Naomi Duijvesteijn

Wageningen University, Wageningen, Gelderland, Netherlands

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Publications (26)34.67 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: We performed a GWAS in order to identify SNPs associated with sperm motility.•A second objective was to find possible candidate genes underling the QTL regions.•We studied two different commercial pig populations (L1 and L2).•For L2, six significant SNPs associated with sperm motility were identified.•The MTFMT gene was selected as a candidate gene in the QTL region.
    Animal Reproduction Science. 10/2014;
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    Frontiers in Genetics 10/2014;
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    ABSTRACT: Pigs may display biting behavior directed at pen mates, resulting in body damage such as tail wounds. We assessed the suitability of jute sacks (hung vertically at wall) to reduce biting behaviors and tail wounds in rearing gilts. Additionally, we assessed several characteristics of different types of tail biters. Tail docked rearing gilts originated from 72 litters, which were kept in partly slatted pens with jute sacks (J) or barren control pens (C) (36 litters per treatment). Tail and ear damage were observed at weaning (4 weeks), and during the weaner and rearing phase (17 J and 19 C pens). Also sow (dam) damage was considered. Biting behaviors (tail, ear and other) were observed during the weaner and rearing phase. Weight was recorded at birth, weaning and end of the weaner phase, and average daily gain was calculated from birth till weaning and from weaning till 9 weeks. Furthermore, estimated breeding values for litter size, litter birth weight, back fat, and growth between birth and ±105 kg, and ±25-105 kg were determined. Jute sacks reduced tail and ear damage at weaning (both P < 0.001) and tended to reduce sow tail damage (P = 0.09). Jute sacks also reduced tail damage post-weaning (P < 0.001-0.03), with a five-fold reduction of (mild) tail wounds at the age of 13 weeks. Biting behaviors directed at pen mates were up to 50 % lower in J pens (P < 0.001-0.04). Higher genotypic litter size, litter birth weight, and growth, and lower back fat seemed associated with higher levels of ear or tail biting behavior (P = 0.002-0.09), albeit dependent on treatment and phase. Higher phenotypic litter sizes were associated with higher levels of biting behaviors (P = 0.004-0.08). High-tail biters and Medium-tail biters (the latter less pronounced) stemmed from larger litters (P = 0.01-0.05), were heavier (P = 0.03-0.04), grew faster (P = 0.05-0.08) and displayed higher levels of all kinds of biting behavior directed to pen mates and the jute sack (P < 0.001-0.10) compared with Non-tail biters, the effect size dependent on treatment and phase of life. To conclude, jute sacks may profoundly reduce damaging behaviors and tail wounds in rearing gilts, probably because they partly meet the behavioral need of pigs for rooting and chewing. Furthermore, (tail) biting is associated with production level of the gilts (phenotypically and genetically) which suggests a role for breeding programs, and additional research focusing on metabolic demands of (tail) biting pigs.
    Journal of animal science. 09/2014;
  • N Duijvesteijn, E F Knol, P Bijma
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    ABSTRACT: Androstenone is one of the compounds causing boar taint of pork, and is highly heritable (∼0.6). Recently, indirect genetic effects (IGEs, also known as associative effects or social genetic effects) were found for androstenone, meaning that pen mates (boars) affect each other's androstenone level genetically. Similar to estimating variance components with a direct-indirect animal model, direct and indirect genetic SNP effects can be estimated for androstenone. This study aims to detect SNPs with significant direct and indirect genetic effects on androstenone. The dataset consisted of 1,282 non-castrated boars (993 boars genotyped), from 184 groups of pen members. After quality control, 46,421 SNPs were included in the analysis. One model for single-SNP regression was fitted, where both the direct SNP-effect of the individual itself and the indirect SNP-effects of its pen mates were included. None of the SNPs (direct or indirect) were found genome-wide significant. One QTL on SSC6 was chromosome-wide significant for the direct effect. A single SNP on SSC9 and two regions and a single SNP on SSC14 were found for the indirect effect. A backwards elimination method and haplotype analysis were used to quantify the variance explained by the SNPs. The backwards elimination method identified four independent regions affecting androstenone. The QTL on SSC6 explained 2.1% and 2.6% of the phenotypic variance using the backwards elimination method or the haplotype analysis. The QTLs on SSC14 explained 3.4% and 2.7% of the phenotypic variance using the backwards eliminations method or the haplotype analysis. The single association on SSC9 explained 2.2% of the phenotypic variance. All significant QTL together explained 7-8% of phenotypic variance, and 40-44% of the total genetic variance available for response to selection. Besides the newly discovered QTL and the confirmation of known QTL, this study also presents a methodology to model SNPs for indirect genetic effects.
    Journal of animal science. 08/2014;
  • Naomi Duijvesteijn, Egbert F. Knol, Piter Bijma
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    ABSTRACT: Abstract Text: Accurate modeling of average daily gain (ADG) can contribute to a better response to selection for feed efficiency in pigs. Inclusion of indirect genetic effects (IGE) has been found to attribute to the heritable variance of this trait. A validation by predicting performance of young animals, has not been performed before. Genetic evaluations using purebred data (sire line S1 and S2) for ADG using an indirect genetic model were performed. Predicted breeding values by removing phenotypes of young animals (classical model vs IGE model) were correlated to corrected phenotypes. Models including IGE had a higher correlation (0.24 compared to 0.22) and the average accuracy of the breeding value was higher (0.52 compared to 0.48). These results illustrate the usefulness of implementation of IGE in pig breeding programs for ADG when sufficient phenotypes have been collected (in this study ~80,000). Keywords: pig; indirect genetic effects; average daily gain
    10th World Congress on Genetics Applied to Livestock Production; 08/2014
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    ABSTRACT: Abstract Text: Selection on indirect genetic effects for production traits may contribute to selection response, but validation through selection experiments is required. Our objective was to determine the consequences of selection for ‘IGE on growth rate’ (IGEg) on production traits and behavior of pigs. Sires (n=24) and dams (n=64) were selected to create a high vs. low contrast for IGEg in the offspring (n=480). The contrast was 2.8 g average daily gain (ADG) per group mate. Offspring were studied in a 2×2 arrangement with IGEg (high/low) and housing conditions (conventional/enriched) to examine genotype-by-environment interactions. Selection did not alter production traits, including ADG. Behavior showed consistent changes, whereby high IGEg pigs showed less biting behavior towards group mates and objects. There were no G×E interactions, but enrichment had a positive additive effect to selection. Despite the lack of response in ADG, behavior improved. Keywords: indirect genetic effect; behaviour; pigs
    10th World Congress on Genetics Applied to Livestock Production; 08/2014
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    ABSTRACT: The objective of this work was to evaluate the efficiency of the supervised independent component regression (SICR) method for the estimation of genomic values and the SNP marker effects for boar taint and carcass traits in pigs. The methods were evaluated via the agreement between the predicted genetic values and the corrected phenotypes observed by cross-validation. These values were also compared with other methods generally used for the same purposes, such as RR-BLUP, SPCR, SPLS, ICR, PCR and PLS. The SICR method was found to have the most accurate prediction values.
    Journal of Animal Breeding and Genetics 07/2014; · 1.65 Impact Factor
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    ABSTRACT: Selection pressure on the number of teats has been applied to be able to provide enough teats for the increase in litter size in pigs. Although many QTL were reported, they cover large chromosomal regions and the functional mutations and their underlying biological mechanisms have not yet been identified. To gain a better insight in the genetic architecture of the trait number of teats, we performed a genome-wide association study by genotyping 936 Large White pigs using the Illumina PorcineSNP60 Beadchip. The analysis is based on deregressed breeding values to account for the dense family structure and a Bayesian approach for estimation of the SNP effects.
    BMC genomics. 06/2014; 15(1):542.
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    ABSTRACT: Production traits such as growth rate may depend on the social interactions between group members. These social interactions might be partly heritable and are referred to as indirect genetic effects (IGE), social-, associative-, or competitive genetic effects. IGE may contribute to heritable variation in traits, and can thus be used to increase the response to selection. This, however, has hardly been tested by selection experiments. Our objective was to determine the effects of one generation of selection on IGE for growth (IGEg) in pigs on ADG, BW, ADFI, feed efficiency, and post-mortem measurements. Sires (n=24) and dams (n=64) were selected to create a high vs. low contrast for IGEg in the offspring (n=480). The IGE difference was 2.8 g ADG per pen mate, corresponding to 14 g higher ADG in high IGEg offspring compared to low IGEg offspring when housed in groups of 6 (i.e. (6-1)×2.8 = 14). Male (barrows) and female (gilts) offspring were housed in groups of 6 of the same IGEg classification, in either barren concrete pens or pen enriched with straw and wood shavings (n=80 pens). Pigs were followed from birth to slaughter. Data were analyzed in a mixed model with pen as random factor. There was no difference in ADG between high and low IGEg pigs during the finishing period (wk 10 to 23). Opposite to expectations, high IGEg tended to have a 17 g lower ADG from weaning to slaughter (P=0.08), which was caused by a higher BW of low IGEg pigs in wk 5 (P=0.008). This led to a 2.3 kg lower carcass weight (P=0.02) and 2.2 mm less muscle depth for high IGEg pigs (P=0.03). High IGEg pigs had a higher stomach wall damage score (P=0.01). Pigs on straw had a 25 g lower ADG during finishing (P=0.03), and less stomach wall damage (P<0.001). Fewer interventions against harmful behavior were required in high IGEg pigs. The unexpected results regarding IGEg may be due to several reasons. Despite initial power calculations showing good power, the IGEg contrast between groups may have been too small. Moreover, measures that were taken to limit harmful behavior may have had a substantial role. Harmful behavior such as tail biting may affect ADG and might underlie the effects of selection on IGEg in pigs. Research under commercial circumstances, where harmful behavior is likely to be more profound, may give more accurate insight into the benefits of selecting for IGEg.
    Journal of Animal Science 03/2014; · 2.09 Impact Factor
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    ABSTRACT: Animal welfare in pig production is frequently a topic of debate and is sensitive in nature. This debate is partly due to differences in values, forms, convictions, interests and knowledge among the stakeholders that constitute differences among their frames of reference with respect to pigs and their welfare. Differences in frames of reference by stakeholder groups are studied widely, but not specifically with respect to animal behaviour or welfare. We explored this phenomenon using a qualitative behaviour assessment (QBA). Participating stakeholders were classified into two expert groups consisting of pig farmers (N = 11) and animal scientists (N = 18) and a lay-group consisting of urban citizens (N = 15). The stakeholders were asked to observe the behaviour of a specific pig in each of the nine videos and to assign a score for each video using 21 predefined terms describing the mood, such as ‘happy’ or ‘irritated’. They were asked to complete two additional questionnaires to obtain information on their frames of reference. Results from the QBA showed that the pig farmers observed the behaviour of pigs more positively than the urban citizens and the animal scientists. This was evident from the consistently higher scores on the positive terms to assess pig behaviour. The questionnaires revealed that the farmers had a different frames of reference regarding pigs and different understanding of welfare, which might explain the differences in assessment. In a follow-up stakeholder workshop, which focussed on differences in observation, QBA showed to be an effective tool to stimulate mutual learning among stakeholders, which is necessary to find shared solutions.
    Journal of Agricultural and Environmental Ethics 01/2014; · 1.30 Impact Factor
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    ABSTRACT: The independent domestication of local wild boar populations in Asia and Europe about 10,000 years ago led to distinct European and Asian pig breeds, each with very different phenotypic characteristics. During the Industrial Revolution, Chinese breeds were imported to Europe to improve commercial traits in European breeds. Here we demonstrate the presence of introgressed Asian haplotypes in European domestic pigs and selection signatures on some loci in these regions, using whole genome sequence data. The introgression signatures are widespread and the Asian haplotypes are rarely fixed. The Asian introgressed haplotypes are associated with regions harbouring genes involved in meat quality, development and fertility. We identify Asian-derived non-synonymous mutations in the AHR gene that associate with increased litter size in multiple European commercial lines. These findings demonstrate that increased fertility was an important breeding goal for early nineteenth century pig farmers, and that Asian variants of genes related to this trait were preferentially selected during the development of modern European pig breeds.
    Nature Communications 01/2014; 5:4392. · 10.74 Impact Factor
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    ABSTRACT: Traditional breeding programs consider an average pairwise kinship between sibs. Based on pedigree information, the relationship matrix is used for genetic evaluations disregarding variation due to Mendelian sampling. Therefore, inbreeding and kinship coefficients are either over or underestimated resulting in reduction of accuracy of genetic evaluations and genetic progress. Single nucleotide polymorphism (SNPs) can be used to estimate pairwise kinship and individual inbreeding more accurately. The aim of this study was to optimize the selection of markers and determine the required number of SNPs for estimation of kinship and inbreeding. A total of 1,565 animals from three commercial pig populations were analyzed for 28,740 SNPs from the PorcineSNP60 Beadchip. Mean genomic inbreeding was higher than pedigree-based estimates in lines 2 and 3, but lower in line 1. As expected, a larger variation of genomic kinship estimates was observed for half and full sibs than for pedigree-based kinship reflecting Mendelian sampling. Genomic kinship between father-offspring pairs was lower (0.23) than the estimate based on pedigree (0.26). Bootstrap analyses using six reduced SNP panels (n=500, 1000, 1500, 2000, 2500 and 3000) showed that 2,000 SNPs were able to reproduce the results very close to those obtained using the full set of unlinked markers (n=7,984-10,235) with high correlations (inbreeding r>0.82 and kinship r>0.96) and low variation between different sets with the same number of SNPs. Variation of kinship between sibs due to Mendelian sampling is better captured using genomic information than the pedigree-based method. Therefore, the reduced sets of SNPs could generate more accurate kinship coefficients between sibs than the pedigree-based method. Variation of genomic kinship of father-offspring pairs is recommended as a parameter to determine accuracy of the method rather than correlation with pedigree-based estimates. Inbreeding and kinship coefficients can be estimated with high accuracy using >=2,000 unlinked SNPs within all three commercial pig lines evaluated. However, a larger number of SNPs might be necessary in other populations or across lines.
    BMC Genetics 09/2013; 14(1):92. · 2.81 Impact Factor
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    ABSTRACT: Pigs housed together in a group influence each other's growth. Part of this effect is genetic and can be represented in a social breeding value. It is unknown, however, which traits are associated with social breeding values. The aim of this study was, therefore, to investigate whether personality and response to novelty could be associated with social breeding values for growth in piglets. Female and castrated male piglets from 80 litters with either an estimated relative positive or negative social breeding value (+SBV or -SBV) for growth were tested individually in a backtest and a novel environment test, and group-wise in a novel object (i.e. a feeder with feed) test and a human approach test. All tests were carried out during the suckling period. No differences between +SBV and -SBV piglets were found for the frequency and latency of struggling and vocalizing in the backtest (at least, P > 0.30). In the novel object test, piglets with a +SBV for growth touched the feeder faster than piglets with a -SBV for growth (P = 0.01) and were more frequently present near the person in the human approach test (P < 0.01). No behavioral differences between +SBV and -SBV piglets were found in the novel environment test (at least, P > 0.40), but piglets that struggled more in the backtest walked more in this test (P = 0.02). Behavior was affected by gender in each test. Female piglets were faster than castrated male piglets to start struggling in the backtest (P = 0.047). In the novel object test, females were faster than males to touch the feeder and to sample the feed and in the human approach test they were also faster than male piglets to touch a person (all, P < 0.001). Females were also more frequently present near the feeder (P < 0.001) and the person (P = 0.03). In the novel environment test, female piglets explored the floor more (P = 0.046), produced less low- (P = 0.04) and high-pitched vocalizations (P = 0.02), and defecated (P = 0.08) and urinated less than male piglets (P < 0.01). It was concluded that +SBV and -SBV piglets do not differ in their response to the backtest and only subtle differences were found in their response to novelty. More research is warranted to identify the traits underlying SBV for growth in pigs. Moreover, castrated male piglets seemed to react more fearfully to each test than female piglets.
    Journal of Animal Science 08/2013; · 2.09 Impact Factor
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    Naomi Duijvesteijn, Egbert F Knol, Piter Bijma
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    ABSTRACT: Background / Purpose: Androstenone is a pheromone that attracts sows, but can also result in boar taint (the off-flavour of pork) when boars are not castrated. This study examined whether indirect genetic effects (where the phenotype of an animal is affected by the genotype of another) influence androstenone excretion. We also investigated whether any of the direct and indirect genetic effects in the genome could be located using a 60k SNPchip. Main conclusion: Indirect effects were present, though the contribution was relatively small. We found known and unknown regions on the genome that are associated with the direct and indirect genetic effects on androstenone excretion.
    4th International Conference of Quantitative Genetics 2012: Understanding Variation in Complex Traits; 08/2012
  • N Duijvesteijn, E F Knol, P Bijma
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    ABSTRACT: In the pig industry, male piglets are surgically castrated early in life to prevent boar taint. Boar taint is mainly caused by androstenone and skatole. Androstenone is a pheromone that can be released from the salivary glands when the boar is sexually aroused. Boars are housed in groups and as a consequence boars can influence and be influenced by the phenotype of other boars by (non-)heritable social interactions. The influence of these social interactions on androstenone is not well understood. The objective of this study is to investigate whether androstenone concentrations are affected by (non-)heritable social interactions and estimate their genetic correlation with growth rate and backfat. The dataset contained 6,245 boars, of which 4,455 had androstenone observations (68%). The average number of animals per pen was 7 and boars were housed in 899 unique pen-groups (boars within a single pen) and 344 unique compartment-groups (boars within a unique 'room' within a barn during time). Four models including different random effects, were compared for androstenone. Direct genetic, associative (also known as social genetic or indirect genetic effects), group, compartment, common environment and residual effects were included as random effects in the full model (M3). Including random pen and compartment effects (non-heritable social effects) significantly improved the model (M2) compared with including only direct, common environment and residual as random effects (M1, P < 0.001), and including associative effects even more (M3, P < 0.001). The sum of the direct and associative variance components determines the total genetic variance of the trait. The associative effect explained 11.7% of the total genetic variance. Backfat thickness was analysed using M2 and growth using M3. The genetic correlation between backfat (direct genetic variance) and total genetic variance for androstenone was close to 0. Backfat and the direct and associative effects for androstenone had genetic correlations of 0.14 ± 0.08 and -0.25 ± 0.18, respectively. The genetic correlation between total genetic variances for growth rate and androstenone was 0.33 ± 0.18. The genetic correlation between direct effects was 0.11 ± 0.09 and between associative effects was 0.42 ± 0.31. The genetic correlations and current selection towards lower backfat and greater growth rate suggest that no major change in androstenone is expected when breeding goals are not changed. For selection against boar taint and therefore also against androstenone , results recommend that at least the social environment of the boars should be considered.
    Journal of Animal Science 02/2012; 90(8):2465-75. · 2.09 Impact Factor
  • Duijvesteijn N, Knol EF, Bijma P
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    ABSTRACT: In the pig industry, male piglets are surgically castrated early in life to prevent boar taint. Boar taint is mainly caused by androstenone and skatole. Androstenone (AND) is a pheromone that can be released from the salivary glands when the boar is sexually aroused. Boars are housed in groups and as a consequence boars can influence each other's phenotype by social interactions ((non-)heritable). The influence of these social interactions on AND are not well understood. The objective of this study is to investigate whether AND levels are affected by (non-) heritable social interactions and estimate its genetic correlation with growth rate and backfat. The dataset contained 6,245 boars, of which 4,455 had AND observations (68%). The average pen size was 7 and boars were housed in 899 unique pen-groups (boars within a single pen) and 344 unique compartment-groups (boars within a unique 'room' within a barn during time). Four models including different random effects were compared for AND. As random effects, direct genetic, associative (also known as social genetic or indirect genetic effects), group, compartment, common environment and residual effects were included in the full model (M3). Including random pen and compartment effects (M2) (non-heritable social effects) significantly improved the model compared to including only direct, common environment and residual as random effects (M1, p<0.001), and including associative effects even more (M3, p<0.001). The sum of the direct and associative variance components determines the total genetic variance of the trait. The associative effect explained 11.7% of the total genetic variance. Backfat thickness was analysed using M2 and growth using M3. The genetic correlation between backfat (direct genetic variance) and total genetic variance for AND was close to zero. Backfat and the direct and associative effects for AND had genetic correlations of 0.14±0.08 and -0.25±0.18, respectively. The genetic correlation between total genetic variances for growth rate and AND was 0.33±0.18. The genetic correlation between direct effects was 0.11±0.09 and between associative effects was 0.42±0.31. The genetic correlations and current selection towards lower backfat and higher growth rate, suggest that no major change in AND is expected when breeding goals are not changed. For selection against boar taint and therefore also against AND, results recommend that at least the social environment of the boars should be considered.
    Journal of Animal Science 02/2012; · 2.09 Impact Factor
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    ABSTRACT: Boar taint is an unpleasant condition of pork, mainly due to the accumulation of androstenone and skatole in male pigs at onset of puberty. This condition is the cause of considerable economic losses in the pig industry and the most common practice to control it is to castrate male piglets. Because of the economic and animal welfare concerns there is interest in developing genetic markers that could be used in selection schemes to decrease the incidence of boar taint. The Porcine 60 K SNP Beadchip was used to genotype 891 pigs from a composite Duroc sire line, for which skatole levels in fat had been collected. The genome-wide association study revealed that 16 SNPs (single nucleotide polymorphisms) located on the proximal region of chromosome 6 were significantly associated with skatole levels. These SNPs are grouped in three separate clusters located in the initial 6 Mb region of chromosome 6. The differences observed between the homozygote genotypes for SNPs in the three clusters were substantial, including a difference of 102.8 ng/g skatole in melted fat between the homozygotes for the ALGA0107039 marker. Single SNPs explain up to 22% of the phenotypic variance. No obvious candidate genes could be pinpointed in the region, which may be due to the need of further annotation of the pig genome. This study demonstrated new SNP markers significantly associated with skatole levels in the distal region of chromosome 6p. These markers defined three independent clusters in the region, which contain a low number of protein-coding genes. The considerable differences observed between the homozygous genotypes for several SNPs may be used in future selection schemes to reduce skatole levels in pigs.
    BMC Genetics 01/2011; 12:35. · 2.81 Impact Factor
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    ABSTRACT: In animal breeding, recording of correct pedigrees is essential to achieve genetic progress. Markers on DNA are useful to verify the on-farm pedigree records (parental verification) but can also be used to assign parents retrospectively (parental identification). This approach could reduce the costs of recording for traits with low incidence, such as those related to diseases or mortality. In this study, SNP were used to assign the true sires of 368 purebred animals from a Duroc-based sire line and 140 crossbred offspring from a commercial pig population. Some of the sires were closely related. There were 3 full sibs and 17 half sibs among the true fathers and 4 full sibs and 35 half sibs among all putative fathers. To define the number of SNP necessary, 5 SNP panels (40, 60, 80, 100, and 120 SNP) were assembled from the Illumina PorcineSNP60 Beadchip (Illumina, San Diego, CA) based on minor allele frequency (>0.3), high genotyping call rate (≥90%), and equal spacing across the genome. For paternal identification considering only the 66 true sires in the data set, 60 SNP resulted in 100% correct assignment of the sire. By including additional putative sires (n = 304), 80 SNP were sufficient for 100% correct assignment of the sire. The following criteria were derived to identify the correct sire for the current data set: the logarithm of odds (LOD) score for assigning the correct sire was ≥5, the number of mismatches was ≤1, and the difference in the LOD score between the first and the second most likely sire was >5. If the correct sire was not present among all putative sires, the mean LOD for the most likely sire was close to zero or negative when using 100 SNP. More SNP would be needed for paternal identification if the number of putative sires increased and the degree of relatedness was greater than in the data set used here. The threshold for the number of mismatches can be adjusted according to the practical situation to account for the trade-off between false negatives and false positives. The latter can be avoided efficiently, ensuring that the correct father is being sampled. Nevertheless, a restriction on the number of putative sires is advisable to reduce the risk of assigning close relatives.
    Journal of Animal Science 01/2011; 89(6):1661-8. · 2.09 Impact Factor
  • A C Bouwman, R Bergsma, N Duijvesteijn, P Bijma
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    ABSTRACT: The aim of this study was to investigate whether there is heritable social variation in ADG from birth until weaning in piglets. Nursing and the establishment of teat order are sources of social interaction among suckling piglets nursed by the same sow. If a heritable social effect is present, but ignored, the selected animals might be the most competitive ones with negative effects on growth of their group mates, resulting in less response to selection than expected. The social interaction model was extended with a maternal component to estimate genetic maternal and social effects. Four different animal models were compared: a basic model with a direct heritable effect only; a social model accounting for direct and social heritable effects; a maternal model with a heritable maternal effect in addition to the basic model; and a social-maternal model accounting for direct, social, and maternal heritable effects. Estimates of direct, maternal, and social heritability were 0.07, 0.06, and around 0.0007 (not significantly different from zero, SE = 0.0005), respectively. Total heritable variance, including direct, social, and maternal heritable variance and their covariances ranged from 0.07 to 0.15 of the phenotypic variation. Both maternal models were significantly better than equivalent nonmaternal models (P <or= 0.005). The social model was not significantly better than the basic model (P = 0.102), and the social-maternal model was also not significantly better than the maternal model (P = 0.486). There was no evidence for heritable social effects among piglets in a group. The generally used maternal model fit the data as well as the social-maternal model. Sufficient cross-fostering is needed to partition social and maternal variation.
    Journal of Animal Science 09/2010; 88(9):2883-92. · 2.09 Impact Factor
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    ABSTRACT: In many countries, male piglets are castrated shortly after birth because a proportion of un-castrated male pigs produce meat with an unpleasant flavour and odour. Main compounds of boar taint are androstenone and skatole. The aim of this high-density genome-wide association study was to identify single nucleotide polymorphisms (SNPs) associated with androstenone levels in a commercial sire line of pigs. The identification of major genetic effects causing boar taint would accelerate the reduction of boar taint through breeding to finally eliminate the need for castration. The Illumina Porcine 60K+SNP Beadchip was genotyped on 987 pigs divergent for androstenone concentration from a commercial Duroc-based sire line. The association analysis with 47,897 SNPs revealed that androstenone levels in fat tissue were significantly affected by 37 SNPs on pig chromosomes SSC1 and SSC6. Among them, the 5 most significant SNPs explained together 13.7% of the genetic variance in androstenone. On SSC6, a larger region of 10 Mb was shown to be associated with androstenone covering several candidate genes potentially involved in the synthesis and metabolism of androgens. Besides known candidate genes, such as cytochrome P450 A19 (CYP2A19), sulfotransferases SULT2A1, and SULT2B1, also new members of the cytochrome P450 CYP2 gene subfamilies and of the hydroxysteroid-dehydrogenases (HSD17B14) were found. In addition, the gene encoding the ss-chain of the luteinizing hormone (LHB) which induces steroid synthesis in the Leydig cells of the testis at onset of puberty maps to this area on SSC6. Interestingly, the gene encoding the alpha-chain of LH is also located in one of the highly significant areas on SSC1. This study reveals several areas of the genome at high resolution responsible for variation of androstenone levels in intact boars. Major genetic factors on SSC1 and SSC6 showing moderate to large effects on androstenone concentration were identified in this commercial breeding line of pigs. Known and new candidate genes cluster especially on SSC6. For one of the most significant SNP variants, the difference in the proportion of animals surpassing the threshold of consumer acceptance between the two homozygous genotypes was as much as 15.6%.
    BMC Genetics 01/2010; 11:42. · 2.81 Impact Factor

Publication Stats

63 Citations
34.67 Total Impact Points

Institutions

  • 2010–2014
    • Wageningen University
      • Animal Breeding and Genomics Centre
      Wageningen, Gelderland, Netherlands
  • 2010–2012
    • Institute for Pig Genetics (IPG)
      Beuningen, Gelderland, Netherlands