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Genome-wide association and genomic prediction for host response to porcine reproductive and respiratory syndrome virus infection.

Boddicker NJ, Bjorkquist A, Rowland RR, Lunney JK, Reecy JM, Dekkers JC - Genet. Sel. Evol. (2014)

Bottom Line: Apart from the SSC4 region, the regions associated with these two traits each explained less than 3% of the genetic variance.Due to the strong linkage disequilibrium in the SSC4 region, only 19 unique haplotypes were identified across all populations, of which four were associated with the favorable phenotype.Accuracies of EBV based on the SSC4 region were high compared to the rest of the genome.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA. jdekkers@iastate.edu.

ABSTRACT

Background: Host genetics has been shown to play a role in porcine reproductive and respiratory syndrome (PRRS), which is the most economically important disease in the swine industry. A region on Sus scrofa chromosome (SSC) 4 has been previously reported to have a strong association with serum viremia and weight gain in pigs experimentally infected with the PRRS virus (PRRSV). The objective here was to identify haplotypes associated with the favorable phenotype, investigate additional genomic regions associated with host response to PRRSV, and to determine the predictive ability of genomic estimated breeding values (GEBV) based on the SSC4 region and based on the rest of the genome. Phenotypic data and 60 K SNP genotypes from eight trials of ~200 pigs from different commercial crosses were used to address these objectives.

Results: Across the eight trials, heritability estimates were 0.44 and 0.29 for viral load (VL, area under the curve of log-transformed serum viremia from 0 to 21 days post infection) and weight gain to 42 days post infection (WG), respectively. Genomic regions associated with VL were identified on chromosomes 4, X, and 1. Genomic regions associated with WG were identified on chromosomes 4, 5, and 7. Apart from the SSC4 region, the regions associated with these two traits each explained less than 3% of the genetic variance. Due to the strong linkage disequilibrium in the SSC4 region, only 19 unique haplotypes were identified across all populations, of which four were associated with the favorable phenotype. Through cross-validation, accuracies of EBV based on the SSC4 region were high (0.55), while the rest of the genome had little predictive ability across populations (0.09).

Conclusions: Traits associated with response to PRRSV infection in growing pigs are largely controlled by genomic regions with relatively small effects, with the exception of SSC4. Accuracies of EBV based on the SSC4 region were high compared to the rest of the genome. These results show that selection for the SSC4 region could potentially reduce the effects of PRRS in growing pigs, ultimately reducing the economic impact of this disease.

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Linkage disequilibrium (r2) plot of the 1 Mb region on Sus scrofa chromosome 4 across trials 1 through 8. Black squares signify r2 = 100% and white squares signify r2 = 0%.
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Figure 2: Linkage disequilibrium (r2) plot of the 1 Mb region on Sus scrofa chromosome 4 across trials 1 through 8. Black squares signify r2 = 100% and white squares signify r2 = 0%.

Mentions: The region on SSC4 spans 1 284 081 base pairs and includes a total of 38 SNPs that are on the 60 k SNP panel, including two that are fixed and two for which no genotypes were called. Figure 2 shows a LD plot of the 34 polymorphic SNPs across trials 1 through 8. Haploview identified five haplotype blocks, including a block (Block 2) of 15 SNPs that spanned 487 kb that had very high LD amongst most SNPs. This block harbors SNP WUR10000125, which captured over 99% of the effects of the SSC4 region on VL and WG [2]. In general, LD is not expected to be the same between breeds and unrelated populations over such long distances. As an example, Amaral et al. [12] found very different LD patterns between a LW population, Ningxiang (a Chinese breed), and the European wild boar, across three different genomic regions. Differences in LD can result from mutation, recombination, selection, and drift. Block 2 is unique in the sense that LD was very high across six unrelated populations that consisted of different breeds (Figure 2).


Genome-wide association and genomic prediction for host response to porcine reproductive and respiratory syndrome virus infection.

Boddicker NJ, Bjorkquist A, Rowland RR, Lunney JK, Reecy JM, Dekkers JC - Genet. Sel. Evol. (2014)

Linkage disequilibrium (r2) plot of the 1 Mb region on Sus scrofa chromosome 4 across trials 1 through 8. Black squares signify r2 = 100% and white squares signify r2 = 0%.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3974599&req=5

Figure 2: Linkage disequilibrium (r2) plot of the 1 Mb region on Sus scrofa chromosome 4 across trials 1 through 8. Black squares signify r2 = 100% and white squares signify r2 = 0%.
Mentions: The region on SSC4 spans 1 284 081 base pairs and includes a total of 38 SNPs that are on the 60 k SNP panel, including two that are fixed and two for which no genotypes were called. Figure 2 shows a LD plot of the 34 polymorphic SNPs across trials 1 through 8. Haploview identified five haplotype blocks, including a block (Block 2) of 15 SNPs that spanned 487 kb that had very high LD amongst most SNPs. This block harbors SNP WUR10000125, which captured over 99% of the effects of the SSC4 region on VL and WG [2]. In general, LD is not expected to be the same between breeds and unrelated populations over such long distances. As an example, Amaral et al. [12] found very different LD patterns between a LW population, Ningxiang (a Chinese breed), and the European wild boar, across three different genomic regions. Differences in LD can result from mutation, recombination, selection, and drift. Block 2 is unique in the sense that LD was very high across six unrelated populations that consisted of different breeds (Figure 2).

Bottom Line: Apart from the SSC4 region, the regions associated with these two traits each explained less than 3% of the genetic variance.Due to the strong linkage disequilibrium in the SSC4 region, only 19 unique haplotypes were identified across all populations, of which four were associated with the favorable phenotype.Accuracies of EBV based on the SSC4 region were high compared to the rest of the genome.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA. jdekkers@iastate.edu.

ABSTRACT

Background: Host genetics has been shown to play a role in porcine reproductive and respiratory syndrome (PRRS), which is the most economically important disease in the swine industry. A region on Sus scrofa chromosome (SSC) 4 has been previously reported to have a strong association with serum viremia and weight gain in pigs experimentally infected with the PRRS virus (PRRSV). The objective here was to identify haplotypes associated with the favorable phenotype, investigate additional genomic regions associated with host response to PRRSV, and to determine the predictive ability of genomic estimated breeding values (GEBV) based on the SSC4 region and based on the rest of the genome. Phenotypic data and 60 K SNP genotypes from eight trials of ~200 pigs from different commercial crosses were used to address these objectives.

Results: Across the eight trials, heritability estimates were 0.44 and 0.29 for viral load (VL, area under the curve of log-transformed serum viremia from 0 to 21 days post infection) and weight gain to 42 days post infection (WG), respectively. Genomic regions associated with VL were identified on chromosomes 4, X, and 1. Genomic regions associated with WG were identified on chromosomes 4, 5, and 7. Apart from the SSC4 region, the regions associated with these two traits each explained less than 3% of the genetic variance. Due to the strong linkage disequilibrium in the SSC4 region, only 19 unique haplotypes were identified across all populations, of which four were associated with the favorable phenotype. Through cross-validation, accuracies of EBV based on the SSC4 region were high (0.55), while the rest of the genome had little predictive ability across populations (0.09).

Conclusions: Traits associated with response to PRRSV infection in growing pigs are largely controlled by genomic regions with relatively small effects, with the exception of SSC4. Accuracies of EBV based on the SSC4 region were high compared to the rest of the genome. These results show that selection for the SSC4 region could potentially reduce the effects of PRRS in growing pigs, ultimately reducing the economic impact of this disease.

Show MeSH
Related in: MedlinePlus