antibiotic records, production parameters and pedigree records of 2238 full-sib pens from two experimental farms in Belgium between 2014 and 2020 were analysed. Heritability estimates were moderate (18-44%) for phenotypes derived from all antibiotic treatments, and low (1-15%) for phenotypes derived from treatments against respiratory diseases only. Moreover, genetic correlations between these new phenotypes and mortality were low to moderate (0.08-0.60) and no strong adverse genetic correlations with production traits were found. The high heritabilities and favourable genetic correlations suggest these new phenotypes, derived from on-farm antibiotics records, to be promising for inclusion in future pig breeding programs to breed for a decrease in antibiotics usage.

Background: Runs of homozygosity (ROH) have become the state-of-the-art method for analysis of inbreeding in animal populations. Moreover, ROH are suited to detect signatures of selection via ROH islands and are used in other applications, such as genomic prediction and genome-wide association studies (GWAS). Currently, a vast amount of single nucleotide polymorphism (SNP) data is available online, but most of these data have never been used for ROH analysis. Therefore, we performed a ROH analysis on large medium-density SNP datasets in eight animal species (cat, cattle, dog, goat, horse, pig, sheep and water buffalo; 442 different populations) and make these results publicly available., Results: The results include an overview of ROH islands per population and a comparison of the incidence of these ROH islands among populations from the same species, which can assist researchers when studying other (livestock) populations or when looking for similar signatures of selection. We were able to confirm many known ROH islands, for example signatures of selection for the myostatin (MSTN) gene in sheep and horses. However, our results also included multiple other ROH islands, which are common to many populations and not identified to date (e.g. on chromosomes D4 and E2 in cats and on chromosome 6 in sheep)., Conclusions: We are confident that our repository of ROH islands is a valuable reference for future studies. The discovered ROH island regions represent a unique starting point for new studies or can be used as a reference for future studies. Furthermore, we encourage authors to add their population-specific ROH findings to our repository.