Thomas Mark

Genome-Wide Association Study Reveals Genetic Architecture of Eating Behavior in Pigs and Its Implications for Humans Obesity by Comparative Mapping

This study was aimed at identifying genomic regions controlling feeding behavior in Danish Duroc boars and its potential implications for eating behavior in humans. Data regarding individual daily feed intake (DFI), total daily time spent in feeder (TPD), number of daily visits to feeder (NVD), average duration of each visit (TPV), mean feed intake per visit (FPV) and mean feed intake rate (FR) were available for 1130 boars. All boars were genotyped using the Illumina Porcine SNP60 BeadChip. The association analyses were performed using the GenABEL package in the R program. Sixteen SNPs were found to have moderate genome-wide significance (p<5E-05) and 76 SNPs had suggestive (p<5E-04) association with feeding behavior traits. MSI2 gene on chromosome (SSC) 14 was very strongly associated with NVD. Thirty-six SNPs were located in genome regions where QTLs have previously been reported for behavior and/or feed intake traits in pigs. The regions: 64–65 Mb on SSC 1, 124–130 Mb on SSC 8, 63–68 Mb on SSC 11, 32–39 Mb and 59–60 Mb on SSC 12 harbored several signifcant SNPs. Synapse genes (GABRR2, PPP1R9B, SYT1, GABRR1, CADPS2, DLGAP2 and GOPC), dephosphorylation genes (PPM1E, DAPP1, PTPN18, PTPRZ1, PTPN4, MTMR4 and RNGTT) and positive regulation of peptide secretion genes (GHRH, NNAT and TCF7L2) were highly significantly associated with feeding behavior traits. This is the first GWAS to identify genetic variants and biological mechanisms for eating behavior in pigs and these results are important for genetic improvement of pig feed efficiency. We have also conducted pig-human comparative gene mapping to reveal key genomic regions and/or genes on the human genome that may influence eating behavior in human beings and consequently affect the development of obesity and metabolic syndrome. This is the first translational genomics study of its kind to report potential candidate genes for eating behavior in humans.

Genetic parameters for different measures of feed efficiency and related traits in boars of three pig breeds

Residual feed intake (RFI) is commonly used as a measure of feed efficiency at a given level of production. A total of 16,872 pigs with their pedigree traced back as far as possible was used to estimate genetic parameters for RFI, growth performance, food conversion ratio (FCR), body conformation, and feeding behavior traits in 3 Danish breeds [Duroc (DD), Landrace (LL), and Yorkshire (YY)]. Two measures of RFI were considered: residual feed intake 1 (RFI1) was calculated based on regression of daily feed intake (DFI) from 30 to 100 kg on initial test weight and ADG from 30 to 100 kg (ADG2). Residual feed intake 2 (RFI2) was as RFI1, except it was also regressed with respect to backfat (BF). The estimated heritabilities for RFI1 and RFI2 were 0.34 and 0.38 in DD, 0.34 and 0.36 in LL, and 0.39 and 0.40 in YY, respectively. The heritabilities ranged from 0.32 (DD) to 0.54 (LL) for ADG2, from 0.54 (DD) to 0.67 (LL) for BF, and from 0.13 (DD) to 0.19 (YY) for body conformation. Feeding behavior traits including DFI, number of visits to feeder per day (NVD), total time spent eating per day (TPD), feed intake rate (FR), feed intake per visit (FPV), and time spent eating per visit (TPV) were moderately to highly heritable. Residual feed intake 2 was genetically independent of ADG2 and BF in all breeds, except it had low genetic correlation to ADG2 in YY (0.2). Residual feed intake 1 was also genetically independent of ADG2 in DD and LL. Both RFI traits had strong genetic correlations with DFI (0.85 to 0.96) and FCR (0.76 to 0.99). They had low or no genetic correlations with feeding behavior traits. Unfavorable genetic correlations were found between ADG2 and both BF and DFI. Among feeding behavior traits, DFI had low genetic correlations to other traits in all breeds. High and negative genetic correlations were also found between TPD with FR (-0.79 in YY to -0.88 in DD), NVD, and TPD (-0.91 in DD to -0.94 in YY) and between NVD and FPV (-0.83 in DD to -0.91 in YY) in all breeds. The genetic trend for feed efficiency was favorable in all breeds regardless of the definition of feed efficiency used. In summary, RFI1 and RFI2 were heritable and selection for reduced RFI2 can be performed without adversely affecting ADG and BF and could replace FCR in the selection index for the Danish pig breeds. Selection could also be based on RFI1 for breeds with fewer concerns about a negative effect of BF or for breeds that do not have BF records.

An F2 pig resource population as a model for genetic studies of obesity and obesity-related diseases in humans: design and genetic parameters

Obesity is a rising worldwide public health problem. Difficulties to precisely measure various obesity traits and the genetic heterogeneity in human have been major impediments to completely disentangle genetic factors causing obesity. The pig is a relevant model for studying human obesity and obesity-related (OOR) traits. Using founder breeds divergent with respect to obesity traits we have created an F2 pig resource population (454 pigs), which has been intensively phenotyped for 36 OOR traits. The main rationale for our study is to characterize the genetic architecture of OOR traits in the F2 pig design, by estimating heritabilities, genetic, and phenotypic correlations using mixed- and multi-trait BLUP animal models. Our analyses revealed high coefficients of variation (15–42%) and moderate to high heritabilities (0.22–0.81) in fatness traits, showing large phenotypic and genetic variation in the F2 population, respectively. This fulfills the purpose of creating a resource population divergent for OOR traits. Strong genetic correlations were found between weight and lean mass at dual-energy x-ray absorptiometry scanning (0.56–0.97). Weight and conformation also showed strong genetic correlations with slaughter traits (e.g., rg between abdominal circumference and leaf fat at slaughtering: 0.66). Genetic correlations between fat-related traits and the glucose level vary between 0.35 and 0.74 and show a strong correlation between adipose tissue and impaired glucose metabolism. Our power calculations showed a minimum of 80% power for QTL detection for all phenotypes. We revealed genetic correlations at population level, for the first time, for several difficult to measure and novel OOR traits and diseases. The results underpin the potential of the established F2 pig resource population for further genomic, systems genetics, and functional investigations to unravel the genetic background of OOR traits.

Comparative Analyses of QTLs Influencing Obesity and Metabolic Phenotypes in Pigs and Humans

The pig is a well-known animal model used to investigate genetic and mechanistic aspects of human disease biology. They are particularly useful in the context of obesity and metabolic diseases because other widely used models (e.g. mice) do not completely recapitulate key pathophysiological features associated with these diseases in humans. Therefore, we established a F2 pig resource population (n = 564) designed to elucidate the genetics underlying obesity and metabolic phenotypes. Segregation of obesity traits was ensured by using breeds highly divergent with respect to obesity traits in the parental generation. Several obesity and metabolic phenotypes were recorded (n = 35) from birth to slaughter (242 ± 48 days), including body composition determined at about two months of age (63 ± 10 days) via dual-energy x-ray absorptiometry (DXA) scanning. All pigs were genotyped using Illumina Porcine 60k SNP Beadchip and a combined linkage disequilibrium-linkage analysis was used to identify genome-wide significant associations for collected phenotypes. We identified 229 QTLs which associated with adiposity- and metabolic phenotypes at genome-wide significant levels. Subsequently comparative analyses were performed to identify the extent of overlap between previously identified QTLs in both humans and pigs. The combined analysis of a large number of obesity phenotypes has provided insight in the genetic architecture of the molecular mechanisms underlying these traits indicating that QTLs underlying similar phenotypes are clustered in the genome. Our analyses have further confirmed that genetic heterogeneity is an inherent characteristic of obesity traits most likely caused by segregation or fixation of different variants of the individual components belonging to cellular pathways in different populations. Several important genes previously associated to obesity in human studies, along with novel genes were identified. Altogether, this study provides novel insight that may further the current understanding of the molecular mechanisms underlying human obesity.

Genetic parameters for pathogen-specific mastitis resistance in Danish Holstein Cattle.

The objective of this study was to estimate heritabilities for and genetic correlations among different pathogen-specific mastitis traits. The traits were unspecific mastitis, which is all mastitis treatments regardless of the causative pathogen as well as mastitis caused by Streptococcus dysgalactiae, Escherichia coli, coagulase-negative staphylococci (CNS), Staphylococcus aureus and Streptococcus uberis. Also groups of pathogens were investigated, Gram-negative v. Gram-positive and contagious v. environmental pathogens. Data from 168 158 Danish Holstein cows calving first time between 1998 and 2006 were used in the analyses. Variances and covariances were estimated using uni- and bivariate threshold models via Gibbs sampling. Posterior means of heritabilities of pathogen-specific mastitis were lower than the heritability of unspecific mastitis, ranging from 0.035 to 0.076 for S. aureus and S. uberis, respectively. The heritabilities of groups of pathogen ranged from 0.053 to 0.087. Genetic correlations among the pathogen-specific mastitis traits ranged from 0.45 to 0.77. These estimates tended to be lowest for bacteria eliciting very different immune responses, which can be considered as the overall pleiotropic effect of genes affecting resistance to a specific pathogen, and highest for bacteria sharing characteristics regarding immune response. The genetic correlations between the groups of pathogens were high, 0.73 and 0.83. Results showed that the pathogen-specific traits used in this study should be considered as different traits. Genetic evaluation for pathogen-specific mastitis resistance may be beneficial despite lower heritabilities than unspecific mastitis because a pathogen-specific mastitis trait is a direct measure of an udder infection, and because the cost of a mastitis case caused by different pathogens has been shown to differ greatly. Sampling bias may be present because there were not pathogen information on all mastitis treatments and because some farms do not record pathogen information. Therefore, improved recording of pathogen information and mastitis treatments in general is critical for a successful genetic evaluation of udder health. Also, economic values have to be specified for each pathogen-specific trait separately.

Genetic parameters for androstenone and skatole as indicators of boar taint and their relationship to production and litter size traits in Danish Landrace.

Boar taint is an offensive odor that affects the smell and taste of cooked pork, resulting mainly from the accumulation of skatole and androstenone in the back fat of intact males. The aim of the study was to estimate genetic parameters for skatole and androstenone and their genetic relationship to production and litter size traits. Concentrations of skatole and androstenone in the back fat were available for approximately 6,000 and 1,000 Landrace boars, respectively. The concentrations were log-transformed to align phenotypic measures to a normal distribution. Heritability estimates for Log(skatole) and Log(androstenone) were 0.33 and 0.59, respectively. The genetic correlation between the 2 measures of boar taint was 0.37, suggesting that genetic selection against boar taint based on only 1 of the chemical compounds could be insufficient. The boar taint compounds had low and mostly favorable genetic correlations with the production traits. Most noticeable, a favorable genetic correlation of -0.20 between meat percentage and Log(skatole) was estimated and hence continued selection for lean pigs can also slowly reduce the level of boar taint if the desired carcass weight is kept constant. The relationship between litter size traits (measured on sows related to boars) and boar taint compounds was low and not significantly different from 0. In conclusion, skatole and androstenone can be reduced through selection without affecting important economical production and litter size traits. Therefore, animal breeding offers an effective and sustainable solution to surgical castration of male piglets.

Genetic parameters for male fertility and its relationship to skatole and androstenone in Danish Landrace boars.

Concerns have been raised regarding selection against the boar taint compounds, androstenone and skatole, due to potential unfavorable genetic correlations with important male fertility traits (i.e., selection of boars with low levels of these boar taint compounds might also reduce male fertility). Hence, the objective of this investigation was to study the genetic association between direct measures of male fertility and the boar taint compounds in Danish Landrace pigs. Concentrations of skatole and androstenone in the back fat were available for approximately 6,000 and 1,000 Landrace boars, respectively. The litter size traits, such as total number born, live piglets at d 5, and piglet survival until d 5 on relatives of the slaughter boars, were extracted from the Danish Landrace breeding program, yielding 35,715 records. Semen volume, sperm concentration, subjective sperm quality score, and total number of sperm were available from 95,267 ejaculates. These ejaculates were collected between 2005 and 2012 and originated from 3,145 Landrace boars from 12 AI stations in Denmark. The traits were analyzed using single and multitrait animal models including univariate random regression models. Skatole and androstenone concentrations were moderate to highly heritable (i.e., 0.33 and 0.59, respectively). The genetic correlation between the two compounds was moderate (0.40). Genetic variance of sperm production per ejaculate increased during the productive life of the boar, resulting in heritability estimates increasing from 0.18 to 0.31. Genetic correlations between sperm production per ejaculate at different ages were high and generally larger than 0.8, indicating that later genetic merit can be predicted from records at an early age. The heritability (based on service-sire genetic component) of both total number of piglets born and survival to d 5 were 0.02, and the correlation between these effects and the additive genetic effect on boar taint ranged from 0.05 to -0.40 (none of these correlations were significantly different from zero). Most importantly, the genetic correlations between skatole and androstenone and the different semen traits tended to be more favorable with increase in age of the boars. In conclusion, these data suggest that concentrations of skatole and androstenone can be reduced through genetic selection without negatively affecting important male fertility traits in Danish Landrace pigs.

Estimation of (co)variances for genomic regions of flexible sizes: application to complex infectious udder diseases in dairy cattle

BackgroundMulti-trait genomic models in a Bayesian context can be used to estimate genomic (co)variances, either for a complete genome or for genomic regions (e.g. per chromosome) for the purpose of multi-trait genomic selection or to gain further insight into the genomic architecture of related traits such as mammary disease traits in dairy cattle.MethodsData on progeny means of six traits related to mastitis resistance in dairy cattle (general mastitis resistance and five pathogen-specific mastitis resistance traits) were analyzed using a bivariate Bayesian SNP-based genomic model with a common prior distribution for the marker allele substitution effects and estimation of the hyperparameters in this prior distribution from the progeny means data. From the Markov chain Monte Carlo samples of the allele substitution effects, genomic (co)variances were calculated on a whole-genome level, per chromosome, and in regions of 100 SNP on a chromosome.ResultsGenomic proportions of the total variance differed between traits. Genomic correlations were lower than pedigree-based genetic correlations and they were highest between general mastitis and pathogen-specific traits because of the part-whole relationship between these traits. The chromosome-wise genomic proportions of the total variance differed between traits, with some chromosomes explaining higher or lower values than expected in relation to chromosome size. Few chromosomes showed pleiotropic effects and only chromosome 19 had a clear effect on all traits, indicating the presence of QTL with a general effect on mastitis resistance. The region-wise patterns of genomic variances differed between traits. Peaks indicating QTL were identified but were not very distinctive because a common prior for the marker effects was used. There was a clear difference in the region-wise patterns of genomic correlation among combinations of traits, with distinctive peaks indicating the presence of pleiotropic QTL.ConclusionsThe results show that it is possible to estimate, genome-wide and region-wise genomic (co)variances of mastitis resistance traits in dairy cattle using multivariate genomic models.

Investigation of candidate regions influencing litter size in Danish Landrace sows.

Selection for increased litter size has been one of the main objectives in Danish pig breeding since 1992. This selection has led to an average increase of 0.30 piglets/litter per year for Landrace and Yorkshire sows, resulting in an average litter size of 15.3 piglets born alive in 2007, with an SD of 3.5 piglets. The objective of this study was to investigate differences in identity by state relationships and allele effects associated with litter size across 17 selected microsatellite marker positions on chromosomes 11, 13, and 15. For this purpose, 357 Danish Landrace sows with high and low EBV for litter size were genotyped. An assignment test showed that 91 and 90% of the sows could be assigned correctly to the group of sows representing high and low EBV, respectively, based on genotype information. Allele effects were estimated separately for each marker by using deregressed EBV and a linear model that include both a polygenic and an allele effect. The investigated region on chromosome 13 was found to have a greater average identity by state relationship compared with the other regions, indicating that selection has taken place in this region. This is supported by an increased average allele effect of microsatellite alleles in the region. In spite of the apparent increased historical selection pressure on chromosome 13, fairly large variation in allele effects was observed, indicating that the markers within the region may be used for marker-assisted selection. However, substantial variation in allele effects was observed for several markers on all 3 investigated chromosomes, indicating that selection should preferably be based on several markers.

Haplotypes on pig chromosome 3 distinguish metabolically healthy from unhealthy obese individuals

We have established a pig resource population specifically designed to elucidate the genetics involved in development of obesity and obesity related co-morbidities by crossing the obesity prone Göttingen Minipig breed with two lean production pig breeds. In this study we have performed genome wide association (GWA) to identify loci with effect on blood lipid levels. The most significantly associated single nucleotide polymorphisms (SNPs) were used for linkage disequilibrium (LD) and haplotype analyses. Three separate haploblocks which influence the ratio between high density lipoprotein cholesterol and total cholesterol (HDL-C/CT), triglycerides (TG) and low density lipoprotein cholesterol (LDL-C) levels respectively were identified on Sus Scrofa chromosome 3 (SSC3). Large additive genetic effects were found for the HDL-C/CT and LDL-C haplotypes. Haplotypes segregating from Göttingen Minipigs were shown to impose a positive effect on blood lipid levels. Thus, the genetic profile of the Göttingen Minipig breed seems to support a phenotype comparable to the metabolic healthy obese (MHO) phenotype in humans.