Using SNP array data to test for host genetic and breed effects on Porcine Reproductive and Respiratory Syndrome Viremia
- Stefano Biffani†1Email author,
- Sara Botti†1,
- Stephen C Bishop2,
- Alessandra Stella1, 3 and
- Elisabetta Giuffra1, 4
© Biffani et al; licensee BioMed Central Ltd. 2011
Published: 3 June 2011
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.
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
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.
Over the last decade the genetics of host susceptibility/resistance to disease has been a major topic of research. For the swine industry PRRS represents one of the most economically important diseases worldwide, causing reproductive failure, abortions, stillbirths, interstitial pneumonia and decreased growth rate . Previous studies investigated the possible role which breed effect may have in determining resistant/susceptibility of pigs to PRRSV. One author  in an experimental “in vivo” study found difference between Duroc, Meishan and Hampshire while two authors [3, 4] with an “in vivo” infection experiment using Large White/Landrace and Hamphshire/Duroc synthetic lines found the former being more resistant to the effects of the virus. Ait-Ali et al studied the innate immune response to PRRSV infection “in vitro”, using used flow cytometry to analyse cells in bronchial alveolar lavage fluid (BALF) from five commercial pig lines. Macrophages from the Landrace line showed significantly reduced virus replication and poor growth of PRRSV than Large White, Pietrain and other two synthetic pig lines. Whilst “in vivo” and “in vitro” experiment can possibly help in dissecting PRRS pathogenesis among breeds, these studies were usually based on relatively small numbers of animals. Moreover, they do not consider environment and management which actually play an important role in the host resistant/susceptibility to PRRSV. Using data collected in commercial pig farms and genotypes obtained by the PorcineSNP60 BeadChip (Illumina, San Diego, CA), the objective of the present study was to cluster animals based on the average similarity among them and to test a possible breed-cluster effect on PRRS viremia.
Number of negative (0) and positive (1) piglets by breed (original dataset)
- call-rate (%) < 99 (if the SNP was available in less than 99% of all genotyped individuals)
- minor allele frequency (MAF) in all individuals < 0.05
Furthermore individuals <99% call rate (maximum percent of missing genotypes in an individual) were eliminated. A total of 14,967 SNPs (24.8%), from the available 60,123 SNPs, were excluded from the case-control analysis if one of the filters indicated a violation of the quality. A total of 77 (0.063%) individuals were excluded: 33 individuals who had low call rates, 3 individuals with too high Identity By State (IBS) and 41 individuals with sex discrepancies. A contemporary group (Herd-Year-Season, HYS) was defined as all piglets reared in the same herd, in the same year and whose samples were collected in the same season. Sampling season was categorized as season 1 (January to April), season 2 (May to August) and season 3 (September to December). Totally, 46 HYS groups were defined whose average size was 9.1. Three breeds were present in twenty HYS (43 %), two breeds in sixteen HYS (35%), four breeds in three HYS (15 %) and only one breed in seven HYS (15 %). A General Linear Mixed Model with a logit link function and binomial distributions was used to investigate the relationship between breed and PRRSV susceptibility using the Glimmix procedure in SAS version 9.1 (SAS Institute Inc., Cary, NC). Breed-clusters were defined using the matrix of genomic kinship between all pairs of piglets computed as:
, where L is the number of loci, pl is the allelic frequency at l-th locus and gl;j is the genotype of j-th individual at the l-th locus, coded as 0, 1=2, and 1, corresponding to the homozygous, heterozygous, and other type of homozygous genotype. Such a matrix was transformed to a distance matrix and the first two principal components were computed by Classical Multidimensional Scaling. The fitted model was: Y ijkl = HYS i + G j + B k + F l + b.age l + e ijkl (1), where Y is the binary trait, HYS is the fixed effect of the ith contemporary group, G is the fixed effect of jth gender class, B is the fixed effect of the kth breed-cluster class, F is the random effect of lth piglet, age is the covariate for age at sampling, with b being the regression coefficient, and e is the random error.
Number of negative (0) and positive (1) piglets by breed-cluster (after SNP editing)
1 (Large White)
Type III text of fixed effects of breed, age, HYS and sex
Pr > F
The idea behind this study was to use SNP to correctly cluster animals based on the average similarity among them and to test a possible breed-cluster effect using a General Linear Mixed model. The model fails to detect a significant breed-cluster effect but highlighted the impact of environment and management on PRRS viremia incidence. Although we cannot formally exclude that incomplete exposure over the observed period may have masked possible breed differences, the genome wide analysis currently in progress could detect a significant genetic variability in host response to PRRSV in the same dataset (Botti, Biffani et al. in preparation).
This study was supported by the MISAGEN project (DG Agriculture of Lombardia Region), the ProZOO project (Cariplo Foundation and DG Agriculture of Lombardia Region ) and SABRE (http://www.sabre-eu.eu, demonstration projects grant (SCAN-IT).
This article has been published as part of BMC Proceedings Volume 5 Supplement 4, 2011: Proceedings of the International Symposium on Animal Genomics for Animal Health (AGAH 2010). The full contents of the supplement are available online at http://www.biomedcentral.com/1753-6561/5?issue=S4.
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