Limits...
Using SNP array data to test for host genetic and breed effects on Porcine Reproductive and Respiratory Syndrome Viremia.

Biffani S, Botti S, Bishop SC, Stella A, Giuffra E - BMC Proc (2011)

Bottom Line: Breed-clusters were defined using the matrix of genomic kinship between all pairs of piglets.Only the contemporary group effect, defined as all piglets reared in the same herd, in the same year and whose samples were collected in the same season, was significant.Incomplete exposure over the observed period may have masked possible breed differences.

View Article: PubMed Central - HTML - PubMed

Affiliation: Parco Tecnologico Padano-Loc, Cascina Codazza, Via A, Einstein, 26900 Lodi Italy. stefano.biffani@tecnoparco.org.

ABSTRACT

Background: The effect of breed on Porcine Reproductive and Respiratory Syndrome Viremia (PRRSV) was tested using data collected in 17 Italian commercial pig farms and 1096 genotypes obtained by the PorcineSNP60 BeadChip. A binomial logistic model was used to investigate the relationship between breed-clusters and PRRSV susceptibility. Breed-clusters were defined using the matrix of genomic kinship between all pairs of piglets.

Results: Only the contemporary group effect, defined as all piglets reared in the same herd, in the same year and whose samples were collected in the same season, was significant. Sex, age and breed-cluster showed no statistically significant effect on PRRS viremia, although the Landrace and Cross breed-clusters showed the lowest Odds-Ratio

Conclusions: The model failed to detect a significant breed-cluster effect, highlighting the impact of environment and management on PRRS viremia incidence. Incomplete exposure over the observed period may have masked possible breed differences.

No MeSH data available.


Related in: MedlinePlus

Multidimensional Scaling Plot – Breed Clustering
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Figure 1: Multidimensional Scaling Plot – Breed Clustering

Mentions: Breed-clusters as a result of "a posteriori" definition based on Kinship analysis are plotted in Figure 1. Each point represents a piglet. As expected, using SNP information, four main clusters can be identified. Those clusters matched with the expected breed, defined by the time of field data recording. However, an additional cluster (cluster 4) can be identified between cluster 1 (Large White) and cluster 5 (Duroc ). Those animals are possibly the result of cross-breeding. Indeed, they belong to farms where both breeds (i.e, Large White and Duroc) were present and where artificial insemination was used. Our hypothesis is that some inconsistencies occurred during the insemination events, i.e. that a limited number of boars was associated to the wrong insemination. According to the breed-cluster classification (Table 2), the observed proportion of affected piglets ranges from 34% (Landrace – Cluster 3) to 52% (Pietrain – Cluster 2). Results from Type III test of fixed effects are shown in table 3. Only the Herd-Year-Season effect (contemporary group) is significant. Sex, age and breed-cluster show no statistically significant effect on PRRS viremia, although the Landrace and Cross clusters show the lowest Odds-Ratio (not shown). Results on breed-cluster effect are contradictory. Some studies reported the existence of differences in susceptibility among breeds [9,10]. Nevertheless, most of those studies were based on in vitro or in vivo experiments, used commercial data from few large farms or analyzed different phenotypes. The present study spanned a 3-year period and used data collected from 17 farms. As Cooper et al. [11] observed, data under controlled experimental conditions do not necessarily support field reports. Physical and environmental factors may affect the immune system and hence determine or change the host response. This is exactly what our results suggest, because the contemporary group effect tries to capture the combined effect of environment and management removing variation due to their conditions over time. Previous findings from MISAGEN data [12] do show the existence of genetic variation but no breed effect. In this case breed was not defined by Kinship analysis. Bishop and Woolliams [13] showed how incomplete exposure to infection can reduce the power of datasets. This is the case of the present study, where records were collected in commercial farms spanning a 3-year period. As can be observed in Figure 2 incidence varies from a minimum of 27 % (September – December 2007) to a maximum of 80 % (September – December 2008).


Using SNP array data to test for host genetic and breed effects on Porcine Reproductive and Respiratory Syndrome Viremia.

Biffani S, Botti S, Bishop SC, Stella A, Giuffra E - BMC Proc (2011)

Multidimensional Scaling Plot – Breed Clustering
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3108223&req=5

Figure 1: Multidimensional Scaling Plot – Breed Clustering
Mentions: Breed-clusters as a result of "a posteriori" definition based on Kinship analysis are plotted in Figure 1. Each point represents a piglet. As expected, using SNP information, four main clusters can be identified. Those clusters matched with the expected breed, defined by the time of field data recording. However, an additional cluster (cluster 4) can be identified between cluster 1 (Large White) and cluster 5 (Duroc ). Those animals are possibly the result of cross-breeding. Indeed, they belong to farms where both breeds (i.e, Large White and Duroc) were present and where artificial insemination was used. Our hypothesis is that some inconsistencies occurred during the insemination events, i.e. that a limited number of boars was associated to the wrong insemination. According to the breed-cluster classification (Table 2), the observed proportion of affected piglets ranges from 34% (Landrace – Cluster 3) to 52% (Pietrain – Cluster 2). Results from Type III test of fixed effects are shown in table 3. Only the Herd-Year-Season effect (contemporary group) is significant. Sex, age and breed-cluster show no statistically significant effect on PRRS viremia, although the Landrace and Cross clusters show the lowest Odds-Ratio (not shown). Results on breed-cluster effect are contradictory. Some studies reported the existence of differences in susceptibility among breeds [9,10]. Nevertheless, most of those studies were based on in vitro or in vivo experiments, used commercial data from few large farms or analyzed different phenotypes. The present study spanned a 3-year period and used data collected from 17 farms. As Cooper et al. [11] observed, data under controlled experimental conditions do not necessarily support field reports. Physical and environmental factors may affect the immune system and hence determine or change the host response. This is exactly what our results suggest, because the contemporary group effect tries to capture the combined effect of environment and management removing variation due to their conditions over time. Previous findings from MISAGEN data [12] do show the existence of genetic variation but no breed effect. In this case breed was not defined by Kinship analysis. Bishop and Woolliams [13] showed how incomplete exposure to infection can reduce the power of datasets. This is the case of the present study, where records were collected in commercial farms spanning a 3-year period. As can be observed in Figure 2 incidence varies from a minimum of 27 % (September – December 2007) to a maximum of 80 % (September – December 2008).

Bottom Line: Breed-clusters were defined using the matrix of genomic kinship between all pairs of piglets.Only the contemporary group effect, defined as all piglets reared in the same herd, in the same year and whose samples were collected in the same season, was significant.Incomplete exposure over the observed period may have masked possible breed differences.

View Article: PubMed Central - HTML - PubMed

Affiliation: Parco Tecnologico Padano-Loc, Cascina Codazza, Via A, Einstein, 26900 Lodi Italy. stefano.biffani@tecnoparco.org.

ABSTRACT

Background: The effect of breed on Porcine Reproductive and Respiratory Syndrome Viremia (PRRSV) was tested using data collected in 17 Italian commercial pig farms and 1096 genotypes obtained by the PorcineSNP60 BeadChip. A binomial logistic model was used to investigate the relationship between breed-clusters and PRRSV susceptibility. Breed-clusters were defined using the matrix of genomic kinship between all pairs of piglets.

Results: Only the contemporary group effect, defined as all piglets reared in the same herd, in the same year and whose samples were collected in the same season, was significant. Sex, age and breed-cluster showed no statistically significant effect on PRRS viremia, although the Landrace and Cross breed-clusters showed the lowest Odds-Ratio

Conclusions: The model failed to detect a significant breed-cluster effect, highlighting the impact of environment and management on PRRS viremia incidence. Incomplete exposure over the observed period may have masked possible breed differences.

No MeSH data available.


Related in: MedlinePlus