INTRODUCTION:Pigs without intestinal receptors for F4 fimbriae are congenitally resistant to F4 fimbriae-bearing enterotoxigenic Escherichia coli (ETEC F4). In general, 50 % and 100 % of piglets born to resistant (RR) sows crossed with hetero- or homozygous susceptible (SR, SS) boars, respectively, are susceptible but do not receive colostral antibodies against F4 fimbriae unless the sows have been vaccinated. The question arises as to whether resistant sows produce protective amounts of F4 antifimbrial antibodies after vaccination. The serum and colostrum antibody titres of 12 resistant and 12 susceptible vaccinated gilts were compared. The effect of the receptor status of the dam and sire on the preweaning performance of 5027 piglets was evaluated using Agroscope's recordings. The sows of the experimental herd, where ETEC F4 was circulating, were vaccinated against ETEC twice during the first pregnancy and once during each following pregnancy. The log2 transformed F4 antibody titres in the serum obtained after the second vaccine injection as well as in the colostrum of the 12 resistant animals were lower than the titres of the susceptible animals (serum: F4ab 11,19 ± 1,44 vs. 12,18 ± 1,33, P = 0,096; F4ac 10,03 ± 1,58 vs. 11,59 ± 1,43, P = 0,019; colostrum: F4ab 12,20 ± 2,41 vs. 14,02 ± 1,31, P = 0,033; F4ac 10,93 ± 2,46 vs. 13,03 ± 5,21, P = 0,006). The heat labile enterotoxin (LT) antibody titres after vaccination did not differ between susceptible and resistant animals (p > 0,10). Preweaning mortality in the offspring of RR sows × SS boars was slightly lower than in the offspring of SS sows × RR boars (P = 0,04), suggesting that the disease risk of susceptible piglets born to vaccinated resistant sows was not increased, even though they received colostrum with a slightly reduced content of antibody against F4 fimbriae.

AbstractHaemorrhagic bowel syndrome (HBS) is one of the most common causes of death in fattening pigs worldwide. The objective of this descriptive study was to systematically assess predictors or causal components for the appearance of HBS using case farms (mortality rate caused by HBS ≥ 1.5%) in comparison with control farms (mortality rate caused by HBS ≤ 0.25%), focusing on feed ingredients, feed quality and size, and gastrointestinal pathogens. The inclusion of sugar beet as a feed component in liquid feeding systems was found to be associated (p = 0.03) with farms identified as HBS cases. Another predictive or causal factor found for liquid feeding systems, but only for those using meal, was particle size. A higher percentage of small particles (< 2 mm) in the meal was associated with a higher risk of being an HBS case farm (p = 0.02), while no relevant association was detected for the use of pellets. Sugar beet in the diet was also associated with the incidence of HBS.The microbial quality of the feed in dry feeding systems, specifically the number of total aerobes at the first and last outlet tubes, was associated with a higher incidence of HBS (p = 0.03). Faecal sample analysis showed a difference (p < 0.05) in the prevalence of B. pilosicoli in the herd category (case vs. control herd). In this descriptive study, five predictive or causal factors were identified for an HBS farm with a mortality rate due to HBS ≥ 1.5%. These included the number of aerobes in dry matter samples from the first and last feeders, the particle diameter of the meal used in liquid feeding systems and sugar beet as a component of liquid feeding rations, and the presence of B. pilosicoli as an infectious agent at animal level. Relevant associations reinforce the findings of the previously published Swiss study that HBS is a multifactorial syndrome involving different aspects of pig production and cannot be attributed to a single cause. Further studies are needed to develop evidenced based causal models for HBS in swine.

Background The porcine haemorrhagic bowel syndrome (HBS) is a multifactorial disease causing fatal gastrointestinal disturbances and sudden death in fattening pigs. HBS is the leading cause of deaths during fattening in Swiss pigs, with unclear etiology. Environmental and management factors are associated with HBS incidence, but recent findings also suggest a potential genetic predisposition. Pigs sired by a Swiss Large White (SLW) line appear more prone to HBS. Here we conduct genome-wide association studies (GWAS) for HBS between cases and controls to investigate potential genetic factors for the disease in Swiss fattening pigs.Results Our study included 1,036 HBS cases and 4,080 controls with available microarray genotypes or whole-genome sequencing data. Variant positions were determined according to the current porcine reference assembly (Sscrofa11.1) or a HiFi-based SLW haplotype assembly which we constructed using trio-binning. GWAS for HBS were conducted using 12.49 to 15.46 million biallelic variants in three mapping cohorts consisting of purebred animals from SLW sire and dam lines, or crosses between these two parental lines. The statistical model applied for the GWAS accounted for animal relatedness, population structure, and an imbalanced case/control ratio. No sequence variants significantly associated with HBS were identified, regardless of the cohort analysed and the reference sequence considered.Conclusions The lack of genetic associations despite a relatively large sample size suggests that susceptibility to HBS in the studied SLW population is not due to large effect variants but may be influenced by numerous small effect genetic variants, in addition to environmental and management factors.### Competing Interest StatementThe authors have declared no competing interest.* BUSCO : Benchmarking Universal Single-Copy Orthologs GRM : Genomic Relationship Matrix GWAS : Genome-Wide Association Studies HBS : Haemorrhagic Bowel Syndrome HiFi : High Fidelity HMW : High Molecular Weight MAF : Minor Allele Frequency QV : Quality Value SLW : Swiss Large White SNP : Single Nucleotide Polymorphism SV : Structural Variation

BACKGROUND:Genetic correlations between complex traits suggest that pleiotropic variants contribute to trait variation. Genome-wide association studies (GWAS) aim to uncover the genetic underpinnings of traits. Multivariate association testing and the meta-analysis of summary statistics from single-trait GWAS enable detecting variants associated with multiple phenotypes. In this study, we used array-derived genotypes and phenotypes for 24 reproduction, production, and conformation traits to explore differences between the two methods and used imputed sequence variant genotypes to fine-map six quantitative trait loci (QTL).RESULTS:We considered genotypes at 44,733 SNPs for 5,753 pigs from the Swiss Large White breed that had deregressed breeding values for 24 traits. Single-trait association analyses revealed eleven QTL that affected 15 traits. Multi-trait association testing and the meta-analysis of the single-trait GWAS revealed between 3 and 6 QTL, respectively, in three groups of traits. The multi-trait methods revealed three loci that were not detected in the single-trait GWAS. Four QTL that were identified in the single-trait GWAS, remained undetected in the multi-trait analyses. To pinpoint candidate causal variants for the QTL, we imputed the array-derived genotypes to the sequence level using a sequenced reference panel consisting of 421 pigs. This approach provided genotypes at 16 million imputed sequence variants with a mean accuracy of imputation of 0.94. The fine-mapping of six QTL with imputed sequence variant genotypes revealed four previously proposed causal mutations among the top variants.CONCLUSIONS:Our findings in a medium-size cohort of pigs suggest that multivariate association testing and the meta-analysis of summary statistics from single-trait GWAS provide very similar results. Although multi-trait association methods provide a useful overview of pleiotropic loci segregating in mapping populations, the investigation of single-trait association studies is still advised, as multi-trait methods may miss QTL that are uncovered in single-trait GWAS.

Background Haemorrhagic bowel syndrome (HBS) is a sporadically occurring disorder characterized by sudden death in pigs in combination with a pale and bloated carcass with no prior signs of disease. Most often HBS is affecting fattening pigs. Due to the good general health and performance before death as well as the time point of disease shortly prior to slaughter, this syndrome means a significant economic impact for the farm and is a major animal welfare concern. Furthermore, the cause or the causing agents have not yet been identified even though it is a worldwide known problem. The aim of this study was to detect possible risk factors for the occurrence of HBS with the focus on risk factors on herd level. Results Management and feeding strategies of 97 Swiss fattening herds with high and low HBS incidence were assessed and examined to identify risk factors for the disease. Having only pigs sired by the PREMO® breed in the herd showed to be a significant risk factor for HBS (Odds Ratio (OR) = 147) as compared to having other breeds or a mixture of multiple breeds. Furthermore, pigs from two or more origins per batch compared to having only one origin per batch significantly increased the disease risk (OR = 52). Farms with 1 decimetre greater feeding place width per finisher pig have a lower HBS incidence (OR = 0.07). The frequency of cleaning of the distribution pipes (split up into categories, e.g. once a month) was associated with being a HBS case farm (p < 0.05). Conclusion The four factors identified in this study for the occurrence of HBS represent different aspects of the environment and management. This leads to the assumption that it is a multifactorial syndrome and a thorough examination of each herd individually is necessary to mitigate disease risk. This study suggests that part of the susceptibility to HBS is genetically determined. The reduction of HBS in the herd should be the main objective to improve the economic status of the herd and improve animal welfare.

We performed single-trait and multi-trait genome-wide association studies (GWAS) to detect quantitative trait loci (QTL) for body length and feed intake in 3,638 Swiss Large White pigs that had genotypes at 43,994 SNPs. Single-trait GWAS (ST-GWAS) revealed two non-overlapping QTL for each trait. Multivariate GWAS implemented with GEMMA software yielded 75 significant SNPs (-log10(p)>6) at the same four QTL. A meta-analysis of summary statistics from the two ST-GWAS resulted in 83 significant SNPs at the same QTL. After including all samples that had at least one phenotype recorded (in total 5,109), the P-values of top variants decreased suggesting higher statistical power due to a larger sample size. Fine mapping using imputed sequence variant genotypes confirmed the presence of three previously reported candidate causal variants in MC4R, VRTN and BMP2 genes among the most significantly associated variants.

Background The key-ancestor approach has been frequently applied to prioritize individuals for whole-genome sequencing based on their marginal genetic contribution to current populations. Using this approach, we selected 70 key ancestors from two lines of the Swiss Large White breed that have been selected divergently for fertility and fattening traits and sequenced their genomes with short paired-end reads. Results Using pedigree records, we estimated the effective population size of the dam and sire line to 72 and 44, respectively. In order to assess sequence variation in both lines, we sequenced the genomes of 70 boars at an average coverage of 16.69-fold. The boars explained 87.95 and 95.35% of the genetic diversity of the breeding populations of the dam and sire line, respectively. Reference-guided variant discovery using the GATK revealed 26,862,369 polymorphic sites. Principal component, admixture and fixation index (F ST ) analyses indicated considerable genetic differentiation between the lines. Genomic inbreeding quantified using runs of homozygosity was higher in the sire than dam line (0.28 vs 0.26). Using two complementary approaches, we detected 51 signatures of selection. However, only six signatures of selection overlapped between both lines. We used the sequenced haplotypes of the 70 key ancestors as a reference panel to call 22,618,811 genotypes in 175 pigs that had been sequenced at very low coverage (1.11-fold) using the GLIMPSE software. The genotype concordance, non-reference sensitivity and non-reference discrepancy between thus inferred and Illumina PorcineSNP60 BeadChip-called genotypes was 97.60, 98.73 and 3.24%, respectively. The low-pass sequencing-derived genomic relationship coefficients were highly correlated ( r > 0.99) with those obtained from microarray genotyping. Conclusions We assessed genetic diversity within and between two lines of the Swiss Large White pig breed. Our analyses revealed considerable differentiation, even though the split into two populations occurred only few generations ago. The sequenced haplotypes of the key ancestor animals enabled us to implement genotyping by low-pass sequencing which offers an intriguing cost-effective approach to increase the variant density over current array-based genotyping by more than 350-fold.

Artificial insemination in pig (Sus scrofa domesticus) breeding involves the evaluation of the semen quality of breeding boars. Ejaculates that fulfill predefined quality requirements are processed, diluted and used for inseminations. Within short time, eight Swiss Large White boars producing immotile sperm that had multiple morphological abnormalities of the sperm flagella were noticed. The eight boars were inbred on a common ancestor suggesting that the novel sperm flagella defect is a recessive trait. Transmission electron microscopy cross-sections revealed that the immotile sperm had disorganized flagellar axonemes. Haplotype-based association testing involving microarray-derived genotypes at 41,094 SNPs of six affected and 100 fertile boars yielded strong association (P=4.22 x 10−15) at chromosome 12. Autozygosity mapping enabled us to pinpoint the causal mutation on a 1.11 Mb haplotype located between 3,473,632 and 4,587,759 bp. The haplotype carries an intronic 13-bp deletion (Chr12:3,556,401-3,556,414 bp) that is compatible with recessive inheritance. The 13-bp deletion excises the polypyrimidine tract upstream exon 56 of DNAH17 (XM_021066525.1:c.8510-17_8510-5del) encoding dynein axonemal heavy chain 17. Transcriptome analysis of the testis of two affected boars revealed that the loss of the polypyrimidine tract causes exon skipping which results in the in-frame loss of 89 amino acids from DNAH17. Disruption of DNAH17 impairs the assembly of the flagellar axoneme and manifests in multiple morphological abnormalities of the sperm flagella. Direct gene testing may now be implemented to monitor the defective allele in the Swiss Large White population and prevent the frequent manifestation of a sterilizing sperm tail disorder in breeding boars.

Artificial insemination in pig (Sus scrofa domesticus) breeding involves the evaluation of the semen quality of breeding boars. Ejaculates that fulfill predefined quality requirements are processed, diluted and used for inseminations. Within short time, eight Swiss Large White boars producing immotile sperm that had multiple morphological abnormalities of the sperm flagella were noticed at a semen collection center. The eight boars were inbred on a common ancestor suggesting that the novel sperm flagella defect is a recessive trait. Transmission electron microscopy cross-sections revealed that the immotile sperm had disorganized flagellar axonemes. Haplotype-based association testing involving microarray-derived genotypes at 41,094 SNPs of six affected and 100 fertile boars yielded strong association (P = 4.22 × 10-15) at chromosome 12. Autozygosity mapping enabled us to pinpoint the causal mutation on a 1.11 Mb haplotype located between 3,473,632 and 4,587,759 bp. The haplotype carries an intronic 13-bp deletion (Chr12:3,556,401-3,556,414 bp) that is compatible with recessive inheritance. The 13-bp deletion excises the polypyrimidine tract upstream exon 56 of DNAH17 (XM_021066525.1: c.8510-17_8510-5del) encoding dynein axonemal heavy chain 17. Transcriptome analysis of the testis of two affected boars revealed that the loss of the polypyrimidine tract causes exon skipping which results in the in-frame loss of 89 amino acids from DNAH17. Disruption of DNAH17 impairs the assembly of the flagellar axoneme and manifests in multiple morphological abnormalities of the sperm flagella. Direct gene testing may now be implemented to monitor the defective allele in the Swiss Large White population and prevent the frequent manifestation of a sterilizing sperm tail disorder in breeding boars.

The F4ac receptor locus (F4acR), which encodes susceptibility or resistance to Escherichia coli diarrhoea, is inherited as an autosomal recessive monogenetic trait. F4acR is localized on pig chromosome 13 (SSC13q41-q44) near the MUC13 gene. Two flanking markers (CHCF1 and ALGA0106330) with a high linkage disequilibrium (LD) with F4acR were found to be effective for the genetic identification of F4ac-resistant pigs in the Swiss Large White breed (one recombinant out of 2034 genotyped pigs). Three recombinant boars, one each from the Duroc, Swiss Landrace and Piétrain breeds, were genotyped with seven different markers and phenotyped by means of a microscopic adhesion test. Only ALGA0072075, CHCF1 and CHCF3 indicated the correct phenotype. To test the effect of the resistance allele on production traits, 530 Large White pigs from the national test station were investigated. A significant difference existed among the F4acR locus genotypes in the intramuscular fat content of the longissimus dorsi muscle, whereas no other production traits were influenced by the resistance allele. The frequency of the CHCF1-C and ALGA0106330-A alleles associated with resistance in the Swiss Large White population was 60%, which is advantageous for implementing this trait in a breeding programme to select for E. coli F4ac-resistant animals. The selection of resistant pigs should start on the male side due to the inability of resistant sows to produce sufficient amounts of protecting antibodies in the colostrum. Selection of genetically F4ac-resistant pigs is a sustainable and suitable alternative to decreasing animal loss and antibiotic use due to diarrhoea.

Osteochondrosis (OC) is an orthopedic syndrome of the joints that occurs in children and adolescents and domestic animals, particularly pigs, horses, and dogs. OC is the most frequent cause of leg weakness in rapidly growing pigs causing animal welfare issues and economic losses. In this study, a genome-wide association study (GWAS) was performed using the Porcine 60k SNPChip in animals of the breed Large White (n = 298) to identify chromosome regions and candidate genes associated with OC lesion scores. A total of 19 SNPs on chromosomes (SSC) 3, 5, 8, 10, 14, and 18 were significantly associated with OC lesion scores (p-values ≤ 10(-5)). The SNPs MARC0098684, MARC00840086, MARC0093124, and ASGA0062794 at SSC14 36.1-38.2 Mb encompass a region of six linkage disequilibrium (LD) blocks. The most significant SNP ASGA0062794 is located in a LD block spanning 465 kb and covering the gene encoding T-box transcription factor 5 (TBX5). A SNP (c.54T > C) identified in TBX5 was significantly associated with OC lesion scores in a single-marker analysis. TBX5 c.54T > C showed highest LD with ASGA00627974 (r (2) = 0.96) and superior association with OC lesion scores over other SNPs when included in the genome scan, whereas its treatment as an additional fixed effect in the GWAS statistical model led to a drop of significance of nearby markers. Moreover, real-time PCR showed different transcript abundance of TBX5 in healthy and defect cartilage. The results imply that the association signal obtained on SCC14 is largely attributable to TBX5 c.54T > C likely to be in LD with a regulatory polymorphism of TBX5. The transcription factor TBX5 interacts with GJA5 and MEF2C both being involved in vascularization. This study provides evidence for epistatic interaction of TBX5 and MEF2C, thus supporting deficiency of blood supply to growth cartilage as being fundamental for the initiation of OC.

Genetically reducing boar taint using low-taint lines is considered the most sustainable and economic long-term alternative to surgical castration of male pigs. Owing to the high heritability of the main boar taint components (androstenone, skatole and indole), breeding is an excellent tool for reducing the number of tainted carcasses. To incorporate boar taint into breeding programmes, standardized performance testing is required. The objective of this study was to develop and formally present a performance test for the main boar taint compounds on live breeding candidates. First, a standardized performance test for boar taint was established. A biopsy device was developed to extract small tissue samples (200 to 300 mg) from breeding candidates. Quantification of boar taint components from these small samples using specialized chemical extraction methods proved accurate and repeatable (r = 0.938). Following establishment of the method, biopsy samples of 516 live boars (100 to 130 kg live weight) were collected in the second step. Various mixed linear models were tested for each boar taint compound; models were ranked in terms of their information content. Pedigree information of 2245 ancestors of biopsied animals was included, and genetic parameters were estimated using univariate and multivariate models. Androstenone (in μg/g liquid fat (LF): mean = 0.578, σ = 0.527), skatole (in μg/g LF: mean = 0.033, σ = 0.002) and indole (in μg/g LF: mean = 0.032, σ = 0.002) levels obtained by biopsy were plausible. Heritability estimates for androstenone calculated with univariate (0.453) and multivariate (0.452) analyses were comparable to those in the literature. Heritabilities for skatole (0.495) and indole (0.550) were higher than that for androstenone. Genetic and phenotypic correlations were similar to those published previously. Our results show that data on boar taint compounds from small adipose samples obtained by biopsy provide similar genetic parameters as that described in the literature for larger samples and are therefore a reliable performance test for boar taint in live breeding candidates.

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The liability to lesions of dysfunctions of bone and joints in pigs, summarized as leg weakness and mostly expressed as osteochondrosis, is an animal welfare and economic issue in pig production. The objective of this study was to identify polymorphisms in the functional and positional candidate genes keratin 8 (KRT8), Fas-associated factor 1 (FAF1) and parathyroid hormone type I receptor (PTH1R) and to evaluate their association with leg weakness traits. Therefore, osteochondrosis lesions were scored in animals of a Duroc × Pietrain F2 population (DuPi; n = 310) and commercial herds of the breed Large White (n = 298). In addition, bone mineralization traits were observed in DuPi population. SNPs were identified in genes KRT8 (g.8,039G > A), FAF1 (g.380,914T > C) and PTH1R (c.1,672C > T). KRT8 showed significant association with bone mineral density and content (P ≤ 0.05). FAF1 was association with OC lesions score of all joints inspected (P ≤ 0.05). PTH1R showed significant dominance effects on OC lesion scores of the distal femur articular cartilage (P = 0.01) and epiphysis of the distal ulna (P = 0.05) as well as sums of scores of all joints (OCsum, P = 0.04) and assignment to groups of either severely or gently affected animals (OCcat, P = 0.01). This study reveals clear genetic-statistical evidence for a link of KRT8, FAF1 and PTH1R with some of leg weakness related traits in pigs.

The breeding scheme of a Swiss sire line was modeled to compare different target traits and information sources for selection against boar taint. The impact of selection against boar taint on production traits was assessed for different economic weights of boar taint compounds. Genetic gain and breeding costs were evaluated using ZPlan+, a software based on selection index theory, gene flow method and economic modeling. Scenario I reflected the currently practiced breeding strategy as a reference scenario without selection against boar taint. Scenario II incorporated selection against the chemical compounds of boar taint, androstenone (AND), skatole (SKA) and indole (IND) with economic weights of -2.74, -1.69 and -0.99 Euro per unit of the log transformed trait, respectively. As information sources, biopsy-based performance testing of live boars (BPT) was compared with genomic selection (GS) and a combination of both. Scenario III included selection against the subjectively assessed human nose score (HNS) of boar taint. Information sources were either station testing of full and half sibs of the selection candidate or GS against HNS of boar taint compounds. In scenario I, annual genetic gain of log-transformed AND (SKA; IND) was 0.06 (0.09; 0.02) Euro, which was because of favorable genetic correlations with lean meat percentage and meat surface. In scenario II, genetic gain increased to 0.28 (0.20; 0.09) Euro per year when conducting BPT. Compared with BPT, genetic gain was smaller with GS. A combination of BPT and GS only marginally increased annual genetic gain, whereas variable costs per selection candidate augmented from 230 Euro (BPT) to 330 Euro (GS) or 380 Euro (both). The potential of GS was found to be higher when selecting against HNS, which has a low heritability. Annual genetic gain from GS was higher than from station testing of 4 full sibs and 76 half sibs with one or two measurements. The most effective strategy to reduce HNS was selecting against chemical compounds by conducting BPT. Because of heritabilities higher than 0.45 for AND, SKA and IND and high genetic correlations to HNS, the (correlated) response in units of the trait could be increased by 62% compared with scenario III with GS and even by 79% compared with scenario III, with station testing of siblings with two measurements. Increasing the economic weights of boar taint compounds amplified negative effects on average daily gain, drip loss and intramuscular fat percentage.

The improvement of meat quality and production traits has high priority in the pork industry. Many of these traits show a low to moderate heritability and are difficult and expensive to measure. Their improvement by targeted breeding programs is challenging and requires knowledge of the genetic and molecular background. For this study we genotyped 192 artificial insemination boars of a commercial line derived from the Swiss Large White breed using the PorcineSNP60 BeadChip with 62,163 evenly spaced SNPs across the pig genome. We obtained 26 estimated breeding values (EBVs) for various traits including exterior, meat quality, reproduction, and production. The subsequent genome-wide association analysis allowed us to identify four QTL with suggestive significance for three of these traits (p-values ranging from 4.99×10⁻⁶ to 2.73×10⁻⁵). Single QTL for the EBVs pH one hour post mortem (pH1) and carcass length were on pig chromosome (SSC) 14 and SSC 2, respectively. Two QTL for the EBV rear view hind legs were on SSC 10 and SSC 16.

The objective of this study was to investigate whether the occurrence of cryptorchidism in a litter is associated with the sex ratio in this litter. The analysis included for dog 1,339 litters of 4 different breeds, of which 12.8% had 1 and 3.1% had 2 cryptorchids, and for pig 119,920 litters of 14 different populations, of which 2.2% had 1 and 0.2% had 2 cryptorchids. The data were analyzed using the GLIMMIX procedure of SAS. In dog, the presence of cryptorchids in a litter does not affect litter size or the stillborn rate. In pig, litter size increases significantly with an increasing number of cryptorchids in a litter. The stillborn rate in pig is larger in litters with cryptorchids than in litters without cryptorchids. To characterize the imbalance of the sexes in a litter, the sex ratio, defined as the number of live males divided by the number of live offspring, and the sex difference, defined as the number of live males minus the number of live females, were used as dependent variables in the analyses. In both dog and pig, the presence of 1 or 2 cryptorchids in a litter clearly goes together with a shift in both the sex ratio and the sex difference in a litter, in favor of male offspring. Our results in dog and pig suggest a common underlying mechanism affecting both cryptorchidism and sex ratio, which may hold true in other mammals as well.

Osteochondrosis might reduce the performance of slaughter pigs, longevity of sows and animal welfare. The aim of the present work was to describe the prevalence in Swiss breeds and to analyse the genetic background of osteochondral lesions. Between January 2002 and December 2005, about 9500 station-tested pigs were examined for several exterior traits before slaughtering at the Swiss pig performance testing station using the Swiss linear description system with a scale from 1 to 7 per trait. The animals belonged to three breeds: Large White dam line, Swiss Landrace and Large White sire line. Additionally, a random sample of these pigs (n = 2622) was examined for osteochondral lesions at seven positions of the carcass after dissection. At first, the surface and shape of the femur, humerus, radius and ulna at the joints were evaluated by a trained person. Afterwards these bones were sawed and the state of the cartilage and the distal epiphyseal cartilage of the ulna was examined at the cutting surface. Osteochondral lesions were scored on a scale from 1 to 6. The prevalence of osteochondral lesions was low at head of humerus, condylus lateralis humeri, radius and ulna proximal and head of femur. Osteochondral lesions at condylus medialis humeri (CMH), distal epiphyseal cartilage of ulna (DEU) and condylus lateralis femoris (CMF) exhibited phenotypic and genetic variance. Their heritabilities ranged from 0.16 to 0.18 using linear mixed animal models. Therefore, it is possible to reduce the prevalence of osteochondral lesions by selection in principle. Exterior traits showed low heritabilities (0.10 to 0.26) but several favourable genetic correlations with osteochondral lesions at CMH, DEU and CMF with low to moderate magnitude. Genetic correlations between osteochondral lesions and production traits were low.

The main objective of this research was to estimate heritabilities of seven osteochondrosis (OC) lesions in station-tested pigs and their genetic and phenotypic correlations with four meat quality (MQ) traits, the percentage of premium cuts (PPC), daily weight gain (DWG), and feed conversion ratio (FCR). Observed OC lesions were on the head of humerus (HK), condylus medialis humeri (CMH), condylus lateralis humeri (CLH), radius and ulna proximal (RUP), distal epiphyseal cartilage of ulna (DEU), head of femur (FK), and condylus medialis femoris (CMF). Meat quality traits were i.m. fat (IMF), muscle pH at 1 h after slaughter (pH1), muscle pH at 30 h after slaughter (pH30), and light reflectance on muscle (H30). The data set comprised 2,710 animals, of which 1,291 animals had OC records. All traits were analyzed by multiple-trait linear mixed model, with the animal's genetic and common litter effects as random. Fixed effects in the model varied between traits. Each OC lesion was further analyzed by a univariate generalized linear mixed model or, equivalently, "threshold models," assuming logistic, probit (normal), and Poisson distributions of the underlying "liability" to the disease. For OC lesions, estimates of heritability were low on the original "incidence" scale (0.06 for HK to 0.16 for CLH) and moderate to high on the liability scale (0.08 to 0.42). Genetic correlations (r(g)) between OC lesions and most MQ traits and PPC were generally unfavorable. Significant r(g) were -0.44 for DWG-CMH, 0.31 for DWG-CMF, 0.40 for FCR-HK, 0.21 for PPC-CLH, 0.32 for PPC-RUP, 0.30 for PPC-CMF, -0.54 for pH1-CLH, 0.47 for pH1-DEU, -0.34 for pH30-CMH, 0.58 for pH30-DEU, -0.50 for H30-HK, -0.31 for H30-DEU, and 0.31 for H30-CMF. Genetic susceptibilities to some OC lesions within the front leg were positively related to each other (r(g) range = 0.57 to 0.69), but r(g) between front and hind leg OC lesions were mostly negative (range = -0.21 to -0.40). Estimated h2 was 0.60 for PPC, and ranged from 0.12 to 0.66 for MQ traits, 0.28 for DWG, and 0.42 for FCR. Genetic correlations among meat quality and quantity traits ranged from -0.66 to 0.37. This is the first study to report genetic and phenotypic correlations between OC lesions and several meat quality and quantity traits in pigs. These findings will be useful to pig industry, especially in designing breeding programs for robust pigs.