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

Bayesian LASSO for population stratification correction in rare haplotype association studies

Population stratification (PS) is one major source of confounding in both single nucleotide polymorphism (SNP) and haplotype association studies. To address PS, principal component regression (PCR) and linear mixed model (LMM) are the current standards for SNP associations, which are also commonly borrowed for haplotype studies. However, the underfitting and overfitting problems introduced by PCR and LMM, respectively, have yet to be addressed. Furthermore, there have been only a few theoretical approaches proposed to address PS specifically for haplotypes. In this paper, we propose a new method under the Bayesian LASSO framework, QBLstrat, to account for PS in identifying rare and common haplotypes associated with a continuous trait of interest. QBLstrat utilizes a large number of principal components (PCs) with appropriate priors to sufficiently correct for PS, while shrinking the estimates of unassociated haplotypes and PCs. We compare the performance of QBLstrat with the Bayesian counterparts of PCR and LMM and a current method, haplo.stats. Extensive simulation studies and real data analyses show that QBLstrat is superior in controlling false positives while maintaining competitive power for identifying true positives under PS.

Searching for new signals for susceptibility to umbilical hernia through genome-wide association analysis in three pig breeds

Umbilical hernia (UH) is a prevalent congenital disorder in pigs, resulting in considerable economic losses and severe animal welfare issues. In the present study, we conducted a genome-wide association study (GWAS) using the GeneSeek 50K Chip in 2777 pigs (Duroc, n = 1267; Landrace, n = 696; and Yorkshire, n = 814) to explore the candidate genes underlying the risk of umbilical hernia in pigs. After quality control analyses, 2748 animals and 48 524 single nucleotide polymorphisms (SNPs) were retained for subsequent GWAS analysis using the FarmCPU model. The heritability of umbilical hernias was estimated to 0.51 ± 0.04, indicating a reasonable basis for investigating genetic markers associated with this disorder. We identified 54 SNPs and 517 candidate genes that showed significant associations with susceptibility to umbilical hernia across the combined population of the three pig breeds. Gene enrichment analyses highlighted several crucial pathways for platelet degranulation, inflammatory mediator regulation of TRP channels and ion transport. These findings provide further insights into the underlying genetic architecture of umbilical hernias in pigs.

Altered Transcript Levels of MMP13 and VIT Genes in the Muscle and Connective Tissue of Pigs with Umbilical Hernia

Umbilical hernia (UH) and inguinal hernia (IH) are among the most common defects in pigs, affecting their welfare and resulting in economic losses. In this study, we aimed to verify the association of previously reported differences in transcript levels of the ACAN, COL6A5, MMP13, and VIT genes with the occurrence of UH and IH. We examined mRNA levels in muscle and connective tissue from 68 animals-34 affected by UH and 34 controls. In a second cohort, we examined inguinal channel samples from 46 pigs (in four groups). We determined DNA methylation levels in muscle tissue for the UH and control animals. The transcript level of MMP13 changed in the UH cases, being upregulated and downregulated in muscle and connective tissue, respectively, and the VIT gene also showed an increased muscular mRNA level. The transcript of the ACAN gene significantly decreased in old pigs with IH. We further observed an increased DNA methylation level for one CpG site within the MMP13 gene in UH individuals. We conclude that these alterations in gene mRNA levels in the UH animals depend on the tissue and can sometimes be a consequence of, not a cause of, the affected phenotype.

Genome-wide population structure, homozygosity, and heterozygosity patterns of Nero Siciliano pig in the framework of Italian and cosmopolitan breeds

Analysis of genomic data is becoming more and more common for the effective management of livestock breeding programmes, even in the case of local populations. In this work, the genome-wide data of Nero Siciliano pig breed were compared to that of wild boar, Italian local and cosmopolitan breeds to investigate its genetic structure, and runs of homozygosity (ROH) and heterozygosity patterns. The Nero Siciliano has been reported to have the highest rate of genetic diversity among the Italian breeds, and a genetic variability comparable to that of the cosmopolitan breeds. Analyses of genomic structure and relationships underlined its proximity to wild boar, and an internal substructure probably linked to different family lines. The breed showed a low value of inbreeding estimated from ROH, and the highest diversity index among the Italian breeds, even if lower than that of the cosmopolitans. Four ROH islands in three chromosomes (SSC8, SSC11, and SSC14) and one heterozygosity-rich region (SSC1) were identified in Nero Siciliano, highlighting genomic regions related to productive QTL. Across breeds, SSC8 and SSC14 were the chromosomes with most ROH islands, with Mora Romagnola and wild boar showing the highest level of autozygosity. Chromosomes SSC2, SSC6, SSC8 and SSC13 showed the majority of runs of heterozygosity regions, mainly found in the cosmopolitan pig breeds, which reported several genes associated with health-related QTL. The outlined results can help to better identify the genomic profile of this local breed in order to plan matings, maintain adequate internal diversity and exploit the production system.

Hernioplasty with Peritoneal Flap for the Surgical Treatment of Umbilical Hernia in Swine

BACKGROUND

Umbilical hernia is one of the most common developmental defects in swine, producing large economic losses for farmers, forced to slaughter animals at a younger age and therefore at a lower weight to prevent fatal complications. This study describes a surgical technique to repair umbilical hernia through the use of autologous prostheses, allowing recovery of the affected animals; Methods: After a general examination of the swine and examination of the lesions, the swine were anesthetized and underwent surgery. The surgery was performed by combining the traditional herniorrhaphy with the inclusion and fixation of a peritoneal flap obtained from the incision of the same hernial sac; Results: Follow-ups were carried out at 7, 30 and 60 days and demonstrated healing in all of the treated subjects; Conclusions: The use of this surgical technique allows for providing resistance to herniorrhaphy performed through the use of a cost-free autologous biomaterial prosthesis, with excellent tissue compatibility. This might allow for reducing significantly the rate of relapses and eliminating the risk of rejection.

Genetic aspects of piglet survival and related traits: a review

In livestock, mortality in general, and mortality of the young, is societal worries and is economically relevant for farm efficiency. Genetic change is cumulative; if it exists for survival of the young and genetic merit can be estimated with sufficient accuracy, it can help alleviate the pressure of mortality. Lack of survival is a moving target; livestock production is in continuous change and labor shortage is a given. There is now ample evidence of clear genetic variance and of models able to provide genomic predictions with enough accuracy for selection response. Underlying traits such as birth weight, uniformity in birth weight, gestation length, number of teats, and farrowing duration all show genetic variation and support selection for survival or, alternatively, be selected for on their own merit.

Direct and indirect contributions of molecular genetics to farm animal welfare: a review

Since domestication, farm animals have played a key role to increase the prosperity of humankind, while animal welfare (AW) is debated even today. This paper aims to comprehensively review the contributions of developing molecular genetics to farm animal welfare (FAW) and to raise awareness among both scientists and farmers about AW. Welfare is a complex trait affected by genetic structure and environmental factors. Therefore, the best welfare status can be achieved not only to enhance environmental factors such as management and feeding practices, but also the genetic structure of animals must be improved. In this regard, advances in molecular genetics have made great contributions to improve the genetic structure of farm animals, which has increased AW. Today, by sequencing and/or molecular markers, genetic diseases may be detected and eliminated in local herds. Additionally, genes related to diseases or adaptations are investigated by molecular techniques, and the frequencies of desired genotypes are increased in farm animals to keep welfare at an optimized level. Furthermore, stress on animals can be reduced with DNA extraction from stool and feather samples which reduces physical contact between animals and veterinarians. Together with molecular genetics, advances in genome editing tools and biotechnology are promising to improve FAW in the future.

A joint analysis using exome and transcriptome data identifiescandidate polymorphisms and genes involved with umbilical hernia in pigs

BACKGROUND

Umbilical Hernia (UH) is characterized by the passage of part of the intestine through the umbilical canal forming the herniary sac. There are several potential causes that can lead to the umbilical hernia such as bacterial infections, management conditions and genetic factors. Since the genetic components involved with UH are poorly understood, this study aimed to identify polymorphisms and genes associated with the manifestation of umbilical hernia in pigs using exome and transcriptome sequencing in a case and control design.

RESULTS

In the exome sequencing, 119 variants located in 58 genes were identified differing between normal and UH-affected pigs, and in the umbilical ring transcriptome, 46 variants were identified, located in 27 genes. Comparing the two methodologies, we obtained 34 concordant variants between the exome and transcriptome analyses, which were located in 17 genes, distributed in 64 biological processes (BP). Among the BP involved with UH it is possible to highlight cell adhesion, cell junction regulation, embryonic morphogenesis, ion transport, muscle contraction, within others.

CONCLUSIONS

We have generated the first exome sequencing related to normal and umbilical hernia-affected pigs, which allowed us to identify several variants possibly involved with this disorder. Many of those variants present in the DNA were confirmed with the RNA-Seq results. The combination of both exome and transcriptome sequencing approaches allowed us to better understand the complex molecular mechanisms underlying UH in pigs and possibly in other mammals, including humans. Some variants found in genes and other regulatory regions are highlighted as strong candidates to the development of UH in pigs and should be further investigated.

Survival of pigs with different characteristics of umbilical outpouching in a prospective cohort study of Danish pigs

Umbilical hernia and other conditions clinically evident as umbilical outpouchings (UOs) affect the welfare and economy in Danish pig production. The objectives of the current study were to characterize the associations between 1) time of detection of the UOs and the odds of dying before scheduled slaughter; 2) time of death, irrespective of the cause, and clinical signs of the UOs, i.e. general condition, size, reducibility, form and skin-color of the UOs; and 3) occurrence of wounds on the UOs and clinical signs: general condition, size, reducibility, form and skin-color. A cohort of Danish conventional pigs with UOs (n = 255) were followed from the detection of an UO until spontaneous death, euthanization or slaughter of the pig. The pigs were clinically examined once a month, and when pigs with an UO died spontaneously, were euthanized or slaughtered, the causes and date of death were recorded. The effects of the clinical manifestations on overall survival were assessed using a Cox proportional hazards model. In total 57 % of the pigs died spontaneously or were euthanized before slaughter. The median age of spontaneous death or euthanasia was 85 days. The UOs were detected at different ages, with half of the pigs (52 %) detected in the farrowing section. No significant association was found between death before scheduled slaughter and the time of detection. Three different clinical manifestations were found to have a prognostic value for overall survival until slaughter, i.e. skin-color of the UO, a general condition of the pig and the size of the UO. An interaction was present between the size and the skin-color of the UO. Wounds on the UO were the most frequent complication resulting in euthanasia (37 %). The odds for developing a wound on the UO were higher for pigs in a general bad condition compared to pigs in a good condition (OR, 5.4; 95 % CL 2.5-11.3), and for pigs with an UO large in size compared to pigs with a small UO (OR, 4.8; 95 % CL 3.0-7.5). The identification of prognostic clinical signs in pigs with an UO is useful in the assessment and decision-making in relation to the future prospects of pigs with UOs.

Genes and SNPs Involved with Scrotal and Umbilical Hernia in Pigs

Hernia is one of the most common defects in pigs. The most prevalent are the scrotal (SH), inguinal (IH) and umbilical (UH) hernias. We compared the inguinal ring transcriptome of normal and SH-affected pigs with the umbilical ring transcriptome of normal and UH-affected pigs to discover genes and pathways involved with the development of both types of hernia. A total of 13,307 transcripts was expressed in the inguinal and 13,302 in the umbilical ring tissues with 94.91% of them present in both tissues. From those, 35 genes were differentially expressed in both groups, participating in 108 biological processes. A total of 67 polymorphisms was identified in the inguinal ring and 76 in the umbilical ring tissue, of which 11 and 14 were novel, respectively. A single nucleotide polymorphism (SNP) with deleterious function was identified in the integrin α M (ITGAM) gene. The microtubule associated protein 1 light chain 3 γ (MAP1LC3C), vitrin (VIT), aggrecan (ACAN), alkaline ceramidase 2 (ACER2), potassium calcium-activated channel subfamily M α 1 (KCNMA1) and synaptopodin 2 (SYNPO2) genes are highlighted as candidates to trigger both types of hernia. We generated the first comparative study of the pig umbilical and inguinal ring transcriptomes, contributing to the understanding of the genetic mechanism involved with these two types of hernia in pigs and probably in other mammals.

Laparoscopy for the Treatment of Congenital Hernia: Use of Surgical Meshes and Mesenchymal Stem Cells in a Clinically Relevant Animal Model

More than a century has passed since the first surgical mesh for hernia repair was developed, and, to date, this is still the most widely used method despite the great number of complications it poses. The purpose of this study was to combine stem cell therapy and laparoscopy for the treatment of congenital hernia in a swine animal model. Porcine bone marrow-derived mesenchymal stem cells (MSCs) were seeded on polypropylene surgical meshes using a fibrin sealant solution as a vehicle. Meshes with (cell group) or without (control group) MSCs were implanted through laparoscopy in Large White pigs with congenital abdominal hernia after the approximation of hernia borders (implantation day). A successive laparoscopic biopsy of the mesh and its surrounding tissues was performed a week after implantation, and surgical meshes were excised a month after implantation. Ultrasonography was used to measure hernia sizes. Flow cytometry, histological, and gene expression analyses of the biopsy and necropsy samples were performed. The fibrin sealant solution was easy to prepare and preserved the viability of MSCs in the surgical meshes. Ultrasonography demonstrated a significant reduction in hernia size 1 week after implantation in the cell group relative to that on the day of implantation (p < 0.05). Flow cytometry of the mesh-infiltrated cells showed a non-significant increase of M2 macrophages when the cell group was compared with the control group 1 week after implantation. A significant decrease in the gene expression of VEGF and a significant increase in TNF expression were determined in the cell group 1 month after implantation compared with gene expressions in the control group (p < 0.05). Here, we propose an easy and feasible method to combine stem cell therapy and minimally invasive surgical techniques for hernia repair. In this study, stem cell therapy did not show a great immunomodulatory or regenerative effect in overcoming hernia-related complications. However, our clinically relevant animal model with congenital hernia closely resembles the clinical human condition. Further studies should be focused on this valuable animal model to evaluate stem cell therapies in hernia surgery.

Transcriptome analysis identifies genes involved with the development of umbilical hernias in pigs

Umbilical hernia (UH) is one of the most frequent defects affecting pig production, however, it also affects humans and other mammals. UH is characterized as an abnormal protrusion of the abdominal contents to the umbilical region, causing pain, discomfort and reduced performance in pigs. Some genomic regions associated to UH have already been identified, however, no study involving RNA sequencing was performed when umbilical tissue is considered. Therefore, here, we have sequenced the umbilical ring transcriptome of five normal and five UH-affected pigs to uncover genes and pathways involved with UH development. A total of 13,216 transcripts were expressed in the umbilical ring tissue. From those, 230 genes were differentially expressed (DE) between normal and UH-affected pigs (FDR <0.05), being 145 downregulated and 85 upregulated in the affected compared to the normal pigs. A total of 68 significant biological processes were identified and the most relevant were extracellular matrix, immune system, anatomical development, cell adhesion, membrane components, receptor activation, calcium binding and immune synapse. The results pointed out ACAN, MMPs, COLs, EPYC, VIT, CCBE1 and LGALS3 as strong candidates to trigger umbilical hernias in pigs since they act in the extracellular matrix remodeling and in the production, integrity and resistance of the collagen. We have generated the first transcriptome of the pig umbilical ring tissue, which allowed the identification of genes that had not yet been related to umbilical hernias in pigs. Nevertheless, further studies are needed to identify the causal mutations, SNPs and CNVs in these genes to improve our understanding of the mechanisms of gene regulation.

Animal-based measures on fattening heavy pigs at the slaughterhouse and the association with animal welfare at the farm level: a preliminary study

Monitoring animal welfare (AW) in pig farms requires both proper indicators and a feasible approach. Animal-based measures (ABMs) are well-established AW indicators. Furthermore, AW screening at the slaughterhouses could be useful for identifying problems on farm. The aim of this study was to evaluate ABMs at the slaughterhouse and, when possible, to compare these ABMs with those collected on the farm. The study was carried out in northern Italy in a commercial abattoir and in a sample of farms. Animal-based measures were recorded on pigs from 62 batches of 54 farms, during ante-mortem (n=10 085 pigs) and post-mortem (n=7952 pigs) inspections. Sixteen of 54 farms were selected to compare ABMs collected at the slaughterhouse with ABMs collected on the farm. Overall, 2295 pigs (mean pigs examined per farm 119±45) were inspected at the slaughterhouse (group S) and 420 pigs (mean pigs per farm 26±5) on the farm (group F). Non-animal-based measures were also collected at the 16 farms. Differences between groups S and F, at the animal level, were assessed by a two-tailed paired Wilcoxon-Mann-Whitney test. Differences at the site of observation level (farm and slaughterhouse) were assessed by Fisher's exact test using a hierarchical log-linear modelling for contingency tables. The most frequent ABMs at the slaughterhouse were manure on the body (47.7%), followed by dermatitis (28.0%), white spot (25.4%) and bursitis (24.7%). Recording ABMs at the slaughterhouse and on the farm usually yielded similar results; however, there were some exceptions. In particular, significant differences were found for non-uniformity of size (P<0.05) and dermatitis (P<0.001), which were higher at the slaughterhouse than on the farm. Results of log-linear modelling underlined the effect of the farm of origin on the percentage of pigs with bursitis, manure on the body and ear injuries that were observed at the slaughterhouse. In group S, significant associations between manure on the body and insufficient presence of clean and dry areas in the corresponding farm were found (P<0.05). Although these results should be interpreted with care due to the limited sample of farms, the slaughterhouse could be a feasible site of observation of ABMs, which could then be integrated in monitoring of AW on farm. Considering the number of slaughtered batches per farm, it would be possible to repeat assessments several times throughout the year for each farm, which could help provide an index for the continuous monitoring of AW.

Genome-wide association study identifies variants in the CAPN9 gene associated with umbilical hernia in pigs

Pig umbilical hernia (UH) affects pig welfare and brings considerable economic loss to the pig industry. To date, the molecular mechanisms underlying pig UH are still poorly understood. To identify potential loci for susceptibility to this disease, we performed a genome-wide association study in an Erhualian × Shaziling F₂ intercross population. A total of 45 animals were genotyped using Illumina Porcine SNP60 BeadChips. We observed a SNP (rs80993347) located in the calpain-9 (CAPN9) gene on Sus scrofa chromosome 14 that was significantly associated with UH (P = 1.97 × 10^-10 ). Then, we identified a synonymous mutation rs321865883 (g.20164T>C) in exon 10 of the CAPN9 gene that distinguished two affected individuals (CC) from their normal full-sibs (TC). Finally, quantitative polymerase chain reaction was explored to investigate the mRNA expression profile of the CAPN9 gene in 12 tissues in Yorkshire pigs at different developmental stages (3, 90 and 180 days). CAPN9 showed high expression levels in the gastrointestinal tract at these three growth stages. The results of this study indicate that the CAPN9 gene might be implicated in UH. Further studies are required to establish a role of CAPN9 in pig UH.