Breeding for resilience in finishing pigs can decrease tail biting, lameness and mortality.

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 (h2 = 25.2 to 36.3%), whereas deviations in weighing order (h2 = 4.2%) and deviations in activity during weighing (h2 = 12.0%) had low heritability estimates. Moreover, deviations in body weight were positively associated and genetically correlated with tail biting wounds (rg = 0.22 to 0.30), lameness (rg = 0.15 to 0.31) and mortality (rg = 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.

Early life jumping traits: Are they good proxies for success in show jumping competitions in Belgian warmblood horses?

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 (rg = 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 (h2 = 0.56-0.65) and moderately to highly correlated with later success in competitions (rg = 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.

Adjusted fence height: an improved phenotype for the genetic evaluation of show jumping performance in Warmblood horses.

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 (rg = 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.

A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species.

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.

Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds.

BACKGROUND: Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV differentiation between breeds may be candidates for population-specific selection. However, CNV differentiation, selection and its population genetics have been poorly explored in horses. RESULTS: We investigated the patterns, population variation and gene annotation of CNV using the Axiom® Equine Genotyping Array (670,796 SNPs) from a large cohort of individuals (N = 1755) belonging to eight European horse breeds, varying from draught horses to several warmblood populations. After quality control, 152,640 SNP CNVs (individual markers), 18,800 segment CNVs (consecutive SNP CNVs of same gain/loss state or both) and 939 CNV regions (CNVRs; overlapping segment CNVs by at least 1 bp) compared to the average signal of the reference (Belgian draught horse) were identified. Our analyses showed that Equus caballus chromosome 12 (ECA12) was the most enriched in segment CNV gains and losses (~ 3% average proportion of the genome covered), but the highest number of segment CNVs were detected on ECA1 and ECA20 (regardless of size). The Friesian horses showed private SNP CNV gains (> 20% of the samples) on ECA1 and Exmoor ponies displayed private SNP CNV losses on ECA25 (> 20% of the samples). The Warmblood cluster showed private SNP CNV gains located in ECA9 and Draught cluster showed private SNP CNV losses located in ECA7. The length of the CNVRs ranged from 1 kb to 21.3 Mb. A total of 10,612 genes were annotated within the CNVRs. The PANTHER annotation of these genes showed significantly under- and overrepresented gene ontology biological terms related to cellular processes and immunity (Bonferroni P-value < 0.05). We identified 80 CNVRs overlapping with known QTL for fertility, coat colour, conformation and temperament. We also report 67 novel CNVRs. CONCLUSIONS: This work revealed that CNV patterns, in the genome of some European horse breeds, occurred in specific genomic regions. The results provide support to the hypothesis that high frequency private CNVs residing in genes may potentially be responsible for the diverse phenotypes seen between horse breeds.

Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity.

BACKGROUND: Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of many species, resulting in more sequence differences between individuals than SNPs. Associations between CNVs and disease phenotypes have been established in several species, but equine CNV studies have been limited. Aim of this study was to identify CNVs and to perform a genome-wide association (GWA) study in Friesian horses to identify genomic loci associated with insect bite hypersensitivity (IBH), a common seasonal allergic dermatitis observed in many horse breeds worldwide. RESULTS: Genotypes were obtained using the Axiom® Equine Genotyping Array containing 670,796 SNPs. After quality control of genotypes, 15,041 CNVs and 5350 CNV regions (CNVRs) were identified in 222 Friesian horses. Coverage of the total genome by CNVRs was 11.2% with 49.2% of CNVRs containing genes. 58.0% of CNVRs were novel (i.e. so far only identified in Friesian horses). A SNP- and CNV-based GWA analysis was performed, where about half of the horses were affected by IBH. The SNP-based analysis showed a highly significant association between the MHC region on ECA20 and IBH in Friesian horses. Associations between the MHC region on ECA20 and IBH were also detected based on the CNV-based analysis. However, CNVs associated with IBH in Friesian horses were not often in close proximity to SNPs identified to be associated with IBH. CONCLUSIONS: CNVs were identified in a large sample of the Friesian horse population, thereby contributing to our knowledge on CNVs in horses and facilitating our understanding of the equine genome and its phenotypic expression. A clear association was identified between the MHC region on ECA20 and IBH in Friesian horses based on both SNP- and CNV-based GWA studies. These results imply that MHC contributes to IBH sensitivity in Friesian horses. Although subsequent analyses are needed for verification, nucleotide differences, as well as more complex structural variations like CNVs, seem to contribute to IBH sensitivity. IBH should be considered as a common disease with a complex genomic architecture.

Conformation Traits and Gaits in the Icelandic Horse are Associated with Genetic Variants in Myostatin (MSTN).

Many genes are known to have an influence on conformation and performance traits; however, the role of one gene, Myostatin (MSTN), has been highlighted in recent studies on horses. Myostatin acts as a repressor in the development and regulation of differentiation and proliferative growth of skeletal muscle. Several studies have examined the link between MSTN, conformation, and performance in racing breeds, but no studies have investigated the relationship in Icelandic horses. Icelandic horses, a highly unique breed, are known both for their robust and compact conformation as well as their additional gaits tölt and pace. Three SNPs (g.65868604G>T [PR8604], g.66493737C>T [PR3737], and g.66495826A>G [PR5826]) flanking or within equine MSTN were genotyped in 195 Icelandic horses. The SNPs and haplotypes were analyzed for association with official estimated breeding values (EBV) for conformation traits (n = 11) and gaits (n = 5). The EBV for neck, withers, and shoulders was significantly associated with both PR8604 and PR3737 (P < 0.05). PR8604 was also associated with EBV for total conformation (P = 0.05). These associations were all supported by the haplotype analysis. However, while SNP PR5826 showed a significant association with EBVs for leg stance and hooves (P < 0.05), haplotype analyses for these traits failed to fully support these associations. This study demonstrates the possible role of MSTN on both the form and function of horses from non-racing breeds. Further analysis of Icelandic horses as well as other non-racing breeds would be beneficial and likely help to completely understand the influence of MSTN on conformation and performance in horses.

On the use of the transmission disequilibrium test to detect pseudo-autosomal variants affecting traits with sex-limited expression.

We herein describe the realization of a genome-wide association study for scrotal hernia and cryptorchidism in Norwegian and Belgian commercial pig populations. We have used the transmission disequilibrium test to avoid spurious associations due to population stratification. By doing so, we obtained genome-wide significant signals for both diseases with SNPs located in the pseudo-autosomal region in the vicinity of the pseudo-autosomal boundary. By further analyzing these signals, we demonstrate that the observed transmission disequilibria are artifactual. We determine that transmission bias at pseudo-autosomal markers will occur (i) when analyzing traits with sex-limited expression and (ii) when the allelic frequencies at the marker locus differ between X and Y chromosomes. We show that the bias is due to the fact that (i) sires will preferentially transmit the allele enriched on the Y (respectively X) chromosome to affected sons (respectively daughters) and (ii) dams will appear to preferentially transmit the allele enriched on the Y (respectively X) to affected sons (respectively daughters), as offspring inheriting the other allele are more likely to be non-informative. We define the conditions to mitigate these issues, namely by (i) extracting information from maternal meiosis only and (ii) ignoring trios for which sire and dam have the same heterozygous genotype. We show that by applying these rules to scrotal hernia and cryptorchidism, the pseudo-autosomal signals disappear, confirming their spurious nature.

The novel IMAGE001 genotyping array as a valuable alternative for genetic diversity screening in chicken: a demonstration in a local chicken breed in Belgium.

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 (Ne = 34). Moreover, a principal component analysis and a genetic differentiation study (FST) 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.

Selection of Escherichia coli heat-labile toxin (LT) inhibitors using both the GM1-ELISA and the cAMP Vero cell assay.

Weaned piglets are very susceptible to diarrhea caused by enterotoxigenic Escherichia coli. In the past, various natural components were proposed to have beneficial effects by reducing the effects of diarrheal infectious diseases in humans and animals, and thus may represent an alternative for the use of (prophylactic) antibiotics. Alternatives may inactivate enterotoxigenic Escherichia coli heat-labile toxin (LT) by interfering with toxin binding to the cellular receptor GM1. In this study, various plants and other natural substances were tested for inhibitory properties, in the GM1 binding assay, and in the LT-induced cAMP production in Vero cells. The toxic dose of each compound was determined in a cell viability assay, and the highest nontoxic concentrations were used in the GM1 and cAMP assays. Results demonstrated that only d-(+)-galactose, lactose, N-acetyl-d-galactosamine, and two tea extracts were able to inhibit the binding of LT to its GM1 receptor. In the cAMP assay, only the two tea extracts showed inhibitory activity. This shows that d-(+)-galactose, lactose, and N-acetyl-d-galactosamine can indeed inhibit LT binding to GM1 based on structural homology with GM1 in the absence of living cells. However, in the cAMP assay, d-(+)-galactose, and lactose, N-acetyl-d-galactosamine are apparently metabolized to below their effective inhibitory concentration, likely predicting limited practical applicability in vivo. Both tea extracts maintained their activity in the presence of cells. The active compounds in both are probably polyphenols, which are not easily metabolized, and most likely work by aggregating the toxin. In conclusion, the combination of methods used here is a convenient and fast method for preselecting natural substances containing potentially toxin-binding compounds. Furthermore, if antidiarrhea activity is attributed to compounds found inactive here, their activity is unlikely based on interference with toxin binding.

A Comparative Study on the Effect of Euthanasia Methods and Sample Storage Conditions on RNA Yield and Quality in Porcine Tissues.

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 (ANOXIATM), 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 (ANOXIATM vs. T-61® injection) and two storage conditions (RNAlater™ 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 RNAlater™ 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 (ANOXIATM) might be considered as a suitable alternative to T-61® for euthanasia of piglets used in research.

A promising resilience parameter for breeding: the use of weight and feed trajectories in growing pigs.

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 (h2 = 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 (rg = 0.78) with low to moderate favourable genetic correlations with feed conversion ratio (rg = 0.39-0.49). Lastly, we showed that some resilience traits, such as the natural logarithm of variances of observed versus predicted body weights (lnvarweight), 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.

The search for the gene mutations underlying enterotoxigenic Escherichia coli F4ab/ac susceptibility in pigs: a review.

Diarrhoea due to enterotoxigenic Escherichia coli with fimbriae F4 (ETEC-F4) is an important problem in neonatal and just weaned piglets and hence for the pig farming industry. There is substantial evidence for a genetic basis for susceptibility to ETEC-F4 since not all piglets suffer from diarrhoea after an ETEC-F4 infection. It is assumed that the wild boar was originally ETEC-F4 resistant and that susceptibility towards ETEC arose after domestication. There are different phenotypes in the pig determined by which of the three existing F4 variants (F4ab, F4ac or F4ad) they are susceptible or resistant for. This suggests that several F4 receptors exist, expressed individually or in combination with each other on the brush border of the piglet's small intestine. As such, the mucin-type glycoproteins (IMTGP) are described as F4ab/ac receptors, while the intestinal neutral glycospingolipid (IGLad) is proposed as an F4ad receptor. GP74 is a putative F4ab receptor. However, the specific genes that encode for the susceptibility are not yet known. In the past decades, linkage analyses revealed that the loci encoding for the receptor(s) for the two most frequent variants F4ab and F4ac were mapped to the 13th chromosome of the pig (Sus scrofa 13, SSC13). After fine mapping, the region of interest was mapped between two microsatellite markers, Sw207 and S0075, and interesting candidate genes surfaced. Numerous SNP analyses and a few expression studies on the three MUC-genes (MUC4, MUC13 and MUC20) and the transferrin receptor gene (TFRC) as well as on some other positional candidate genes have been performed in order to find the causative mutation for the ETEC-F4ab/ac receptor(s). However, until today, the exact mutation causing susceptibility to ETEC-F4 remains unknown.

Estimating genetics of body dimensions and activity levels in pigs using automated pose estimation.

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 (rg = 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.

Genome-Wide Association Analyses of Osteochondrosis in Belgian Warmbloods Reveal Candidate Genes Associated With Chondrocyte Development.

Osteochondrosis (OC) is an important skeletal disease causing profound welfare concerns in horses. Although numerous studies have explored the genetics underlying OC in various breeds, the Belgian Warmblood (BW) remains unstudied despite having a concerning prevalence of 32.0%. As a result, this study aimed to conduct genome-wide association (GWA) analyses to identify candidate variants associated with OC in BWs. To achieve this, blood samples and radiographs were collected from 407 Belgian Warmbloods registered to one of two BW studbooks (Belgisch Warmbloedpaard and Zangersheide), and genotyping was performed using the 670K Axiom Equine Genotyping Array. GWA analyses using a principle component approach were then performed on OC status (OCS; presence or absence of OC at any joint), hock OC status (HOC) and stifle OC status (SOC). These analyses yielded significantly associated (P < .01) SNPs on Equus caballus chromosome (ECA) 3, ECA 12, and ECA 18 for OCS; however, no single nucleotide polymorphisms (SNPs) reached significance for HOC or SOC. Subsequent analysis of candidate genes within 500 kilobases of the significant SNPs revealed functions broadly related to cell differentiation and chondrocyte development. While this study represents another step forward in uncovering variants and biological pathways associated with OC, additional studies are needed to validate the newly identified candidate SNPs for OC in BWs. Further studies of OC in BWs, as well as other breeds, are critical in our efforts to fully understand the disease's etiopathogenesis and ultimately provide breeding programs better equipped to improve horse health and well-being.

Genomics Confirm an Alarming Status of the Genetic Diversity of Belgian Red and Belgian White Red Cattle.

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 Fst 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, Fst 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, Fst 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.

High Heritabilities for Antibiotic Usage Show Potential to Breed for Disease Resistance in Finishing Pigs.

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.

A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig.

Most traits and disorders have a multifactorial background indicating that they are controlled by environmental factors as well as an unknown number of quantitative trait loci (QTLs). The identification of mutations underlying QTLs is a challenge because each locus explains only a fraction of the phenotypic variation. A paternally expressed QTL affecting muscle growth, fat deposition and size of the heart in pigs maps to the IGF2 (insulin-like growth factor 2) region. Here we show that this QTL is caused by a nucleotide substitution in intron 3 of IGF2. The mutation occurs in an evolutionarily conserved CpG island that is hypomethylated in skeletal muscle. The mutation abrogates in vitro interaction with a nuclear factor, probably a repressor, and pigs inheriting the mutation from their sire have a threefold increase in IGF2 messenger RNA expression in postnatal muscle. Our study establishes a causal relationship between a single-base-pair substitution in a non-coding region and a QTL effect. The result supports the long-held view that regulatory mutations are important for controlling phenotypic variation.

Developing and Understanding Olfactory Evaluation of Boar Taint.

Trained expert panels are used routinely in boar taint research, with varying protocols for training of panelists and scoring methods. We describe a standardized process for training and scoring, to contribute to standardize the olfactory detection of boar taint. Three experiments are described in which we (1) evaluate the importance of training and the effect of the previous sample, (2) determine detection thresholds on strips and in fat for our panel, and (3) test priming panelists before boar taint evaluation. For the final evaluation of boar taint, we propose a consistent three-person evaluation scoring on a 0-4 scale using a final mean score of 0.5 as the cut-off for boar taint. This gave an optimal sensitivity of 0.81 and a specificity of 0.56 compared to chemical cut-offs. Even limited training proved useful, but priming assessors with strips did not improve the evaluation of fat samples. Detection thresholds were higher in fat compared to strips, except for indole. We recommend panelists to always smell a non-tainted control sample after a tainted one as a 'reset' mechanism, before continuing. For longitudinal studies, we additionally advise to set up an expert panel with a fixed number of assessors performing each evaluation in duplicate.

Full sib pens of pigs are not suitable to identify variance component of associative effect: a simulation study using Gibbs Sampling.

BACKGROUND: Accounting for and quantifying the associative effect of each animal could improve both welfare of animals and response to selection. Because of the limitation of REML, Gibbs Sampling could be an alternative technique to estimate the variance component of the associative effect. The objective of this study was to investigate the estimation accuracy of the variance component of associative effect by using simulation via Gibbs Sampling. The simulated data comprised five generations of pigs. The breeding animals of each generation were selected randomly. In the simulation, variations were introduced for the methods of assigning pens (random, mixed sib and full sib), the number of pigs per pen (5 or 10), the number of breeding animals per generation (162 or 324) and the correlation between genetic direct effect and genetic associative effect (-0.5, 0.1 or +0.5). Each set of simulation was run for 30 replications. RESULTS: Random assignment or mixed sib assignment resulted in bias of estimated variance components in only 3 of 24 combinations. Furthermore, these 3 cases occurred with 162 breeding animals. With full sib assignment, 9 out of 12 groups of estimates significantly deviated from the true parameter value. The Root Mean Square Errors obtained with the full sib assignment were higher than with the other two methods of pen assignment in most of the cases. The Root Mean Square Errors obtained with datasets with 324 breeding animals were notably smaller than the datasets from 162 breeding animals. Within each method of pen assignment, the relative bias of the associative effect was significantly smaller with group size 10 than with group size 5. CONCLUSION: Full sib assignment caused difficulties to estimate variance components in most of the cases, due to a lack of identifiability. With random and mixed assignment, most data structures yielded unbiased results but increasing the number of breeding animals or group size improves the estimation. Thus to get identifiable and unbiased estimates of the genetic associative effect, it is recommended to avoid close genetic relationship between animals within one pen and to use sufficient numbers of breeding animals and sufficient group sizes.