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.

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.

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.

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.

Preimplantation Genetic Testing for Aneuploidy (PGT-A) Reveals High Levels of Chromosomal Errors in In Vivo-Derived Pig Embryos, with an Increased Incidence When Produced In Vitro.

Preimplantation genetic testing for aneuploidy (PGT-A) is widespread, but controversial, in humans and improves pregnancy and live birth rates in cattle. In pigs, it presents a possible solution to improve in vitro embryo production (IVP), however, the incidence and origin of chromosomal errors remains under-explored. To address this, we used single nucleotide polymorphism (SNP)-based PGT-A algorithms in 101 in vivo-derived (IVD) and 64 IVP porcine embryos. More errors were observed in IVP vs. IVD blastocysts (79.7% vs. 13.6% p < 0.001). In IVD embryos, fewer errors were found at blastocyst stage compared to cleavage (4-cell) stage (13.6% vs. 40%, p = 0.056). One androgenetic and two parthenogenetic embryos were also identified. Triploidy was the most common error in IVD embryos (15.8%), but only observed at cleavage, not blastocyst stage, followed by whole chromosome aneuploidy (9.9%). In IVP blastocysts, 32.8% were parthenogenetic, 25.0% (hypo-)triploid, 12.5% aneuploid, and 9.4% haploid. Parthenogenetic blastocysts arose from just three out of ten sows, suggesting a possible donor effect. The high incidence of chromosomal abnormalities in general, but in IVP embryos in particular, suggests an explanation for the low success of porcine IVP. The approaches described provide a means of monitoring technical improvements and suggest future application of PGT-A might improve embryo transfer success.

Protein profiling of testicular tissue from boars with different levels of hyperactive sperm motility.

Hyperactive sperm motility is important for successful fertilization. In the present study, a proteome profiling approach was performed to identify the differences between Landrace boars with different levels of hyperactive sperm motility in liquid extended semen. Two contrasts were studied: (i) high versus low levels of sperm hyperactivity at semen collection day and (ii) high versus low change in levels of sperm hyperactivity after 96 h semen storage. Testicular samples were analyzed on a Q Exactive mass spectrometer and more than 6000 proteins were identified in the 13 samples. The most significant differentially expressed proteins were mediator complex subunit 28 (MED28), cell division cycle 37 like 1 (CDC37L1), ubiquitin specific peptidase 10 (USP10), zinc finger FYVE-type containing 26 (ZFYVE26), protein kinase C delta (PRKCD), actinin alpha 4 (ACTN4), N(alpha)-acetyltransferase 30 (NAA30), C1q domain-containing (LOC110258309) and uncharacterized LOC100512926. Of the differentially expressed proteins, 11 have previously been identified as differentially expressed at the corresponding mRNA transcript level using the same samples and contrasts. These include sphingosine kinase 1 isoform 2 (SPHK1), serine and arginine rich splicing factor 1 (SRSF1), and tubulin gamma-1 (TUBG1) which are involved in the acrosome reaction and sperm motility. A mass spectrometry approach was applied to investigate the protein profiles of boars with different levels of hyperactive sperm motility. This study identified several proteins previously shown to be involved in sperm motility and quality, but also proteins with no known function for sperm motility. Candidates that are differentially expressed on both mRNA and protein levels are especially relevant as biological markers of semen quality.

Follicular fluid steroid hormones and in vitro embryo development in Duroc and Landrace pigs.

The Duroc sire line has a smaller litter size compared to the Landrace dam line and we have previously observed fewer surface follicles on Duroc ovaries one day after weaning. In that same study, a broader cumulus expansion and faster nuclear maturation were observed for Duroc oocytes at 20 h of in vitro maturation (IVM), while Landrace oocytes showed more advanced stages of cortical granule distributions. However, no differences between breeds were observed after the final IVM period. The aim of this study was to assess subsequent in vitro embryo production (IVP) in Duroc and Landrace. Furthermore, follicle diameter and steroid hormone levels in follicular fluid (FF) were measured to study possible relation to oocyte developmental competence. Follicular phase sow ovaries were collected one day after weaning and follicle size of the 10 largest follicles were measured per ovary before aspiration. Cumulus-oocyte complexes (COCs) were matured in vitro, and cumulus expansion was analysed by assessing individual COC areas at 0 and 20 h. Fertilization of Duroc and Landrace oocytes was performed with sperm from both a Duroc and a Landrace boar. A larger follicle diameter was observed for Landrace animals (5.7 vs. 4.8 mm, P < 0.0001) and individual COC area was additionally larger at 0 h after aspiration (P < 0.0001) compared to Duroc. Contrary, cumulus expansion from 0 to 20 h of maturation was broader for Duroc oocytes than for Landrace (407 ± 67% vs. 319 ± 31%, P < 0.0001). After fertilization, cleavage rate was higher for Duroc oocytes, and the highest blastocyst yield was obtained for Duroc oocytes fertilized with the Landrace sperm. Steroid hormone analysis of the follicular fluid showed differences in the pathways between breeds with a higher total level of estrogens (P = 0.01) and aromatase products/substrates ratio (P < 0.01) in Landrace compared to Duroc. In conclusion, results suggest that Duroc oocytes have a better in vitro oocyte developmental competence when cultured under the same in vitro conditions and breed differences in steroidogenesis were found in the early follicular phase.

Fine Mapping of a Major Backfat QTL Reveals a Causal Regulatory Variant Affecting the CCND2 Gene.

Backfat is an important trait in pork production, and it has been included in the breeding objectives of genetic companies for decades. Although adipose tissue is a good energy storage, excessive fat results in reduced efficiency and economical losses. A large QTL for backfat thickness on chromosome 5 is still segregating in different commercial pig breeds. We fine mapped this QTL region using a genome-wide association analysis (GWAS) with 133,358 genotyped animals from five commercial populations (Landrace, Pietrain, Large White, Synthetic, and Duroc) imputed to the porcine 660K SNP chip. The lead SNP was located at 5:66103958 (G/A) within the third intron of the CCND2 gene, with the G allele associated with more backfat, while the A allele is associated with less backfat. We further phased the QTL region to discover a core haplotype of five SNPs associated with low backfat across three breeds. Linkage disequilibrium analysis using whole-genome sequence data revealed three candidate causal variants within intronic regions and downstream of the CCND2 gene, including the lead SNP. We evaluated the association of the lead SNP with the expression of the genes in the QTL region (including CCND2) in a large cohort of 100 crossbred samples, sequenced in four different tissues (lung, spleen, liver, muscle). Results show that the A allele increases the expression of CCND2 in an additive way in three out of four tissues. Our findings indicate that the causal variant for this QTL region is a regulatory variant within the third intron of the CCND2 gene affecting the expression of CCND2.

A high-throughput study of visceral organs in CT-scanned pigs.

It has been debated whether intensive selection for growth and carcass yield in pig breeding programmes can affect the size of internal organs, and thereby reduce the animal's ability to handle stress and increase the risk of sudden deaths. To explore the respiratory and circulatory system in pigs, a deep learning based computational pipeline was built to extract the size of lungs and hearts from CT-scan images. This pipeline was applied on CT images from 11,000 boar selection candidates acquired during the last decade. Further, heart and lung volumes were analysed genetically and correlated with production traits. Both heart and lung volumes were heritable, with h2 estimated to 0.35 and 0.34, respectively, in Landrace, and 0.28 and 0.4 in Duroc. Both volumes were positively correlated with lean meat percentage, and lung volume was negatively genetically correlated with growth (rg = - 0.48 ± 0.07 for Landrace and rg = - 0.44 ± 0.07 for Duroc). The main findings suggest that the current pig breeding programs could, as an indirect response to selection, affect the size of hearts- and lungs. The presented methods can be used to monitor the development of internal organs in the future.

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.

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.

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.

Ovarian characteristics and in vitro nuclear and cytoplasmic oocyte maturation in Duroc and Landrace pigs.

Differences in total number of piglets born per litter are observed between the Norwegian Duroc (ND) sire and Norwegian Landrace (NL) dam line. The aim of this study was to evaluate ovarian characteristics, and in vitro nuclear and cytoplasmic oocyte maturation in both breeds. One day after weaning, follicular phase ovaries were collected. Ovary length and weight were measured and the number of follicles (< 3 mm and 3-8 mm) was counted. Cumulus-oocyte complexes (COCs) were collected and matured for 48 hr. To assess cumulus expansion, COC area was analysed at 0 and 20 hr. Nuclear maturation and cortical granule (CG) distribution were analysed at 20 and 48 hr, and total glutathione (GSH) was measured at 48 hr to further elucidate cytoplasmic maturation. In first parity sows, a smaller ovary length and fewer 3 to 8 mm follicles were observed in ND compared to NL. For all sows, ND COCs covered a significantly smaller area at 0 hr, but a higher cumulus expansion ratio was observed at 20 hr compared to NL (364 ± 46% versus. 278 ± 27%, p < 0.001). At 20 hr, more ND oocytes exhibited advanced stages of nuclear maturation, while more NL oocytes showed advanced stages of CG distribution. Nuclear maturation to MII stage at 48 hr did not differ between ND and NL oocytes (90.1% and 87.7%, respectively). Moreover, no significant differences were observed for GSH content or CG distribution after maturation. In conclusion, differences with regard to ovarian characteristics as well as to cumulus expansion, and nuclear and cytoplasmic oocyte maturation at 20 hr were observed between the breeds. Further studies are required to determine if this subsequently affects in vitro fertilization and embryo development.

Predicting survival and longevity of sows using purebred and crossbred data.

Survival and longevity are very important traits in pig breeding. From an economic standpoint, it is favorable to keep the sows for another parity instead of replacing them and, from the animal's perspective, better welfare is achieved if they do not experience health problems. It is challenging to record longevity in purebred (PB) nucleus herds because animals are more likely to be replaced based on breeding value and high replacement rates rather than inability to produce. Crossbred (CB) sows are, however, submitted to lower replacement rates and are more likely to be kept in the farm longer if they can produce large and robust litters. Therefore, the objective of this study was to investigate whether the use of CB phenotypes could improve prediction accuracy of longevity for PBs. In addition, a new definition of survival was investigated. The analyzed data included phenotypes from two PB dam lines and their F1 cross. Three traits were evaluated: 1) whether or not the sow got inseminated for a second litter within 85 d of first farrowing (Longevity 1-2), 2) how many litters the sow can produce within 570 d of first farrowing [Longevity 1-5 (LGY15)], and 3) a repeatability trait that indicates whether or not the sow survived until the next parity (Survival). Traits were evaluated both as the same across breeds and as different between breeds. Results indicated that longevity is not the same trait in PB and CB animals (low genetic correlation). In addition, there were differences between the two PB lines in terms of which trait definition gave the greatest prediction accuracy. The repeatability trait (Survival) gave the greatest prediction accuracy for breed B, but LGY15 gave the greatest prediction accuracy for breed A. Prediction accuracy for CBs was generally poor. The Survival trait is recorded earlier in life than LGY15 and seemed to give a greater prediction accuracy for young animals than LGY15 (until own phenotype was available). Thus, for selection of young animals for breeding, Survival would be the preferred trait definition. In addition, results indicated that lots of data were needed to get accurate estimates of breeding values and that, if CB performance is the breeding goal, CB phenotypes should be used in the genetic evaluation.

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.

Association between single-nucleotide polymorphisms within candidate genes and fertility in Landrace and Duroc pigs.

Finding effective predictors of traits related to boar fertility is essential for increasing the efficiency of artificial insemination systems in pig breeding. The objective of this study was to find associations between single-nucleotide polymorphisms (SNPs) within candidate genes and fertility in the breeds Landrace and Duroc. Animals with breeding values for total number of piglets born, were re-sequenced for exonic regions of 14 candidate genes related to male and female fertility using samples from 16 Landrace boars and 16 Duroc boars (four with high and four with low breeding value of total number of piglets born for each breed for male fertility, and the same for female fertility) to detect genetic variants. Genotyping for the detected SNPs was done in 619 Landrace boars and 513 Duroc boars. Two SNPs in BMPR1 and one SNP in COX-2 were found significantly associated with the total number of piglets born in Landrace. In Duroc, two SNPs in PLCz, one SNP in VWF and one SNP in ZP3 were found significantly associated with total number of piglets born. These SNPs explained between 0.27% and 1.18% of the genetic variance. These effects are too low for being used directly for selection purposes but can be of interest in SNP-panels used for genomic selection.

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.

A QTL for Number of Teats Shows Breed Specific Effects on Number of Vertebrae in Pigs: Bridging the Gap Between Molecular and Quantitative Genetics.

Modern breeding schemes for livestock species accumulate a large amount of genotype and phenotype data which can be used for genome-wide association studies (GWAS). Many chromosomal regions harboring effects on quantitative traits have been reported from these studies, but the underlying causative mutations remain mostly undetected. In this study, we combine large genotype and phenotype data available from a commercial pig breeding scheme for three different breeds (Duroc, Landrace, and Large White) to pinpoint functional variation for a region on porcine chromosome 7 affecting number of teats (NTE). Our results show that refining trait definition by counting number of vertebrae (NVE) and ribs (RIB) helps to reduce noise from other genetic variation and increases heritability from 0.28 up to 0.62 NVE and 0.78 RIB in Duroc. However, in Landrace, the effect of the same QTL on NTE mainly affects NVE and not RIB, which is reflected in reduced heritability for RIB (0.24) compared to NVE (0.59). Further, differences in allele frequencies and accuracy of rib counting influence genetic parameters. Correction for the top SNP does not detect any other QTL effect on NTE, NVE, or RIB in Landrace or Duroc. At the molecular level, haplotypes derived from 660K SNP data detects a core haplotype of seven SNPs in Duroc. Sequence analysis of 16 Duroc animals shows that two functional mutations of the Vertnin (VRTN) gene known to increase number of thoracic vertebrae (ribs) reside on this haplotype. In Landrace, the linkage disequilibrium (LD) extends over a region of more than 3 Mb also containing both VRTN mutations. Here, other modifying loci are expected to cause the breed-specific effect. Additional variants found on the wildtype haplotype surrounding the VRTN region in all sequenced Landrace animals point toward breed specific differences which are expected to be present also across the whole genome. This Landrace specific haplotype contains two missense mutations in the ABCD4 gene, one of which is expected to have a negative effect on the protein function. Together, the integration of largescale genotype, phenotype and sequence data shows exemplarily how population parameters are influenced by underlying variation at the molecular level.

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.