Effects of reference population size and structure on genomic prediction of maternal traits in two pig lines using whole-genome sequence-, high-density- and combined annotation-dependent depletion genotypes.

The aim of this study was to investigate the reference population size required to obtain substantial prediction accuracy within- and across-lines and the effect of using a multi-line reference population for genomic predictions of maternal traits in pigs. The data consisted of two nucleus pig populations, one pure-bred Landrace (L) and one Synthetic (S) Yorkshire/Large White line. All animals were genotyped with up to 30 K animals in each line, and all had records on maternal traits. Prediction accuracy was tested with three different marker data sets: High-density SNP (HD), whole genome sequence (WGS), and markers derived from WGS based on pig combined annotation dependent depletion-score (pCADD). Also, two different genomic prediction methods (GBLUP and Bayes GC) were compared for four maternal traits; total number piglets born (TNB), total number of stillborn piglets (STB), Shoulder Lesion Score and Body Condition Score. The main results from this study showed that a reference population of 3 K-6 K animals for within-line prediction generally was sufficient to achieve high prediction accuracy. However, when the number of animals in the reference population was increased to 30 K, the prediction accuracy significantly increased for the traits TNB and STB. For multi-line prediction accuracy, the accuracy was most dependent on the number of within-line animals in the reference data. The S-line provided a generally higher prediction accuracy compared to the L-line. Using pCADD scores to reduce the number of markers from WGS data in combination with the GBLUP method generally reduced prediction accuracies relative to GBLUP using HD genotypes. The BayesGC method benefited from a large reference population and was less dependent on the different genotype marker datasets to achieve a high prediction accuracy.

Liquid storage of porcine in vitro-produced blastocysts; a practical approach for short storage.

Commercial application of embryo transfer in pig breeding is dependent on the storage of embryos. The aim of this study was to assess the embryo quality of in vitro-produced blastocysts after 3 h liquid storage at 37°C in CO2-free medium by evaluating morphology, in vitro developmental capacity and apoptosis. Blastocysts at days 5 and 6 post-fertilization were randomly allocated to the storage group (HEPES-buffered NCSU-23 medium including bovine serum albumin in a portable embryo transport incubator at 37°C) or a control group (porcine blastocyst medium in a conventional culture incubator). Thereafter, blastocysts were evaluated for morphology and stained to assess apoptosis straight after the 3 h storage period or after a further 24 h conventional incubation. There was no significant difference between the storage and control group after 3 h storage and the further 24 h conventional incubation for any of the parameters, nor for apoptosis straight after the 3 h storage. Embryos that reached the blastocyst stage at day 5 showed less apoptosis (6.6% vs 10.9%, P = 0.01) and a trend for a higher rate of developmental capacity (70.6% vs 51.5%, P = 0.089) than embryos reaching the blastocyst stage on day 6. In conclusion, in vitro-produced porcine blastocysts can be stored for 3 h at physiological temperature in transportable incubators using a CO2-independent medium without compromising quality.

Osteochondrosis and other lesions in all intervertebral, articular process and rib joints from occiput to sacrum in pigs with poor back conformation, and relationship to juvenile kyphosis.

BACKGROUND: Computed tomography (CT) is used to evaluate body composition and limb osteochondrosis in selection of breeding boars. Pigs also develop heritably predisposed abnormal curvature of the spine including juvenile kyphosis. It has been suggested that osteochondrosis-like changes cause vertebral wedging and kyphosis, both of which are identifiable by CT. The aim of the current study was to examine the spine from occiput to sacrum to map changes and evaluate relationships, especially whether osteochondrosis caused juvenile kyphosis, in which case CT could be used in selection against it. Whole-body CT scans were collected retrospectively from 37 Landrace or Duroc boars with poor back conformation scores. Spine curvature and vertebral shape were evaluated, and all inter-vertebral, articular process and rib joints from the occiput to the sacrum were assessed for osteochondrosis and other lesions. RESULTS: Twenty-seven of the 37 (73%) pigs had normal spine curvature, whereas 10/37 (27%) pigs had abnormal curvature and all of them had wedge vertebrae. The 37 pigs had 875 focal lesions in articular process and rib joints, 98.5% of which represented stages of osteochondrosis. Five of the 37 pigs had focal lesions in other parts of vertebrae, mainly consisting of vertebral body osteochondrosis. The 10 pigs with abnormal curvature had 21 wedge vertebrae, comprising 10 vertebrae without focal lesions, six ventral wedge vertebrae with ventral osteochondrosis lesions and five dorsal wedge vertebrae with lesions in the neuro-central synchondrosis, articular process or rib joints. CONCLUSIONS: Computed tomography was suited for identification of wedge vertebrae, and kyphosis was due to ventral wedge vertebrae compatible with heritably predisposed vertebral body osteochondrosis. Articular process and rib joint osteochondrosis may represent incidental findings in wedge vertebrae. The role of the neuro-central synchondrosis in the pathogenesis of vertebral wedging warrants further investigation.

Loss of function mutations in essential genes cause embryonic lethality in pigs.

Lethal recessive alleles cause pre- or postnatal death in homozygous affected individuals, reducing fertility. Especially in small size domestic and wild populations, those alleles might be exposed by inbreeding, caused by matings between related parents that inherited the same recessive lethal allele from a common ancestor. In this study we report five relatively common (up to 13.4% carrier frequency) recessive lethal haplotypes in two commercial pig populations. The lethal haplotypes have a large effect on carrier-by-carrier matings, decreasing litter sizes by 15.1 to 21.6%. The causal mutations are of different type including two splice-site variants (affecting POLR1B and TADA2A genes), one frameshift (URB1), and one missense (PNKP) variant, resulting in a complete loss-of-function of these essential genes. The recessive lethal alleles affect up to 2.9% of the litters within a single population and are responsible for the death of 0.52% of the total population of embryos. Moreover, we provide compelling evidence that the identified embryonic lethal alleles contribute to the observed heterosis effect for fertility (i.e. larger litters in crossbred offspring). Together, this work marks specific recessive lethal variation describing its functional consequences at the molecular, phenotypic, and population level, providing a unique model to better understand fertility and heterosis in livestock.

Effect of two 'progressively motile sperm-oocyte' ratios on porcine in vitro fertilization and embryo development.

Sperm motility and viability of cryopreserved semen vary between boars and straws, which influences the outcomes of in vitro embryo production (IVEP). However, progressive motility is usually not considered during IVEP. The aim of this study was to assess fertilization with a 500:1 and 250:1 'progressively motile sperm to oocyte' ratio on IVEP outcomes using semen from three Duroc and three Landrace boars. Frozen-thawed sperm was centrifuged through a 45/90% Percoll® density gradient and sperm quality parameters were assessed. In vitro matured oocytes were fertilized at the two ratios, a portion was stained 10-12 h after start of fertilization to analyze fertilization and polyspermy, while the remaining zygotes were cultured up to day 7. The 500:1 ratio resulted in a higher fertilization and blastocyst yield on day 6 compared with the 250:1 ratio, but no effect of ratio was observed for polyspermy, cleavage rate or blastocyst cell number. Individual differences between boars were observed for fertilization, cleavage and blastocyst rates, but not for the other IVEP outcomes. In conclusion, a higher fertilization and blastocyst yield was obtained with the 500:1 ratio compared with the 250:1 ratio, while polyspermy level was consistent across ratios. Differences in IVEP outcomes were still observed between the individual boars although adjusted for progressive motility. Promising blastocyst yields and high total blastocyst cell counts were obtained with sperm from both breeds.

Accuracy of genomic prediction of maternal traits in pigs using Bayesian variable selection methods.

The aim of this study was to compare three methods of genomic prediction: GBLUP, BayesC and BayesGC for genomic prediction of six maternal traits in Landrace sows using a panel of 660 K SNPs. The effects of different priors for the Bayesian methods were also investigated. GBLUP does not take the genetic architecture into account as all SNPs are assumed to have equally sized effects and relies heavily on the relationships between the animals for accurate predictions. Bayesian approaches rely on both fitting SNPs that describe relationships between animals in addition to fitting single SNP effects directly. Both the relationship between the animals and single SNP effects are important for accurate predictions. Maternal traits in sows are often more difficult to record and have lower heritabilities. BayesGC was generally the method with the higher accuracy, although its accuracy was for some traits matched by that of GBLUP and for others by that of BayesC. For piglet mortality within 3 weeks, BayesGC achieved up to 9.2% higher accuracy. For many of the traits, however, the methods did not show significant differences in accuracies.

Transcriptome profiling of porcine testis tissue reveals genes related to sperm hyperactive motility.

BACKGROUND: Sperm hyperactive motility has previously been shown to influence litter size in pigs, but little is known about the underlying biological mechanisms. The aim of this study was to use RNA sequencing to investigate gene expression differences in testis tissue from Landrace and Duroc boars with high and low levels of sperm hyperactive motility. Boars with divergent phenotypes were selected based on their sperm hyperactivity values at the day of ejaculation (day 0) (contrasts (i) and (ii) for Landrace and Duroc, respectively) and on their change in hyperactivity between day 0 and after 96 h liquid storage at 18 °C (contrast (iii)). RESULTS: RNA sequencing was used to measure gene expression in testis. In Landrace boars, 3219 genes were differentially expressed for contrast (i), whereas 102 genes were differentially expressed for contrast (iii). Forty-one differentially expressed genes were identified in both contrasts, suggesting a functional role of these genes in hyperactivity regardless of storage. Zinc finger DNLZ was the most up-regulated gene in contrasts (i) and (iii), whereas the most significant differentially expressed gene for the two contrasts were ADP ribosylation factor ARFGAP1 and solute carrier SLC40A1, respectively. For Duroc (contrast (ii)), the clustering of boars based on their gene expression data did not reflect their difference in sperm hyperactivity phenotypes. No results were therefore obtained for this breed. A case-control analysis of variants identified in the Landrace RNA sequencing data showed that SNPs in NEU3, CHRDL2 and HMCN1 might be important for sperm hyperactivity. CONCLUSIONS: Differentially expressed genes were identified in Landrace boars with high and low levels of sperm hyperactivity at the day of ejaculate collection and high and low change in hyperactivity after 96 h of sperm storage. The results point towards important candidate genes, biochemical pathways and sequence variants underlying sperm hyperactivity in pigs.

Effects of heterozygosity on performance of purebred and crossbred pigs.

BACKGROUND: In pigs, crossbreeding aims at exploiting heterosis, but heterosis is difficult to quantify. Heterozygosity at genetic markers is easier to measure and could potentially be used as an indicator of heterosis. The objective of this study was to investigate the effect of heterozygosity on various maternal and production traits in purebred and crossbred pigs. The proportion of heterozygosity at genetic markers across the genome for each individual was included in the prediction model as a fixed regression across or within breeds. RESULTS: Estimates of regression coefficients of heterozygosity showed large effects for some traits. For maternal traits, regression coefficient estimates were always in a favourable direction, while for production, meat and slaughter quality traits, they were both favourable and unfavourable. Traits with the largest estimated effects of heterozygosity were total number born, litter weight at 3 weeks, weight at 150 days, and age at 40 kg. Estimates of regression coefficients on heterozygosity differed between breeds. Traits with the largest effect of heterozygosity also showed a significant (P < 0.05) increase in prediction accuracy when heterozygosity was included in the model compared to the model without heterozygosity. CONCLUSIONS: For traits with the largest estimates of regression coefficients on heterozygosity, the inclusion of heterozygosity in the model improved prediction accuracy. Using models that include heterozygosity would result in selecting different animals for breeding, which has the potential to improve genetic gain for these traits. This is most beneficial when crossbreds or several breeds are included in the estimation of breeding values and is relevant to all species, not only pigs. Thus, our results show that including heterozygosity in the model is beneficial for some traits, likely due to dominant gene action.

Computed tomographic development of physeal osteochondrosis in pigs.

BACKGROUND: Articular osteochondrosis follows a dynamic development pattern. Lesions arise, in incidence peaks compatible with failure of cartilage canal vessels during incorporation into bone, and can also resolve. Lesions that resolve before examination at a single time point will constitute false-negative diagnoses. The aim of the study was to identify physeal osteochondrosis lesions in pigs and monitor their development by computed tomography (CT), to determine if they follow a similar dynamic development pattern to articular osteochondrosis. RESULTS: Thirteen physes were evaluated bilaterally in up to eight biweekly CT scans from 18 male Landrace pigs age 70-180 days (total: 112 scans), generating 2912 scores. There were 1754 (60%) lesion-negative scores and 1158 (40%) lesion-positive scores. Positive scores comprised 138 lesions present at the start and 235 lesions that developed during the study, from 4 to 32 lesions per physis (median: 15 lesions). There were 1-2 peaks in the incidence curves for 12/13 examined physes, the exception being the proximal humerus. Positive scores also included 785 times that lesions persisted, from 1.3-4.8 examination intervals per lesion (median: 2.8 intervals). Negative scores included 190 times that lesions resolved, from 19 to 100% of lesions per physis (median: 65%). Lesions resolved by filling with bone from marginal sclerosis and reparative ossification centres. In the distal scapula and distal fibula, perichondrial new bone formation occurred that led to permanent enlargement of physeal regions. Angular limb deformity was not identified in any pig. CONCLUSIONS: Physeal osteochondrosis followed a similar dynamic development pattern to articular osteochondrosis. There were peaks in the incidence curves, compatible with failure of vessels during incorporation into bone. In some physes, osteochondrosis led to permanent enlargement, potentially relevant for decubital ulcers. The relationship between physeal osteochondrosis and angular limb deformity must be examined further in pigs over 6 months old in future.

Osteochondrosis in the Distal Femoral Physis of Pigs Starts With Vascular Failure.

Articular osteochondrosis (OC) arises due to vascular failure and ischemic chondronecrosis. The aim of the study was to describe the histological and computed tomographic (CT) characteristics of changes in the distal femoral physis of pigs, to determine if they represented OC lesions and if the pathogenesis was the same as for articular OC. The material included 19 male Landrace pigs bred for predisposition to OC. One or 2 pigs were euthanized and CT-scanned at 2-week intervals from 82 to 180 days of age. Material from 10 pigs was available for histological validation. The CT scans revealed 31 lesions confirmed in 3 planes and 1 additional macroscopically visible lesion confirmed in 2 CT planes. Twelve of the lesions were histologically validated. All lesions were compatible with OC. Cartilage canal and eosinophilic streak morphological changes corresponded to failure of end arteries coursing from the epiphysis, toward the metaphysis. The location of lesions was compatible with failure at the point of vessel incorporation into bone. Vascular failure was associated with retention of viable hypertrophic chondrocytes and delayed ossification but not cartilage necrosis. Lesion width ranged from 1.1% to 45.6% of the physis. Several lesions were expected to resolve due to small size and evidence of CT-identifiable, reparative ossification. Angular limb deformity was not detected in any pig. The pathogenesis of physeal OC started with vascular failure that was morphologically identical to articular OC. The heritable predisposition may therefore be the same. The association between lesions and limb deformity should be studied further in older pigs in future.

Sperm DNA integrity in Landrace and Duroc boar semen and its relationship to litter size.

The sperm chromatin structure assay is a method for assessment of sperm DNA fragmentation, a parameter reported to be negatively related to field fertility in several mammal species. This method calculates a DNA fragmentation index (DFI) whose high values indicate abnormal chromatin structure. In this study, running from March 2010 until June 2017, the aim was to assess sperm DFI in stored liquid extended semen from two different pig breeds, Norwegian Landrace (NL; n = 693) and Norwegian Duroc (ND; n = 655), and to evaluate the influence on total number of piglets born (TNB). There was a significantly higher median DFI (p < 0.0001) in ejaculates from the 478 ND boars compared to the 452 NL boars. Data from 19,496 NL litters and 3,877 ND litters of the same boars were retrieved. For either breed, sow herd (p < 0.0001), parity (p < 0.05) and DFI (p < 0.05) showed significant effects on TNB. The DFI was negatively correlated to TNB in both breeds. The boars with the 5% lowest TNB had a least square means DFI of 3.05% and 2.24% in NL and ND, respectively, compared to 1.67% and 1.23% for the boars with the 5% highest TNB (p < 0.01). The DFI and the motility of the same semen samples were negatively correlated (p < 0.0001), and the high and low TNB groups showed significant differences in motility. However, this difference could not be used for practical prediction of TNB group (92.1% vs. 89.7%; p = 0.0038 and 92.3% vs. 89.5%; p = 0.018; NL and ND, respectively). In conclusion, our results indicate that sperm DNA integrity in semen with good motility and morphology may be an additional prediction parameter for fertility in pigs.

Genome-wide association study reveals a QTL and strong candidate genes for umbilical hernia in pigs on SSC14.

BACKGROUND: Umbilical hernia is one of the most prevalent congenital defect in pigs, causing economic losses and substantial animal welfare problems. Identification and implementation of genomic regions controlling umbilical hernia in breeding is of great interest to reduce incidences of hernia in commercial pig production. The aim of this study was to identify such regions and possibly identify causative variation affecting umbilical hernia in pigs. A case/control material consisting of 739 Norwegian Landrace pigs was collected and applied in a GWAS study with a genome-wide distributed panel of 60 K SNPs. Additionally candidate genes were sequenced to detect additional polymorphisms that were used for single SNP and haplotype association analyses in 453 of the pigs. RESULTS: The GWAS in this report detected a highly significant region affecting umbilical hernia around 50 Mb on SSC14 (P < 0.0001) explaining up to 8.6% of the phenotypic variance of the trait. The region is rather broad and includes 62 significant SNPs in high linkage disequilibrium with each other. Targeted sequencing of candidate genes within the region revealed polymorphisms within the Leukemia inhibitory factor (LIF) and Oncostatin M (OSM) that were significantly associated with umbilical hernia (P < 0.001). CONCLUSIONS: A highly significant QTL for umbilical hernia in Norwegian Landrace pigs was detected around 50 Mb on SSC14. Resequencing of candidate genes within the region revealed SNPs within LIF and OSM highly associated with the trait. However, because of extended LD within the region, studies in other populations and functional studies are needed to determine whether these variants are causal or not. Still without this knowledge, SNPs within the region can be used as genetic markers to reduce incidences of umbilical hernia in Norwegian Landrace pigs.

Genome-wide association study confirm major QTL for backfat fatty acid composition on SSC14 in Duroc pigs.

BACKGROUND: Fatty acid composition contributes importantly to meat quality and is essential to the nutritional value of the meat. Identification of genetic factors underlying levels of fatty acids can be used to breed for pigs with healthier meat. The aim of this study was to conduct genome-wide association studies (GWAS) to identify QTL regions affecting fatty acid composition in backfat from the pig breeds Duroc and Landrace. RESULTS: Using data from the Axiom porcine 660 K array, we performed GWAS on 454 Duroc and 659 Landrace boars for fatty acid phenotypes measured by near-infrared spectroscopy (NIRS) technology (C16:0, C16:1n-7, C18:0, C18:1n-9, C18:2n-6, C18:3n-3, total saturated fatty acids, monounsaturated fatty acids and polyunsaturated fatty acids). Two QTL regions on SSC4 and SSC14 were identified in Duroc for the de novo synthesized fatty acids traits, whereas one QTL on SSC8 was detected in Landrace for C16:1n-7. The QTL region on SSC14 has been reported in previous studies and a putative causative mutation has been suggested in the promoter region of the SCD gene. Whole genome re-sequencing data was used for genotype imputation and to fine map the SSC14 QTL region in Norwegian Duroc. This effort confirms the location of the QTL on this chromosome as well as suggesting other putative candidate genes in the region. The most significant single nucleotide polymorphisms (SNPs) located on SSC14 explain between 55 and 76% of the genetic variance and between 27 and 54% of the phenotypic variance for the de novo synthesized fatty acid traits in Norwegian Duroc. For the QTL region on SSC8 in Landrace, the most significant SNP explained 19% of the genetic variance and 5% of the phenotypic variance for C16:1n-7. CONCLUSIONS: This study confirms a major QTL affecting fatty acid composition on SSC14 in Duroc, which can be used in genetic selection to increase the level of fatty acid desaturation. The SSC14 QTL was not segregating in the Landrace population, but another QTL on SSC8 affecting C16:1n-7 was identified and might be used to increase the level of desaturation in meat products from this breed.

Fine mapping of a QTL affecting levels of skatole on pig chromosome 7.

BACKGROUND: Previous studies in the Norwegian pig breeds Landrace and Duroc have revealed a QTL for levels of skatole located in the region 74.7-80.5 Mb on SSC7. Skatole is one of the main components causing boar taint, which gives an undesirable smell and taste to the pig meat when heated. Surgical castration of boars is a common practice to reduce the risk of boar taint, however, a selection for boars genetically predisposed for low levels of taint would help eliminating the need for castration and be advantageous for both economic and welfare reasons. In order to identify the causal mutation(s) for the QTL and/or identify genetic markers for selection purposes we performed a fine mapping of the SSC7 skatole QTL region. RESULTS: A dense set of markers on SSC7 was obtained by whole genome re-sequencing of 24 Norwegian Landrace and 23 Duroc boars. Subsets of 126 and 157 SNPs were used for association analyses in Landrace and Duroc, respectively. Significant single markers associated with skatole spanned a large 4.4 Mb region from 75.9-80.3 Mb in Landrace, with the highest test scores found in a region between the genes NOVA1 and TGM1 (p < 0.001). The same QTL was obtained in Duroc and, although less significant, with associated SNPs spanning a 1.2 Mb region from 78.9-80.1 Mb (p < 0.01). The highest test scores in Duroc were found in genes of the granzyme family (GZMB and GZMH-like) and STXBP6. Haplotypes associated with levels of skatole were identified in Landrace but not in Duroc, and a haplotype block was found to explain 2.3% of the phenotypic variation for skatole. The SNPs in this region were not associated with levels of sex steroids. CONCLUSIONS: Fine mapping of a QTL for skatole on SSC7 confirmed associations of this region with skatole levels in pigs. The QTL region was narrowed down to 4.4 Mb in Landrace and haplotypes explaining 2.3% of the phenotypic variance for skatole levels were identified. Results confirmed that sex steroids are not affected by this QTL region, making these markers attractive for selection against boar taint.

RNA sequencing reveals candidate genes and polymorphisms related to sperm DNA integrity in testis tissue from boars.

BACKGROUND: Sperm DNA is protected against fragmentation by a high degree of chromatin packaging. It has been demonstrated that proper chromatin packaging is important for boar fertility outcome. However, little is known about the molecular mechanisms underlying differences in sperm DNA fragmentation. Knowledge of sequence variation influencing this sperm parameter could be beneficial in selecting the best artificial insemination (AI) boars for commercial production. The aim of this study was to identify genes differentially expressed in testis tissue of Norwegian Landrace and Duroc boars, with high and low sperm DNA fragmentation index (DFI), using transcriptome sequencing. RESULTS: Altogether, 308 and 374 genes were found to display significant differences in expression level between high and low DFI in Landrace and Duroc boars, respectively. Of these genes, 71 were differentially expressed in both breeds. Gene ontology analysis revealed that significant terms in common for the two breeds included extracellular matrix, extracellular region and calcium ion binding. Moreover, different metabolic processes were enriched in Landrace and Duroc, whereas immune response terms were common in Landrace only. Variant detection identified putative polymorphisms in some of the differentially expressed genes. Validation showed that predicted high impact variants in RAMP2, GIMAP6 and three uncharacterized genes are particularly interesting for sperm DNA fragmentation in boars. CONCLUSIONS: We identified differentially expressed genes between groups of boars with high and low sperm DFI, and functional annotation of these genes point towards important biochemical pathways. Moreover, variant detection identified putative polymorphisms in the differentially expressed genes. Our results provide valuable insights into the molecular network underlying DFI in pigs.

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.

On the distance of genetic relationships and the accuracy of genomic prediction in pig breeding.

BACKGROUND: With the advent of genomic selection, alternative relationship matrices are used in animal breeding, which vary in their coverage of distant relationships due to old common ancestors. Relationships based on pedigree (A) and linkage analysis (GLA) cover only recent relationships because of the limited depth of the known pedigree. Relationships based on identity-by-state (G) include relationships up to the age of the SNP (single nucleotide polymorphism) mutations. We hypothesised that the latter relationships were too old, since QTL (quantitative trait locus) mutations for traits under selection were probably more recent than the SNPs on a chip, which are typically selected for high minor allele frequency. In addition, A and GLA relationships are too recent to cover genetic differences accurately. Thus, we devised a relationship matrix that considered intermediate-aged relationships and compared all these relationship matrices for their accuracy of genomic prediction in a pig breeding situation. METHODS: Haplotypes were constructed and used to build a haplotype-based relationship matrix (GH), which considers more intermediate-aged relationships, since haplotypes recombine more quickly than SNPs mutate. Dense genotypes (38 453 SNPs) on 3250 elite breeding pigs were combined with phenotypes for growth rate (2668 records), lean meat percentage (2618), weight at three weeks of age (7387) and number of teats (5851) to estimate breeding values for all animals in the pedigree (8187 animals) using the aforementioned relationship matrices. Phenotypes on the youngest 424 to 486 animals were masked and predicted in order to assess the accuracy of the alternative genomic predictions. RESULTS: Correlations between the relationships and regressions of older on younger relationships revealed that the age of the relationships increased in the order A, GLA, GH and G. Use of genomic relationship matrices yielded significantly higher prediction accuracies than A. GH and G, differed not significantly, but were significantly more accurate than GLA. CONCLUSIONS: Our hypothesis that intermediate-aged relationships yield more accurate genomic predictions than G was confirmed for two of four traits, but these results were not statistically significant. Use of estimated genotype probabilities for ungenotyped animals proved to be an efficient method to include the phenotypes of ungenotyped animals.

Consequences of the natural course of articular osteochondrosis in pigs for the suitability of computed tomography as a screening tool.

BACKGROUND: A significant heritability has been documented for articular osteochondrosis. Selection against osteochondrosis has historically been based on macroscopic evaluation, but as computed tomography (CT) now is used to select boars with optimal body composition it can potentially also be used to screen for osteochondrosis. False negative diagnosis will occur if defects have not developed or have resolved prior to screening at a single time point. The aim of the current study was to assess the suitability of the use of CT at a single point in time as a screening tool in piglets for articular osteochondrosis, which is known to be a highly dynamic condition in which lesions develop and resolve over time. METHODS: Male Landrace piglets (n = 18) were serial CT scanned from 2-8 times at biweekly intervals from 70-180 days of age. At each interval, 1-2 piglets were euthanased and the left distal femur processed for histological validation. RESULTS: A total of 795 defects were identified in the 112 available CT scans. Within the hind and fore limbs, the incidence of defects was highest in the stifle (n = 321) and elbow joints (n = 110), respectively. Ninety-eight per cent of the defects in the stifle and elbow joints had developed by the 7th examination interval when the piglets were a mean age of 159 days old. The proportion of defects that resolved was lowest in the stifle joint at 51% and highest in the elbow joint at 69%. CONCLUSIONS: Scanning of the current piglets at an age of 159 days resulted in detection of 98% of the total number of defects that developed up to the maximum age of 180 days. The proportion of defects that resolved ranged from 51-69% for different joints, but may not adversely affect prevalence as this category of false negative diagnosis will result in selection of pigs that are disposed for healing. Optimally timed CT is a powerful screening tool for osteochondrosis.

Genetic analyses of nutrient digestibility measured by fecal near-infrared spectroscopy in pigs.

Improved nutrient digestibility is an important trait in genetic improvement in pigs due to global resource scarcity, increased human population and greenhouse gas emissions from pork production. Further, poor nutrient digestibility represents a direct nutrient loss, which affects the profit of the farmer. The aim of this study was to estimate genetic parameters for apparent total tract digestibility of nitrogen (ATTDn), crude fat (ATTDCfat), dry matter (ATTDdm), and organic matter (ATTDom) and to investigate their genetic relationship to other relevant production traits in pigs. Near-infrared spectroscopy was used for prediction of total nitrogen content and crude fat content in feces. The predicted content was used to estimate apparent total tract digestibility of the different nutrients by using an indicator method, where acid insoluble ash was used as an indigestible marker. Average ATTDdm, ATTDom, ATTDn, and ATTDCfat ranged from 61% to 75.3%. Moderate heritabilities was found for all digestibility traits and ranged from 0.15 to 0.22. The genetic correlations among the digestibility traits were high (>0.8), except for ATTDCfat, which had no significant genetic correlation to the other digestibility traits. Significant genetic correlations were found between ATTDn and feed consumption between 40 and 120 kg live weight (F40120) (-0.54 ± 0.11) and ATTDdm and F40120 (-0.35 ± 0.12) and ATTDom and F40120 (-0.28 ± 0.13). No significant genetic correlations were found between digestibility traits and loin depth at 100 kg, nor backfat thickness at 100 kg (BF), except between BF and ATTDn (-0.31 ± 0.14). These results suggested that selection for improved feed efficiency through reduced feed intake within a weight interval, also has led to improved ATTDdm, ATTDom, and ATTDn. Further, the digestibility traits are heritable, but mainly related to feed intake and general function of the intestines, as opposed to allocation of feed resources to different tissues in the body.

Improved nutrient digestibility is an important trait in genetic improvement of pigs due to global resource scarcity, increased human population and greenhouse gas emissions from pork production. The main aim of this study was to investigate whether nutrient digestibility traits in pigs are heritable, and if they are genetically linked to other production traits. The results showed that digestibility of dry matter, organic matter, nitrogen, and crude fat are heritable, and can be selected for in a pig breeding program. The traits are genetically linked to other relevant production traits, such as feed intake, but not to carcass traits, such as loin depth. The results suggest that nutrient digestibility are traits that can be selected for, and that the traits are under indirect selection through other traits in the pig breeding program. The results also indicate that the nutrient digestibility traits express how well the animal utilizes consumed feed, rather than allocating feed to different tissue deposition.

Cumulus Cell and Oocyte Gene Expression in Prepubertal Gilts and Sows Identifies Cumulus Cells as a Prime Informative Parameter of Oocyte Quality.

Cumulus cells (CCs) are pivotal during oocyte development. This study aimed to identify novel marker genes for porcine oocyte quality by examining the expression of selected genes in CCs and oocytes, employing the model of oocytes from prepubertal animals being of reduced quality compared to those from adult animals. Total RNA was extracted either directly after follicle aspiration or after in vitro maturation, followed by RT-qPCR. Immature gilt CCs accumulated BBOX1 transcripts, involved in L-carnitine biosynthesis, to a 14.8-fold higher level (p < 0.05) relative to sows, while for CPT2, participating in fatty acid oxidation, the level was 0.48 (p < 0.05). While showing no differences between gilt and sow CCs after maturation, CPT2 and BBOX1 levels in oocytes were higher in gilts at both time points. The apparent delayed lipid metabolism and reduced accumulation of ALDOA and G6PD transcripts in gilt CCs after maturation, implying downregulation of glycolysis and the pentose phosphate pathway, suggest gilt cumulus-oocyte complexes have inadequate ATP stores and oxidative stress balance compared to sows at the end of maturation. Reduced expression of BBOX1 and higher expression of CPT2 in CCs before maturation and higher expression of G6PD and ALDOA after maturation are new potential markers of oocyte quality.