Abstract
The purpose of this study was to detect significant SNPs for blood components that were related to immunity using high single nucleotide polymorphism (SNP) density panels in a Korean native pig (KNP)×Yorkshire (YK) cross population. A reciprocal design of KNP×YK produced 249 F2 individuals that were genotyped for a total of 46,865 available SNPs in the Illumina porcine 60K beadchip. To perform whole genome association analysis (WGA), phenotypes were regressed on each SNP under a simple linear regression model after adjustment for sex and slaughter age. To set up a significance threshold, 0.1% point-wise p value from F distribution was used for each SNP test. Among the significant SNPs for a trait, the best set of SNP markers were determined using a stepwise regression procedure with the rates of inclusion and exclusion of each SNP out of the model at 0.001 level. A total of 54 SNPs were detected; 10, 6, 4, 4, 5, 4, 5, 10, and 6 SNPs for neutrophil, lymphocyte, monocyte, eosinophil, basophil, atypical lymph, immunoglobulin, insulin, and insulin-like growth factor-I, respectively. Each set of significant SNPs per trait explained 24 to 42% of phenotypic variance. Several pleiotropic SNPs were detected on SSCs 4, 13, 14 and 15.
Highlights
The purpose of this study was to detect significant SNPs for blood components that were related to immunity using high single nucleotide polymorphism (SNP) density panels in a Korean native pig (KNP) Yorkshire (YK) cross population
Animals and phenotypes Data were collected from the quantitative trait loci (QTL) experimental population that was produced by crossing Korean Native (KNP) boars and Yorkshire (YK) sows at National Livestock Research Institute (NLRI), Cheju, Korea
The number of SNPs (6,622) was the greatest in Sus scrofa chromosome (SSC) 1, while SSC12 had the smallest number of SNPs (1,098)
Summary
The purpose of this study was to detect significant SNPs for blood components that were related to immunity using high single nucleotide polymorphism (SNP) density panels in a Korean native pig (KNP) Yorkshire (YK) cross population. Porcine disease resistance, application of biomarkers, e.g. epidemic diarrhea (PED) and porcine reproductive and quantitative trait loci (QTL) or SNPs that are related to respiratory syndrome (PRRS) cause serious damage in pig immune response, can be a good option to avoid damages farms each year. Annual costs for treating epidemics are increasing in pork industry, causing loss of productivity and high reported to find QTL for blood components that were related to immune response using microsatellites or high density SNP panels (Cho et al, 2011; Lu et al, 2011; Reiner et al, 2011).
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