Evidence of a major gene from Bayesian segregation analyses of liability to osteochondral diseases in pigs

High physiological demands in intensively raised pigs: impact on health and welfare

Genetic selection and better control of the environment of the pigs have resulted in increased production levels concerning both reproduction and growth. Such high performances imply high physiological demands that may deteriorate health and welfare. The aims of this paper are to review the physiological challenges that pigs are facing, to identify possible consequences on health and welfare, to propose ways of detecting and correcting problems whenever possible. At weaning, piglets are submitted to abrupt changes in food supply, housing and social environment. Behavioural changes and efficient adaptations of the digestive tract are critical for their health and welfare. Physiological demands to support these adaptations and risks of failure are inversely related to the age of the pigs. During fattening, modern pigs have high daily weight gain especially of lean tissue as well as elevated feed conversion rate. These high growth performances are suspected to favour stress and disease susceptibility, undesirable behaviours as well as leg weakness, but further experimental data are necessary to validate these effects and find their origin. In reproductive females, high prolificacy generates elevated foetal demands for nutrients and space that are not fully met as shown by an increased number of light piglets having difficulties to adapt successfully to the neonatal life. During lactation, sows with high milk production have high nutrient requirements leading to intense catabolism that may affect their health, welfare and future reproductive abilities.

Genetic parameters of infectious bovine keratoconjunctivitis and its relationship with weight and parasite infestations in Australian tropical Bos taurus cattle

Background

Infectious bovine keratoconjunctivitis (IBK) or ‘pinkeye’ is an economically important ocular disease that significantly impacts animal performance. Genetic parameters for IBK infection and its genetic and phenotypic correlations with cattle tick counts, number of helminth (unspecified species) eggs per gram of faeces and growth traits in Australian tropically adapted Bos taurus cattle were estimated.

Methods

Animals were clinically examined for the presence of IBK infection before and after weaning when the calves were 3 to 6 months and 15 to 18 months old, respectively and were also recorded for tick counts, helminth eggs counts as an indicator of intestinal parasites and live weights at several ages including 18 months.

Results

Negative genetic correlations were estimated between IBK incidence and weight traits for animals in pre-weaning and post-weaning datasets. Genetic correlations among weight measurements were positive, with moderate to high values. Genetic correlations of IBK incidence with tick counts were positive for the pre-weaning and negative for the post-weaning datasets but negative with helminth eggs counts for the pre-weaning dataset and slightly positive for the post-weaning dataset. Genetic correlations between tick and helminth eggs counts were moderate and positive for both datasets. Phenotypic correlations of IBK incidence with helminth eggs per gram of faeces were moderate and positive for both datasets, but were close to zero for both datasets with tick counts.

Conclusions

Our results suggest that genetic selection against IBK incidence in tropical cattle is feasible and that calves genetically prone to acquire IBK infection could also be genetically prone to have a slower growth. The positive genetic correlations among weight traits and between tick and helminth eggs counts suggest that they are controlled by common genes (with pleiotropic effects). Genetic correlations between IBK incidence and tick and helminth egg counts were moderate and opposite between pre-weaning and post-weaning datasets, suggesting that the environmental and (or) maternal effects differ between these two growth phases. This preliminary study provides estimated genetic parameters for IBK incidence, which could be used to design selection and breeding programs for tropical adaptation in beef cattle.

Bayesian inference to study genetic control of resistance to gray leaf spot in maize

Gray leaf spot (GLS) is a major maize disease in Brazil that significantly affects grain production. We used Bayesian inference to investigate the nature and magnitude of gene effects related to GLS resistance by evaluation of contrasting lines and segregating populations. The experiment was arranged in a randomized block design with three replications and the mean values were analyzed using a Bayesian shrinkage approach. Additive-dominant and epistatic effects and their variances were adjusted in an over-parametrized model. Bayesian shrinkage analysis showed to be an excellent approach to handle complex models in the study of genetic control in GLS, since this approach allows to handle overparametrized models (main and epistatic effects) without using model-selection methods. Genetic control of GLS resistance was predominantly additive, with insignificant influence of dominance and epistasis effects.

Association and expression study of MMP3, TGFβ1 and COL10A1 as candidate genes for leg weakness-related traits in pigs

The present study was aimed to determine the association between metalloproteinase 3 (MMP3), transforming growth factor beta 1 (TGFβ1) and collagen type X alpha I (COL10A1) gene polymorphisms with traits related to leg weakness in pigs. Three hundred Duroc × Pietrain cross breds (DuPi) and 299 pigs of a commercial population (CP) were used for the experiment. DuPi animals were examined for 10 different traits describing leg and feet structure, osteochondrosis (OC) scores and bone density status. Data of OC score at condylus medialis humeri, condylus medialis femoris and distal epiphysis ulna regions of CP were used for association analysis. Significant association (P < 0.05) was found for MMP3 SNP (g.158 C>T) with OC at head of femur and bone mineral density in the DuPi population. Association (P < 0.05) was found between SNP of TGFβ1 (g.180 G>A) with rear leg score and the principle component denoting both OC and feet and leg scores in the DuPi population. No association was found between COL10A1 (g.72 C>T) and leg weakness related traits. The associations of SNPs with OC traits could not be confirmed in the commercial population. Expression analysis of the three candidate genes was performed to compare between healthy and OC. TGFβ1 was found to be highly expressed (P < 0.05) in the OC compared to healthy cartilages, but no significant different expressions were observed for MMP3 and COL10A1 genes. The present finding suggested that TGFβ1 and MMP3 genes variants have an effect on some of the leg weakness related traits.

Quantitative trait loci analysis for leg weakness-related traits in a Duroc × Pietrain crossbred population

Background

Leg weakness issues are a great concern for the pig breeding industry, especially with regard to animal welfare. Traits associated with leg weakness are partly influenced by the genetic background of the animals but the genetic basis of these traits is not yet fully understood. The aim of this study was to identify quantitative trait loci (QTL) affecting leg weakness in pigs.

Methods

Three hundred and ten F₂ pigs from a Duroc × Pietrain resource population were genotyped using 82 genetic markers. Front and rear legs and feet scores were based on the standard scoring system. Osteochondrosis lesions were examined histologically at the head and the condylus medialis of the left femur and humerus. Bone mineral density, bone mineral content and bone mineral area were measured in the whole ulna and radius bones using dual energy X-ray absorptiometry. A line-cross model was applied to determine QTL regions associated with leg weakness using the QTL Express software.

Results

Eleven QTL affecting leg weakness were identified on eight autosomes. All QTL reached the 5% chromosome-wide significance level. Three QTL were associated with osteochondrosis on the humerus end, two with the fore feet score and two with the rear leg score. QTL on SSC2 and SSC3 influencing bone mineral content and bone mineral density, respectively, reached the 5% genome-wide significance level.

Conclusions

Our results confirm previous studies and provide information on new QTL associated with leg weakness in pigs. These results contribute towards a better understanding of the genetic background of leg weakness in pigs.

Use of serum biomarkers to predict the development and severity of osteochondrosis lesions in the distal portion of the femur in pigs

OBJECTIVE

To evaluate the use of serum biomarkers of cartilage and bone metabolism to predict the occurrence and severity of osteochondrosis (OC) lesions in the distal portion of the femur in growing swine.

ANIMALS

71 gilts.

PROCEDURES

At an abattoir, serum samples for analysis of 10 biomarkers indicative of cartilage and bone metabolism were obtained prior to processing of the pigs. The distal portion of each pig's left femur was directly examined and cut into longitudinal sections to evaluate the number and severity of abnormalities on the external surface, articular cartilage, and growth plate. Each specimen was categorized as with (n = 56) or without (15) OC, and an overall OC severity score was assigned to affected pigs. Logistic and linear regression analyses were performed to predict odds of OC on the basis of biomarker concentrations and predict the severity of OC values in affected pigs, respectively.

RESULTS

Compared with values in unaffected pigs, serum concentrations of C-propeptide of type II collagen (CPII) and cartilage oligomeric matrix protein were significantly increased and concentrations of carboxy-terminal telopeptide of type II collagen 3/4-length fragment (C2C) and pyridinoline cross-links were significantly decreased in affected pigs. A 2-fold increase in CPII concentration increased the odds of pigs having OC by a factor of 97 (95% confidence interval, 6 to infinity). Changes in serum C2C concentration accounted for 49% of the variation in overall OC severity score.

CONCLUSIONS AND CLINICAL RELEVANCE

Assessment of serum biomarker concentrations may be useful in the diagnosis of OC and aid in reduction of lameness in swine herds.

Evidence of major genes affecting resistance to bacterial cold water disease in rainbow trout using Bayesian methods of segregation analysis

Bacterial cold water disease (BCWD) causes significant economic loss in salmonid aquaculture. We previously detected genetic variation for BCWD resistance in our rainbow trout population, and a family-based selection program to improve resistance was initiated at the National Center for Cool and Cold Water Aquaculture (NCCCWA). This study investigated evidence of major trait loci affecting BCWD resistance using only phenotypic data (without using genetic markers) and Bayesian methods of segregation analysis (BMSA). A total of 10,603 juvenile fish from 101 full-sib families corresponding to 3 generations (2005, 2007, and 2009 hatch years) of the NCCCWA population were challenged by intraperitoneal injection with Flavobacterium psychrophilum, the bacterium that causes BCWD. The results from single- and multiple-QTL models of BMSA suggest that 6 to 10 QTL explaining 83 to 89% of phenotypic variance with either codominant or dominant disease-resistant alleles plus polygenic effects may underlie the genetic architecture of BCWD resistance. This study also highlights the importance of polygenic background effects in the genetic variation of BCWD resistance. The polygenic heritability on the observed scale of survival status is slightly larger than that previously reported for rainbow trout BCWD resistance. These findings provide the basis for designing informative crosses for QTL mapping and carrying out genome scans for QTL affecting BCWD resistance in rainbow trout.

Analysis of the existence of major genes affecting alpaca fiber traits

The aim of this study was to determine the presence of major genes for fiber diameter (FD), SD of FD (SDFD), CV of FD, and comfort factor (CF) in Huacaya (HU) and Suri (SU) Peruvian alpaca breeds. Bayesian segregation analyses with relaxed transmission probabilities were performed using 1,906 and 6,592 available records for SU and HU breeds. Evidence for the presence of major genes was statistically supported when the 95% posterior density did not include zero. Significant major genes were found associated with decreased FD, SDFD, CV values, and increased CF values. Additive effects of the major genes were 4.18 and 4.23 μm for FD, 1.67 and 1.61 μm for SDFD, 3.32 and 3.76% for CV, and 15.03 and 14.90% for CF in HU and SU breeds, respectively. Dominance effects were -1.98 and -2.03 μm for FD, -0.88 and -1.11 μm for SDFD, -1.37 and -2.17% for CV, and 13.0 and 11.8% for CF in HU and SU breeds, respectively. Major gene variance was larger than the polygenic variance for all traits. Major gene allelic frequencies for FD, SDFD, and CV ranged from 0.81 to 0.86 for HU breed and from 0.70 to 0.77 for the SU breed and were 0.24 and 0.36, respectively, for CF. It can be concluded that a major gene affecting these traits could be segregating. Then, molecular identification and monitoring of animals carrying favorable genes throughout the worldwide alpaca population would allow for a quick genetic improvement.

Molecular characterization and methylation study of matrix gla protein in articular cartilage from pig with osteochondrosis

Osteochondrosis (OC) or leg weakness is an economically important disease of young fast growing pigs and is a concern of animal welfare. The etiology and pathogenesis of osteochondrosis is not fully understood yet, but any abnormalities in the formation of hypertrophic chondrocytes and disrupted blood supply to the growth cartilage are very important predisposing factors. Matrix gla protein (MGP) as a potential calcification inhibitor of extracellular matrix might contribute to the development of OC. Molecular characterization, polymorphisms analysis, methylation at promoter region and expression of MGP gene and protein were performed in both healthy and OC cartilage collected from a DurocxPietrain resource population. The porcine MGP gene consists of 4 exons and 3 introns. The full-length MGP cDNA isolated from articular cartilage consists of 606 bp with a 69-bp 5' UTR, a 312-bp open reading frame with a start codon, a 225-bp 3' UTR. Three single-nucleotide polymorphisms (SNP) were detected in the intron 1 (A-115G, C-1073T and C-1135A) and one in the 3'UTR (C-3767T). The relative abundance of MGP mRNA was lower (P<0.05) in OC compared with healthy cartilage. Moreover, the intensity of MGP band was lower (P<0.05) in OC group when quantified by western blot. Furthermore, one CpG region was identified in MGP promoter and DNA methylation of three CG sites were higher in OC compared with normal cartilage. This suggested that the high DNA methylation at specific CG sites in the MGP promoter might be involved in the down regulation of MGP in OC. Immunofluorescence of normal cartilage collected from pigs of different ages revealed that MGP signals were higher in younger pigs and decreased in the older pigs. The MGP protein was expressed more near to the cartilage canals. These results suggest that the MGP gene might be a potential candidate gene for the development of OC in pigs.

Hereditary hydrocephalus internus in a laboratory strain of golden hamsters ( Mesocricetus auratus)

Golden hamsters of one common laboratory strain had a high incidence of hydrocephalus internus. When a severity score of hydrocephalus was used, a major autosomal recessive locus could be identified. However, when a binary score (hydrocephalus, no hydrocephalus) was used, no such major locus could be detected and results of test matings were not consistent with Mendelian inheritance. Golden hamsters with severe forms of hydrocephalus had a dorsally compressed and ventrally intact hippocampus. Implications for the behavior and well-being of affected hamsters are unknown but researchers using this strain should be aware of the likely presence of hydrocephalus.

Heritability and complex segregation analysis of deafness in Jack Russell Terriers

BACKGROUND

The association between patterns of pigmentation and deafness in the dog has a long-documented history, with reports dating back over one hundred years. Long suspected of having a genetic basis, the search for loci with a pronounced influence in the expression of hearing loss in the dog has yet to be successful. No studies in the dog to date have found a possible influence of a specific colour locus associated with deafness. The present study is intended to evaluate the heritability of deafness in the Jack Russell Terrier (JRT), characterize the mode of inheritance, and evaluate the existence of a sex, coat colour, or coat texture influence on the expression of sensorineural deafness.

RESULTS

The estimation of heritability of deafness in the JRT was 0.22 when deafness was considered a binary (normal/deaf) trait and 0.31 when deafness was considered a three-category (normal/unilateral/bilateral deafness). The influence of coat colour in the incidence of JRT deafness was statistically significant, indicating that dogs with more white are more likely to be deaf. The influence of sex or coat texture was not statistically significant in the incidence of JRT deafness. Complex segregation analysis revealed a model of a single locus with a large effect on the binary measure of hearing loss is not supported.

CONCLUSION

This is the first attempt, to our knowledge, to characterize a genetic component responsible for deafness in the JRT. The heritability of deafness in the JRT was found to be 0.22 and 0.31 considering deafness to be a two-category or three-category trait, respectively. There appears to be an influence of coat colour on the expression of deafness. In an attempt to characterize the mode of inheritance of deafness in the JRT, a model of a single locus with a large effect on hearing loss is not supported with this data. Further study is needed to determine if a single locus may be influencing deafness in the JRT. While the absence of a clear mode of inheritance complicates genetic dissection of deafness in the JRT, the assembling of this pedigree provides a tool for eventually defining the genetic bases of this disorder.

Genome-wide search for markers associated with osteochondrosis in Hanoverian warmblood horses

A genome-wide scan was performed to detect quantitative trait loci (QTLs) for osteochondrosis (OC) and osteochondrosis dissecans (OCD) in horses. The marker set comprised 260 microsatellites. We collected data from 211 Hanoverian warmblood horses consisting of 14 paternal half-sib families. Traits used were OC (fetlock and/or hock joints affected), OCD (fetlock and/or hock joints affected), fetlock OC, fetlock OCD, hock OC, and hock OCD. The first genome scan included 172 microsatellite markers. In a second step 88 additional markers were chosen to refine putative QTLs found in the first scan. Genome-wide significant QTLs were located on equine chromosomes 2, 4, 5, and 16. QTLs for fetlock OC and hock OC partly overlapped on the same chromosomes, indicating that these traits may be genetically related. QTLs reached the chromosome-wide significance level on eight different equine chromosomes: 2, 3, 4, 5, 15, 16, 19, and 21. This whole-genome scan was a first step toward the identification of candidate genome regions harboring genes responsible for equine OC. Further investigations are necessary to refine the map positions of the QTLs already identified for OC.

Clinical features and heritability of hypoadrenocorticism in Nova Scotia Duck Tolling Retrievers: 25 cases (1994-2006)

OBJECTIVE

To evaluate the clinical features and heritability of naturally occurring hypoadrenocorticism in Nova Scotia Duck Tolling Retrievers (NSDTRs).

DESIGN

Retrospective case series.

ANIMALS

25 NSDTRs with hypoadrenocorticism.

PROCEDURES

Questionnaires completed by owners of NSDTRs with hypoadrenocorticism and medical records from veterinarians were reviewed for information regarding diagnosis, age at diagnosis, concurrent diseases, age at death, and cause of death. Pedigrees were analyzed for heritability and mode of inheritance of hypoadrenocorticism (including complex segregation analysis of pedigrees of 1,515 dogs).

RESULTS

On the basis of results of ACTH stimulation testing, hypoadrenocorticism was diagnosed in 16 female and 9 male NSDTRs (including 6 full siblings). Median age at diagnosis was 2.6 years; the diagnosis was made prior to 2 years of age in 11 dogs. Seventeen dogs had hyponatremia, hyperkalemia, or both, and serum electrolyte concentrations were within reference ranges for 8 dogs at the time of diagnosis. Median survival time after diagnosis for 4 dogs that died or were euthanized as a result of medical causes was 1.6 years. Heritability was calculated at 0.98 with no sex effect, and complex segregation analysis fit a major gene model with an autosomal recessive mode of inheritance.

CONCLUSIONS AND CLINICAL RELEVANCE

In NSDTRs, hypoadrenocorticism was diagnosed at an earlier age, compared with published reports of age at diagnosis among the general dog population. Among the study dogs, 32% had no serum electrolyte abnormalities at the time of diagnosis, and the disease appeared to have an autosomal recessive mode of inheritance in the breed.

Investigation of major gene for milk yield, milking speed, dry matter intake, and body weight in dairy cattle

The main aim of this study was to determine if there exist any major gene for milk yield (MY), milking speed (MS), dry matter intake (DMI), and body weight (BW) recorded at various stages of lactation in first-lactation dairy cows (2543 observations from 320 cows) kept at the research farm of the Swiss Federal Institute of Technology between April 1994 and April 2004. Data were modelled based a simple repeatability covariance structure and analysed by using Bayesian segregation analyses. Gibbs sampling was used to make statistical inferences on posterior distributions; inferences were based on a single run of the Markov chain for each trait with 500,000 samples, with each 10th sample collected because of the high correlation among the samples. The posterior mean (+/-SD) of major gene variance was 2.61 (+/-2.46) for MY, 0.83 (+/-1.26) for MS, 4.37 (+/-2.34) for DMI, and 2056.43 (+/-665.67) for BW. Highest posterior density regions for 3 of the 4 traits did not include 0 (except MS), which supported the evidence for major gene. With additional tests for agreement with Mendelian transmission probabilities, we could only confirm the existence of a major gene for MY, but not for MS, DMI, and BW. Expected Mendelian transmission probabilities and their model fits were also compared.

Population and systems genetics analyses of cortisol in pigs divergently selected for stress

This study presents a systems genetic analysis on the physiology of cortisol in mice and pigs with an aim to show the potential of a comprehensive computational approach to quickly identify candidate genes and avoid a costly whole-genome quantitative trait locus (QTL) mapping. Population genetics analyses were performed on measurements of cortisol from a pig selection experiment. Expression QTL were mapped and gene networks were built using gene expressions for Crhr1 (corticotrophin-releasing hormone receptor) gene and single nucleotide polymorphisms from public mouse data. Results from mouse data were used to infer potential candidate regulatory genes involved in pig cortisol regulation, using a comparative or translational systems genetics approach. The pig data used were from a 10-yr divergent genetic selection experiment, providing data on 417 individuals. Population genetics analysis showed that cortisol is highly genetically determined with heritabilities of 0.40-0.70. Furthermore, a major gene with an additive effect of 86 ng/ml is segregating. Genetical-genomics investigations revealed two trans-acting eQTL for Crhr1 gene expression on chromosomes 2 and 13. Candidate gene search under trans-eQTL peaks yielded 63 genes for Crhr1 expression phenotypes. Functional links for Crhr1 genes with other genes/proteins in the gene network using mouse data were shown for the first 10 statistically significant genes involved. Results show translational or comparative systems genetics approaches reduce costs and time in large-scale genetics and "-omics" investigations. This is the first study to report a strong genetic basis for cortisol physiology using a systems approach.

From genetical genomics to systems genetics: potential applications in quantitative genomics and animal breeding

This article reviews methods of integration of transcriptomics (and equally proteomics and metabolomics), genetics, and genomics in the form of systems genetics into existing genome analyses and their potential use in animal breeding and quantitative genomic modeling of complex traits. Genetical genomics or the expression quantitative trait loci (eQTL) mapping method and key findings in this research are reviewed. Various procedures and potential uses of eQTL mapping, global linkage clustering, and systems genetics are illustrated using actual analysis on recombinant inbred lines of mice with data on gene expression (for diabetes- and obesity-related genes), pathway, and single nucleotide polymorphism (SNP) linkage maps. Experimental and bioinformatics difficulties and possible solutions are discussed. The main uses of this systems genetics approach in quantitative genomics were shown to be in refinement of the identified QTL, candidate gene and SNP discovery, understanding gene-environment and gene-gene interactions, detection of candidate regulator genes/eQTL, discriminating multiple QTL/eQTL, and detection of pleiotropic QTL/eQTL, in addition to its use in reconstructing regulatory networks. The potential uses in animal breeding are direct selection on heritable gene expression measures, termed “expression assisted selection,” and genetical genomic selection of both QTL and eQTL based on breeding values of the respective genes, termed “expression-assisted evaluation.”

Genetic evaluation of Addison's disease in the Portuguese Water Dog

BACKGROUND

Addison's disease, also known as hypoadrenocorticism, has been reported in many individual dogs, although some breeds exhibit a greater incidence than the population as a whole. Addison's is presumed to be an autoimmune mediated hereditary defect but the mode of inheritance remains unclear. In particular, the heritability and mode of inheritance have not been defined for the Portuguese Water Dog although Addison's is known to be prevalent in the breed.

RESULTS

The analyses present clear evidence that establishes Addison's disease as an inherited disorder in the Portuguese Water Dog with an estimate of heritability of 0.49 (+/- 0.16); there were no differences in risk for disease across sexes (p > 0.49). Further, the complex segregation analysis provides suggestive evidence that Addison's disease in the Portuguese Water Dog is inherited under the control of a single, autosomal recessive locus.

CONCLUSION

The high heritability and mode of inheritance of Addison's disease in the Portuguese Water Dog should enable the detection of segregating markers in a genome-wide scan and the identification of a locus linked to Addison's. Though the confirmation of Addison's disease as an autosomal recessive disorder must wait until the gene is identified, breeders of these dogs may wish to keep the present findings in mind as they plan their breeding programs to select against producing affected dogs.