A Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Blood Components (Immunity) in a Cross between Korean Native Pig and Yorkshire
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...
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Asian-Australasian Association of Animal Production Societies
2012-12-01
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doaj-c2900c345873405f8619c6e867027fc22020-11-25T00:50:09ZengAsian-Australasian Association of Animal Production SocietiesAsian-Australasian Journal of Animal Sciences1011-23671976-55172012-12-0125121674168010.5713/ajas.2012.1250322861A Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Blood Components (Immunity) in a Cross between Korean Native Pig and YorkshireY.-M. LeeM. AlamB. H. Choi0K.-S. Kim1J.-J. Kim Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon, .Korea Department of Animal Science, Chungbuk National University, Cheongju, .KoreaThe 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.http://www.ajas.info/upload/pdf/25-218.pdfWGASNPImmunityKorean Native PigYorkshire |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Y.-M. Lee M. Alam B. H. Choi K.-S. Kim J.-J. Kim |
spellingShingle |
Y.-M. Lee M. Alam B. H. Choi K.-S. Kim J.-J. Kim A Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Blood Components (Immunity) in a Cross between Korean Native Pig and Yorkshire Asian-Australasian Journal of Animal Sciences WGA SNP Immunity Korean Native Pig Yorkshire |
author_facet |
Y.-M. Lee M. Alam B. H. Choi K.-S. Kim J.-J. Kim |
author_sort |
Y.-M. Lee |
title |
A Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Blood Components (Immunity) in a Cross between Korean Native Pig and Yorkshire |
title_short |
A Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Blood Components (Immunity) in a Cross between Korean Native Pig and Yorkshire |
title_full |
A Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Blood Components (Immunity) in a Cross between Korean Native Pig and Yorkshire |
title_fullStr |
A Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Blood Components (Immunity) in a Cross between Korean Native Pig and Yorkshire |
title_full_unstemmed |
A Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Blood Components (Immunity) in a Cross between Korean Native Pig and Yorkshire |
title_sort |
whole genome association study to detect single nucleotide polymorphisms for blood components (immunity) in a cross between korean native pig and yorkshire |
publisher |
Asian-Australasian Association of Animal Production Societies |
series |
Asian-Australasian Journal of Animal Sciences |
issn |
1011-2367 1976-5517 |
publishDate |
2012-12-01 |
description |
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. |
topic |
WGA SNP Immunity Korean Native Pig Yorkshire |
url |
http://www.ajas.info/upload/pdf/25-218.pdf |
work_keys_str_mv |
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