Genome-wide linkage analysis of inguinal hernia in pigs using affected sib pairs

The downregulation of genes encoding muscle proteins have a potential role in the development of scrotal hernia in pigs

BACKGROUND

Testicular descent is a physiological process regulated by many factors. Eventually, disturbances in the embryological/fetal development path facilitate the occurrence of scrotal hernia, a congenital malformation characterized by the presence of intestinal portions within the scrotal sac due to the abnormal expansion of the inguinal ring. In pigs, some genes have been related to this anomaly, but the genetic mechanisms involved remain unclear. This study aimed to investigate the expression profile of a set of genes potentially involved with the manifestation of scrotal hernia in the inguinal ring tissue.

METHODS AND RESULTS

Tissue samples from the inguinal ring/canal of normal and scrotal hernia-affected male pigs with approximately 30 days of age were used. Relative expression analysis was performed using qPCR to confirm the expression profile of 17 candidate genes previously identified in an RNA-Seq study. Among them, the Myosin heavy chain 1 (MYH1), Desmin (DES), and Troponin 1 (TNNI1) genes were differentially expressed between groups and had reduced levels of expression in the affected animals. These genes encode proteins involved in the formation of muscle tissue, which seems to be important for increasing the resistance of the inguinal ring to the abdominal pressure, which is essential to avoid the occurrence of scrotal hernia.

CONCLUSIONS

The downregulation of muscular candidate genes in the inguinal tissue clarifies the genetic mechanisms involved with this anomaly in its primary site, providing useful information for developing strategies to control this malformation in pigs and other mammals.

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.

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.

Postweaning mortality in commercial swine production. I: review of non-infectious contributing factors

Postweaning mortality is a complex causal matrix involving animal, environment, and infectious etiologic factors. Despite advances in swine productivity such as total pigs born, growth rate, feed intake, and efficiency, there have been modest to no improvements in postweaning mortality rates over the last several years. Industry averages for postweaning mortality range from four to eight percent for each the nursery, grow-finish, or wean-finish stages. Retrospective mortality causal analyses of individual databases have been performed. However, little information derived from meta-analysis, systematic review, or comprehensive literature reviews are available. In order to develop and evaluate strategies to comprehensively manage and reduce postweaning mortality, addressing the complexity and range of impact that factors have on mortality is necessary to identify and prioritize such contributing factors. Our objective is to describe the current state of knowledge regarding non-infectious causes of postweaning mortality, focusing on estimates of frequency and magnitude of effect where available. Postweaning mortality can be generalized into non-infectious and infectious causes, with non-infectious factors further classified into anatomic abnormalities, toxicity, animal factors, facility factors, nutritional inadequacies, season, and management factors. Important non-infectious factors that have been identified through review of literature include birth weight, pre-weaning management, weaning age and weight, and season. Additionally, reasons for mortality with a low incidence but a high magnitude include abdominal organ torsion/volvulus, sodium ion or ionophore toxicosis, or dietary imbalance due to feed formulation or manufacture error. Many interactive effects are present between and among infectious and non-infectious factors, but an important trend is the impact that non-infectious factors have on the incidence, severity, and resolution of infectious disease. Strategies to reduce postweaning mortality must consider the dynamic, complex state that forms the causal web. Control of postweaning mortality through understanding of the complexity, evaluation of mortality reduction strategies through rigorous scientific evaluation, and implementation remains an area of opportunity for continued growth and development in the global swine industry.

Inguinal Ring RNA Sequencing Reveals Downregulation of Muscular Genes Related to Scrotal Hernia in Pigs

Scrotal hernias (SH) are common congenital defects in commercial pigs, characterized by the presence of abdominal contents in the scrotal sac, leading to considerable production and animal welfare losses. Since the etiology of SH remains obscure, we aimed to identify the biological and genetic mechanisms involved in its occurrence through the whole transcriptome analysis of SH affected and unaffected pigs’ inguinal rings. From the 22,452 genes annotated in the pig reference genome, 13,498 were expressed in the inguinal canal tissue. Of those, 703 genes were differentially expressed (DE, FDR < 0.05) between the two groups analyzed being, respectively, 209 genes upregulated and 494 downregulated in the SH-affected group. Thirty-seven significantly overrepresented GO terms related to SH were enriched, and the most relevant biological processes were muscular system, cell differentiation, sarcome reorganization, and myofibril assembly. The calcium signaling, hypertrophic cardiomyopathy, dilated cardiomyopathy, and cardiac muscle contraction were the major pathways possibly involved in the occurrence of the scrotal hernias. The expression profile of the DE genes was associated with the reduction of smooth muscle differentiation, followed by low calcium content in the cell, which could lead to a decreased apoptosis ratio and diminished muscle contraction of the inguinal canal region. We have demonstrated that genes involved with musculature are closely linked to the physiological imbalance predisposing to scrotal hernia. According to our study, the genes MYBPC1, BOK, SLC25A4, SLC8A3, DES, TPM2, MAP1CL3C, and FGF1 were considered strong candidates for future evaluation.

Rediscover and Refine QTLs for Pig Scrotal Hernia by Increasing a Specially Designed F3 Population and Using Whole-Genome Sequence Imputation Technology

Pig scrotal hernia is one of the most common congenital defects triggered by both genetic and environmental factors, leading to severe economic loss as well as poor animal welfare in the pig industry. Identification and implementation of genomic regions controlling scrotal hernia in breeding is of great appeal to reduce incidences of hernia in pig production. The aim of this study was to identify such regions or molecular markers affecting scrotal hernia in pigs. First of all, we summarized and analyzed the results of some international teams on scrotal hernia and designed a specially population which contains 246 male individuals. We then performed genome-wide association study (GWAS) in this specially designed population using two scenarios, i.e., the target panel data before and after imputation, which contain 42,365 SNPs and 18,756,672 SNPs, respectively. In addition, a series of methods including genetic differentiation analysis, linkage disequilibrium and linkage analysis (LDLA), and haplotype sharing analysis were appropriate to provide for further analysis to identify the potential gene underlying the QTL. The GWAS in this report detected a highly significant region affecting scrotal hernia within a 24.8Mb region (114.1-138.9Mb) on SSC8. And the result of genetic differentiation analysis also showed a strong genetic differentiation signal between 116.1 and 132.7Mb on SSC8. In addition, the QTL interval was refined to 2.99Mb by combining LDLA and genetic differentiation analysis. Finally, two susceptibility haplotypes were identified through haplotype sharing analysis, with one potential causal gene in it. Our study provided deeper insights into the genetic architecture of pig scrotal hernia and contributed to further fine-mapping and characterize haplotype and gene that influence scrotal hernia in pigs.

Identification of endogenous normalizing genes for expression studies in inguinal ring tissue for scrotal hernias in pigs

The use of reference genes is required for relative quantification in gene expression analysis and since the stability of these genes could be variable depending on the experimental design, it has become indispensable to test the reliability of endogenous genes. Therefore, this study evaluated 10 reference candidate genes in two different experimental conditions in order to obtain stable genes to be used as reference in expression studies related to scrotal hernias in pigs. Two independent experiments were performed: one with 30 days-old MS115 pigs and the other with 60 days-old Landrace pigs. The inguinal ring/canal was collected, frozen and further submitted to real-time PCR analysis (qPCR). For the reference genes stability evaluation, four tools were used: GeNorm in the SLqPCR, BestKeeper, NormFinder and Comparative CT. A general ranking was generated using the BruteAggreg function of R environment. In this study, the RPL19 was one of the most reliable endogenous genes for both experiments. The breed/age effects influenced the expression stability of candidate reference genes evaluated in the inguinal ring of pigs. Therefore, this study reinforces the importance of evaluating the stability of several endogenous genes previous their use, since a consensual set of reference genes is not easily obtained. Here, two sets of genes are recommended: RPL19, RPL32 and H3F3A for 30-days MS115 and PPIA and RPL19 for the 60 days-old Landrace pigs. This is the first study using the inguinal ring tissue and the results can be useful as an indicative for other studies working with gene expression in this tissue.

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.

Identification of Genetic Regions Associated with Scrotal Hernias in a Commercial Swine Herd

In this paper, we have used two approaches to detect genetic associations with scrotal hernias in commercial pigs. Firstly, we have investigated the effects of runs of homozygosity (ROH) with the appearance of scrotal hernias, followed by a Genome Wide Association Study (GWAS). The phenotype classification was based on visual appearance of scrotal hernias. Each affected animal was matched to a healthy control from the same pen. In the total, 68 animals were genotyped using the Porcine SNP60 Beadchip, out of those, 41 animals had the presence of hernias and 27 were healthy animals. Fifteen animals were removed from the analysis due to differences in genetic background, leaving 18 healthy animals and 35 piglets with scrotal hernia. Further, the detection of extended haplotypes shared ROH were conducted for health (control) and affected (case) animals and a permutation test was used to test whether the ROH segments were more frequent in case/case pairs than non-case/case pairs. Using the ROH, we have identified an association (p = 0.019) on chromosome 2(SSC2) being segregated on animals with the presence of scrotal hernias. Using a GWAS, a region composed by 3 SNPs on the sexual chromosome X (SSCX) were associated with scrotal hernias (p < 1.6 × 10^-5), this region harbors the Androgen Receptor Gene (AR).

The effects of amoxicillin treatment of newborn piglets on the prevalence of hernias and abscesses, growth and ampicillin resistance of intestinal coliform bacteria in weaned pigs

This study investigated the effects of a single amoxicillin treatment of newborn piglets on the prevalence of hernias and abscesses until the age of nine weeks. We also studied whether the treatment was associated with growth and mortality, the need for treatment of other diseases, the proportions of ampicillin resistant coliforms and antimicrobial resistance patterns of intestinal Escherichia coli (E. coli). A total of 7156 piglets, from approximately 480 litters, were divided into two treatment groups: ANT (N = 3661) and CON (N = 3495), where piglets were treated with or without a single intramuscular injection of 75 mg amoxicillin one day after birth, respectively. The umbilical and inguinal areas of weaned pigs were palpated at four and nine weeks of age. At the same time, altogether 124 pigs with hernias or abscesses and 820 non-defective pigs from three pens per batch were weighed individually. Mortality and the need to treat piglets for other diseases were recorded. Piglet faecal samples were collected from three areas of the floors of each pen at four weeks of age. The prevalence of umbilical hernias or abscesses did not differ between the groups at four weeks of age, but it was higher in the CON group than in the ANT group at nine weeks of age (2.3% vs. 0.7%, P < 0.05). Numbers of inguinal hernias and abscesses did not differ between the groups at four or nine weeks of age. The ANT group, when it compared with the CON group, increased the weight gain between four and nine weeks of age (LS means ± SE; 497.5 g/d ± 5.0 vs. 475.3 g/d ± 4.9, P < 0.01), and decreased piglet mortality (19.5% ± 1.0 vs. 6.9% ± 1.0, P < 0.05) and the need to treat the piglets for leg problems (3.4% ± 0.3 vs. 1.9% ± 0.3%, P < 0.01) but not for other diseases by the age of four weeks. The proportion of ampicillin resistant intestinal coliform bacteria and the resistance patterns of the E. coli isolates were not different between the ANT and CON groups. In conclusion, our results showed that the amoxicillin treatment of new-born piglets produced statistically significant effect in some of the parameters studied. However, as these effects were only minor, we did not find grounds to recommend preventive antibiotic treatment. Further, continuous antimicrobial treatment of newborn piglets could negatively influence the development of the normal microbiota of the piglet and promote selection of antimicrobial resistance genes in herds. Therefore we suggest rejection of the use of routine administration of antimicrobial agents at birth.

Screening of BCL-2 associated X protein gene polymorphism associated with scrotal hernia in domesticated swine using polymerase chain reaction-restriction fragment length polymorphism

Objective

This study was conducted to screen scrotal hernia in domesticated swine from selected breeders in the Philippines. This defect is associated with a cytosine to thymine mutation in the BCL-2 associated X protein (BAX) gene of swine.

Methods

Genetic screening was done by DNA extraction followed by amplification and digestion using polymerase chain reaction-restriction fragment length polymorphism, amplifying the 416 bp region of the BAX gene that was subjected to digestion using the Ear I enzyme. Sequencing was also conducted to validate the results.

Results

Results revealed that out of 538 samples tested, 411 (76.4%) of the samples were found to be normal whereas the remaining were carriers of the mutation in which 80 (14.9%) were heterozygous mutants and 47 (8.7%) were homozygous mutants. Pietrain breed was found to have the highest incidence.

Conclusion

Having a scrotal hernia eliminates the chances of using the boar as a breeder stock because the following generations arising from it would most likely exhibit herniation. It is therefore advised to establish a genetic screening method for Scrotal Hernia in the Philippines to eliminate the negative gene from the herd.

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.

Genome-wide association study using deregressed breeding values for cryptorchidism and scrotal/inguinal hernia in two pig lines

BACKGROUND

Cryptorchidism and scrotal/inguinal hernia are the most frequent congenital defects in pigs. Identification of genomic regions that control these congenital defects is of great interest to breeding programs, both from an animal welfare point of view as well as for economic reasons. The aim of this genome-wide association study (GWAS) was to identify single nucleotide polymorphisms (SNPs) that are strongly associated with these congenital defects. Genotypes were available for 2570 Large White (LW) and 2272 Landrace (LR) pigs. Breeding values were estimated based on 1 359 765 purebred and crossbred male offspring, using a binary trait animal model. Estimated breeding values were deregressed (DEBV) and taken as the response variable in the GWAS.

RESULTS

Heritability estimates were equal to 0.26 ± 0.02 for cryptorchidism and to 0.31 ± 0.01 for scrotal/inguinal hernia. Seven and 31 distinct QTL regions were associated with cryptorchidism in the LW and LR datasets, respectively. The top SNP per region explained between 0.96% and 1.10% and between 0.48% and 2.77% of the total variance of cryptorchidism incidence in the LW and LR populations, respectively. Five distinct QTL regions associated with scrotal/inguinal hernia were detected in both LW and LR datasets. The top SNP per region explained between 1.22% and 1.60% and between 1.15% and 1.46% of the total variance of scrotal/inguinal hernia incidence in the LW and LR populations, respectively. For each trait, we identified one overlapping region between the LW and LR datasets, i.e. a region on SSC8 (Sus scrofa chromosome) between 65 and 73 Mb for cryptorchidism and a region on SSC13 between 34 and 37 Mb for scrotal/inguinal hernia.

CONCLUSIONS

The use of DEBV in combination with a binary trait model was a powerful approach to detect regions associated with difficult traits such as cryptorchidism and scrotal/inguinal hernia that have a low incidence and for which affected animals are generally not available for genotyping. Several novel QTL regions were detected for cryptorchidism and scrotal/inguinal hernia, and for several previously known QTL regions, the confidence interval was narrowed down.

Shared and nonshared familial susceptibility to surgically treated inguinal hernia, femoral hernia, incisional hernia, epigastric hernia, and umbilical hernia

BACKGROUND

The familial risk of abdominal wall hernia (AWH) is largely unknown. In addition, it is unknown whether inguinal hernia (IH), femoral hernia (FH), incisional hernia (INH), epigastric hernia (EH), and umbilical hernia (UH) share familial susceptibility. The aim of this nationwide study was to determine the familial risks of concordant AWH (same disease in proband and exposed relative) and discordant AWH (different disease in proband and exposed relative).

STUDY DESIGN

Data from the Swedish Multigeneration Register on individuals aged 0 to 78 years were linked to the Swedish hospital discharge register and the Swedish outpatient register for the period from 1964 to 2010. Standardized incidence ratios (SIRs) and 95% CIs for surgically treated IH (n = 209,814 cases), FH (n = 4,576), INH (n = 19,494), EH (n = 8,257), and UH (n = 22,761) were calculated for siblings of individuals with hernia compared with the siblings of unaffected individuals. The procedure was repeated for spouses.

RESULTS

All concordant and most discordant familial sibling risks were increased. Familial concordant SIRs for siblings were IH = 1.97 (95% CI, 1.94-1.99), FH = 3.40 (95% CI, 2.44-4.62), INH = 2.24 (95% CI, 2.04-2.46), EH = 5.57 (95% CI, 4.64-6.64), and UH = 3.61 (95% CI, 3.33-3.91). Concordant familial risks were higher than discordant risks. For example, when the proband sibling had IH, the discordant SIRs were FH = 1.74 (95% CI, 1.61-1.88), INH = 1.22 (95% CI, 1.16-1.28), EH = 1.30 (95% CI, 1.20-1.40), and UH = 1.35 (95% CI, 1.29-1.41). Concordant SIRs for spouses were lower: IH = 1.23 (95% CI, 1.20-1.26), FH = 0.97 (95% CI, 0.64-1.36), INH = 1.56 (95% CI, 1.41-1.71), EH = 1.70 (95% CI, 1.09-2.45), and UH = 1.31 (95% CI, 1.09-1.56).

CONCLUSIONS

Family history of surgically treated AWH is an important risk factor for surgical treatment of AWH. The 5 forms of AWH studied share familial susceptibility, but site-specific familial factors might exist. Several spouse risks were increased, suggesting the possibility of a nongenetic contribution to familial risks.

High incidence of scrotal hernias in a closed colony of FVB mice

Although inguinal hernias are rarely reported to occur in mice, a high incidence of scrotal hernias was observed in a closed breeding colony of FVB/N mice. Unilateral or bilateral hernias occurred in more than 20% of the male mice in the colony that were available for necropsy over 3 inbred and 1 outcross generations; no female mice were affected. Organs commonly present within the hernial sac included the cecum and seminal vesicles. Hernias did not adversely affect the fertility or lifespan of the affected male mice. Although the condition was heritable, no clear pattern of transmission was evident.

Association of the porcine transforming growth factor beta type I receptor (TGFBR1) gene with growth and carcass traits

BACKGROUND

Growth and carcass traits are of great economic importance in livestock production. A large number of quantitative trait loci (QTL) have been identified for growth and carcass traits on porcine chromosome one (SSC1). A key positional candidate for this chromosomal region is TGFBR1 (transforming growth factor beta type I receptor). This gene plays a key role in inherited disorders at cardiovascular, craniofacial, neurocognitive, and skeletal development in mammals.

RESULTS

In this study, 27 polymorphic SNPs in the porcine TGFBR1 gene were identified on the University of Illinois Yorkshire × Meishan resource population. Three SNPs (SNP3, SNP43, SNP64) representing major polymorphic patterns of the 27 SNPs in F1 and F0 individuals of the Illinois population were selected for analyses of QTL association and genetic diversity. An association analysis for growth and carcass traits was completed using these three representative SNPs in the Illinois population with 298 F2 individuals and a large commercial population of 1008 animals. The results indicate that the TGFBR1 gene polymorphism (SNP64) is significantly associated (p < 0.05) with growth rates including average daily gains between birth and 56 kg (p = 0.049), between 5.5 and 56 kg (p = 0.024), between 35 and 56 kg (p = 0.021). Significant associations (p < 0.05) were also identified between TGFBR1 gene polymorphisms (SNP3/SNP43) and carcass traits including loin-eye-area (p = 0.022) in the Illinois population, and back-fat thickness (p = 0.0009), lean percentage (p = 0.0023) and muscle color (p = 0.021) in the commercial population. These three SNPs were also used to genotype a diverse panel of 130 animals representing 11 pig breeds. Alleles SNP3_T and SNP43_G were fixed in Pietrain and Sinclair pig breeds. SNP64_G allele was uniquely identified in Chinese Meishan pigs. Strong evidence of association (p < 0.01) between both SNP3 and SNP64 alleles and reproductive traits including gestation length and number of corpora lutea were also observed in the Illinois population.

CONCLUSION

This study gives the first evidence of association between the porcine TGFBR1 gene and traits of economic importance and provides support for using TGFBR1 markers for pig breeding and selection programs. The genetic diversities in different pig breeds would be helpful to understand the genetic background and migration of the porcine TGFBR1 gene.

Association and haplotype analysis of candidate genes in five genomic regions linked to sow maternal infanticide in a white Duroc × Erhualian resource population

Background

Maternal infanticide is an extreme and failed maternal behavior, which is defined as an active attack on piglets using the jaws, resulting in serious or fatal bite wounds. It brings big economic loss to the pig industry and severe problems to piglets' welfare. But little is known about the genetic background of this behavior. Quantitative trait loci (QTL) for maternal infanticide were identified in a White Duroc × Erhualian intercross by a non-parametric linkage analysis (NPL) in our previous study. In this study, associations of 194 microsatellite markers used in NPL analysis with maternal infanticide behavior were further analyzed by transmission-disequilibrium test (TDT). On this basis, seven genes (ESR2, EAAT2, BDNF, OXTR, 5-HTR2C, DRD1 and GABRA6) at five genomic regions were selected and further analyzed. Associations of single nucleotide polymorphisms (SNPs) and haplotypes in each gene with maternal infanticide behavior were evaluated.

Results

Microsatellite markers on pig chromosome (SSC) 2, 13, 15, and X displayed significance at P < 0.05 by both TDT and NPL. Of the seven candidate genes, three ESR2 SNPs had nominal evidence for association (P < 0.05). Allele A at EAAT2 g. 233G > A and allele T at DRD1 g.1013C > G > T also showed evidence of overtransmission to infanticidal sows. In the overall tests of association of haplotypes, candidate genes of ESR2, EAAT2 and DRD1 achieved overall significance level (P < 0.05). Haplotype [A; A; G], [G; A; G], [A; G; G] and [C; C], respectively, from ESR2, EAAT2 and DRD1 showed higher frequencies to infanticidal sows (P < 0.05). Alleles among haplotypes and SNPs which showed an overtransmission to infanticidal sows were from White Duroc.

Conclusions

From association tests of SNPs and haplotypes, ESR2, EAAT2 and DRD1 showed significant associations with maternal infanticide. This result supported the existence of QTL for maternal infanticide behavior on SSC1, SSC2 and SSC16.

Association of HOXA10, ZFPM2, and MMP2 genes with scrotal hernias evaluated via biological candidate gene analyses in pigs

OBJECTIVE

To evaluate the associations between 14 biological candidate genes and scrotal hernias in pigs.

ANIMALS

1,534 Pietrain-based pigs, including 692 individuals from 298 pig families and 842 male pigs without family information.

PROCEDURES

Pigs were classified as affected or unaffected for scrotal hernias. Single nucleotide polymorphisms of candidate genes were analyzed via PCR assays and genotyped. Statistical analyses were performed on the family-trio and the case-control data.

RESULTS

2 genes involved in collagen metabolism (homeobox A10 [HOXA10] and matrix metalloproteinases 2 [MMP2]) and 1 gene encoding zinc finger protein multitype 2 (ZFPM2, important in the development of diaphragmatic hernia) were significantly associated with hernias. Pigs with these genotypes had high odds of developing scrotal hernias in the case and control groups (2 ZFPM2 variants: odds ratio, 4.3 [95% confidence interval, 2.78 to 6.64] and 4.45[95%confidenceinterval,2.88to6.88]). Anothergene, collagentypeII A 1(COL2A1),was potentially involved in hernia development.

CONCLUSIONS AND CLINICAL RELEVANCE

HOXA10, ZFPM2, MMP2, and COL2A1 could have important roles in pig hernia development and potentially be useful for marker-assisted selection in the pig industry.

IMPACT FOR HUMAN MEDICINE

Pigs are used for the study of many human diseases because of their physiologic similarities. Genes associated with scrotal hernias in this study may be directly used in understanding the molecular mechanisms underlying this defect in humans.

Using microarrays to identify positional candidate genes for QTL: the case study of ACTH response in pigs

BACKGROUND

Microarray studies can supplement QTL studies by suggesting potential candidate genes in the QTL regions, which by themselves are too large to provide a limited selection of candidate genes. Here we provide a case study where we explore ways to integrate QTL data and microarray data for the pig, which has only a partial genome sequence. We outline various procedures to localize differentially expressed genes on the pig genome and link this with information on published QTL. The starting point is a set of 237 differentially expressed cDNA clones in adrenal tissue from two pig breeds, before and after treatment with adrenocorticotropic hormone (ACTH).

RESULTS

Different approaches to localize the differentially expressed (DE) genes to the pig genome showed different levels of success and a clear lack of concordance for some genes between the various approaches. For a focused analysis on 12 genes, overlapping QTL from the public domain were presented. Also, differentially expressed genes underlying QTL for ACTH response were described. Using the latest version of the draft sequence, the differentially expressed genes were mapped to the pig genome. This enabled co-location of DE genes and previously studied QTL regions, but the draft genome sequence is still incomplete and will contain many errors. A further step to explore links between DE genes and QTL at the pathway level was largely unsuccessful due to the lack of annotation of the pig genome. This could be improved by further comparative mapping analyses but this would be time consuming.

CONCLUSION

This paper provides a case study for the integration of QTL data and microarray data for a species with limited genome sequence information and annotation. The results illustrate the challenges that must be addressed but also provide a roadmap for future work that is applicable to other non-model species.

A genome-wide scan reveals candidate susceptibility loci for pig hernias in an intercross between White Duroc and Erhualian

Pig scrotal/inguinal and umbilical hernias are the most prevalent congenital disorders in pigs and often cause animal welfare problems and economic loss. To identify susceptibility loci for these traits, a genome-wide scan with 194 microsatellite markers covering the pig genome was performed in a White Duroc x Erhualian resource population with 23 scrotal/inguinal F(2) animals, 50 umbilical F(2) animals, and their unaffected siblings. A sex-average linkage map with a total length of 2,350.3 cM and an average marker interval of 12.84 cM was constructed. Both nonparametric genome-wide linkage (NPL) analysis and transmission disequilibrium test (TDT) were implemented to detect closely linked markers. The NPL analysis revealed 11 chromosomal regions on SSC1, 2, 3, 6, 7, 8, 10, and 11 for umbilical hernia and 5 regions on SSC2, 4, 8, 13, and 16 for scrotal/inguinal hernia, whereas the TDT test identified susceptibility loci for umbilical hernia on SSC1, 2, 4, 7, 10, 13, 14, and 15 and for scrotal/inguinal hernias on SSC2, 8, 10, and 18. The most promising loci were SWR1928 on SSC7 and SW830 on SSC10 for umbilical hernia, and SW933 on SSC8 for scrotal hernia, which were consistently detected by both NPL and TDT. Several previously reported chromosomal regions for scrotal/inguinal hernia were confirmed, and new evidence for linkage with this pig defect was found. Moreover, susceptibility loci for pig umbilical hernia were detected for the first time.

Association and haplotype analyses of positional candidate genes in five genomic regions linked to scrotal hernia in commercial pig lines

Scrotal hernia in pigs is a complex trait likely affected by genetic and environmental factors. A large-scale association analysis of positional and functional candidate genes was conducted in four previously identified genomic regions linked to hernia susceptibility on Sus scrofa chromosomes 2 and 12, as well as the fifth region around 67 cM on chromosome 2, respectively. In total, 151 out of 416 SNPs discovered were genotyped successfully. Using a family-based analysis we found that four regions surrounding ELF5, KIF18A, COL23A1 on chromosome 2, and NPTX1 on chromosome 12, respectively, may contain the genetic variants important for the development of the scrotal hernia in pigs. These findings were replicated in another case-control dataset. The SNPs around the ELF5 region were in high linkage disequilibrium with each other, and a haplotype containing SNPs from ELF5 and CAT was highly significantly associated with hernia development. Extensive re-sequencing work focused on the KIF18A gene did not detect any further SNPs with extensive association signals. These genes may be involved in the estrogen receptor signaling pathway (KIF18A and NPTX1), the epithelial-mesenchymal transition (ELF5) and the collagen metabolism pathway (COL23A1), which are associated with the important molecular characteristics of hernia pathophysiology. Further investigation on the molecular mechanisms of these genes may provide more molecular clues on hernia development in pigs.

Primary mesh augmentation with fibrin glue for abdominal wall closure--investigations on a biomechanical model

BACKGROUND

The occurrence of incisional hernias after various types of abdominal procedures and incisions continues to be a problem. A number of studies conducted for diverse risk groups have identified a beneficial role for the prophylactic use of mesh augmentation. To what extent this affects the stability of a suture was tested in our biomechanical model.

MATERIALS AND METHODS

To that effect, we compared three groups, carrying out six measurements in each case: (1) single suture in a muscle specimen, (2) suture and additional reinforcement with fibrin glue, and (3) suture and additional reinforcement with a mesh fixed with fibrin glue (Tissucol, Tisseel; with an overlap of 2 cm to all sides).

RESULTS

The single suture conferred a tensile strength, which in our model, was just above the prescribed maximum abdominal pressure of 32 N (37.3 N). The additional use of fibrin glue did not have any significant impact on this result (41.8 N). Only through mesh augmentation with fibrin glue was it possible to achieve a significantly greater tensile strength (64.5 N, p = 0.003).

CONCLUSIONS

The prophylactic use of meshes for stabilization of laparotomy closures appears to be effective. Adequate mesh fixation can be achieved with fibrin glue alone. Further experimental studies and in particular randomized clinical trials are needed to demonstrate proof of the long-term advantages of mesh augmentation in risk groups.

USP26 gene variations in fertile and infertile men

BACKGROUND

The human X chromosome is enriched with testis-specific genes that may be crucial for male fertility. One is the ubiquitin-specific protease 26 (USP26). Five frequent mutations have been identified: 1737G>A, 1090C > T, 370-371insACA, 494T > C and 1423C>T (with the latter three usually detected in a cluster). Their role in infertility is still controversial. This study assesses the association of the most frequent USP26 mutations with male infertility and male infertility etiology factors.

METHODS

The study included 300 infertile and 287 fertile men. Data were collected on ethnicity (according to maternal origin) and family history of reproduction. Clinical records from 235 infertile and 62 fertile (sperm bank donors) men were available and summarized. The five mutations were investigated by bioinformatic tools and their frequencies were assessed by restriction analysis. The results were correlated with clinical findings. Segregation of the mutations in four families was analyzed.

RESULTS

The five analyzed mutations were detected in 44 men from both fertile and infertile groups. The cluster and the 1090C>T mutations showed the highest frequency among Arabs and Sephardic Jews of the infertile group, respectively. Inheritance studies showed that mutations were not always associated with the infertility trait. Mutations 1090C>T and 1737G>A were significantly associated with a history of inguinal hernia (P = 0.007 and P = 0.043, respectively). The prevalence of inguinal hernia among men with the 1090C > T mutation was 33.3% (5/15 men), higher than that reported in infertile men (6.7%).

CONCLUSIONS

Mutation 1090C > T may be a new genetic risk factor for developing inguinal hernia which may be associated with impaired male fertility.

Genetic sequence variations and ADPRT haplotype analysis in French Canadian families with high risk of breast cancer

The poly(ADP-ribose) polymerase (PARP/ADPRT) protein family catalyzes the synthesis of cellular poly(ADP-ribose) following DNA damage and is involved in genomic integrity by regulating cellular responses to DNA damage and apoptosis. Moreover, ADPRT inhibition contributes to a protective effect against cancer development. These findings render ADPRT an attractive candidate susceptibility gene for breast cancer, and thus the goal of this study was to evaluate the possible involvement of ADPRT sequence variations in breast cancer susceptibility. The complete sequence of the 23 exons and flanking intronic sequences of the ADPRT gene was analyzed in 54 affected individuals from distinct high-risk non-BRCA1/2 French Canadian families. No deleterious truncating mutation was identified in the coding region. However, 34 sequence variations were identified, among which seven are coding variants and seven are novel changes. All coding variants and intronic changes located in the vicinity of the coding variants identified in the case series were also analyzed in a cohort of 73 unrelated healthy French Canadian individuals. Interestingly, one missense variant (Pro377Ser) was observed in three different breast cancer cases but was not present among unaffected individuals. We have conducted here an exhaustive detailed mutation and haplotype tagging analysis of the ADPRT gene with regard to breast cancer, providing useful data for other large-scale association studies. Additional studies in other cohorts and other populations are however needed to further evaluate the implication of the Pro377Ser missense variant with regard to breast cancer susceptibility.

Haplotype analysis of ?-actin gene for its association with sperm quality and boar fertility

beta-actin (ACTB) was examined as a direct functional candidate gene for the possible association with sperm concentration, motility (MOT), semen volume per ejaculate, plasma droplet rate, abnormal sperm rate (ASR) and the fertility traits, non-return rate and number of piglets born alive (NBA). Three polymorphisms in intron 3 (T>C) and one polymorphism in exon 4 (T>C) of porcine ACTB gene were identified by comparative sequencing of animals of the breeds Pietrain and Hampshire. Association analysis revealed that haplotypes affected the variation of the traits MOT, ASR and NBA. The beneficial haplotypes may provide considerable improvement of sperm quality and fertility in the tested commercial boar population.