Imputation-Based Whole-Genome Sequence Association Study Rediscovered the Missing QTL for Lumbar Number in Sutai Pigs

Abstract Resequencing a number of individuals of various breeds as reference population and imputing the whole-genome sequences of individuals that were genotyped with medium-density chips to perform an association study is a very efficient strategy. Previously, we performed a genome-wide associatio...

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Autores principales:	Guorong Yan, Ruimin Qiao, Feng Zhang, Wenshui Xin, Shijun Xiao, Tao Huang, Zhiyan Zhang, Lusheng Huang
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2cd595002d4842c08f231e5df377820d
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spelling	oai:doaj.org-article:2cd595002d4842c08f231e5df377820d2021-12-02T16:06:15ZImputation-Based Whole-Genome Sequence Association Study Rediscovered the Missing QTL for Lumbar Number in Sutai Pigs10.1038/s41598-017-00729-02045-2322https://doaj.org/article/2cd595002d4842c08f231e5df377820d2017-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-00729-0https://doaj.org/toc/2045-2322Abstract Resequencing a number of individuals of various breeds as reference population and imputing the whole-genome sequences of individuals that were genotyped with medium-density chips to perform an association study is a very efficient strategy. Previously, we performed a genome-wide association study (GWAS) of lumbar number using 60K SNPs from the porcine Illumina chips in 418 Sutai pigs and did not detect any significant signals. Therefore, we imputed the whole-genome sequences of 418 Sutai individuals from 403 deeply resequenced reference individuals and performed association tests. We identified a quantitative trait locus (QTL) for lumbar number in SSC1 with a P value of 9.01E-18 that was close to the potential causative gene of NR6A1. The result of conditioning on the top SNP association test indicated that only one QTL was responsible for this trait in SSC1. The linkage disequilibrium (LD) drop test result for the condition of the reported potential causative mutation (c.575T > C missense mutation of NR6A1) indicated that this mutation was probably not the underlying mutation that affected lumbar number in our study. As the first trial of imputed whole-genome sequence GWAS in swine, this approach can be also powerful to investigate complex traits in pig like in human and cattle.Guorong YanRuimin QiaoFeng ZhangWenshui XinShijun XiaoTao HuangZhiyan ZhangLusheng HuangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Guorong Yan Ruimin Qiao Feng Zhang Wenshui Xin Shijun Xiao Tao Huang Zhiyan Zhang Lusheng Huang Imputation-Based Whole-Genome Sequence Association Study Rediscovered the Missing QTL for Lumbar Number in Sutai Pigs
description	Abstract Resequencing a number of individuals of various breeds as reference population and imputing the whole-genome sequences of individuals that were genotyped with medium-density chips to perform an association study is a very efficient strategy. Previously, we performed a genome-wide association study (GWAS) of lumbar number using 60K SNPs from the porcine Illumina chips in 418 Sutai pigs and did not detect any significant signals. Therefore, we imputed the whole-genome sequences of 418 Sutai individuals from 403 deeply resequenced reference individuals and performed association tests. We identified a quantitative trait locus (QTL) for lumbar number in SSC1 with a P value of 9.01E-18 that was close to the potential causative gene of NR6A1. The result of conditioning on the top SNP association test indicated that only one QTL was responsible for this trait in SSC1. The linkage disequilibrium (LD) drop test result for the condition of the reported potential causative mutation (c.575T > C missense mutation of NR6A1) indicated that this mutation was probably not the underlying mutation that affected lumbar number in our study. As the first trial of imputed whole-genome sequence GWAS in swine, this approach can be also powerful to investigate complex traits in pig like in human and cattle.
format	article
author	Guorong Yan Ruimin Qiao Feng Zhang Wenshui Xin Shijun Xiao Tao Huang Zhiyan Zhang Lusheng Huang
author_facet	Guorong Yan Ruimin Qiao Feng Zhang Wenshui Xin Shijun Xiao Tao Huang Zhiyan Zhang Lusheng Huang
author_sort	Guorong Yan
title	Imputation-Based Whole-Genome Sequence Association Study Rediscovered the Missing QTL for Lumbar Number in Sutai Pigs
title_short	Imputation-Based Whole-Genome Sequence Association Study Rediscovered the Missing QTL for Lumbar Number in Sutai Pigs
title_full	Imputation-Based Whole-Genome Sequence Association Study Rediscovered the Missing QTL for Lumbar Number in Sutai Pigs
title_fullStr	Imputation-Based Whole-Genome Sequence Association Study Rediscovered the Missing QTL for Lumbar Number in Sutai Pigs
title_full_unstemmed	Imputation-Based Whole-Genome Sequence Association Study Rediscovered the Missing QTL for Lumbar Number in Sutai Pigs
title_sort	imputation-based whole-genome sequence association study rediscovered the missing qtl for lumbar number in sutai pigs
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/2cd595002d4842c08f231e5df377820d
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Imputation-Based Whole-Genome Sequence Association Study Rediscovered the Missing QTL for Lumbar Number in Sutai Pigs

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