Genome-wide association studies using haplotypes and individual SNPs in Simmental cattle.

Recent advances in high-throughput genotyping technologies have provided the opportunity to map genes using associations between complex traits and markers. Genome-wide association studies (GWAS) based on either a single marker or haplotype have identified genetic variants and underlying genetic mec...

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Autores principales:	Yang Wu, Huizhong Fan, Yanhui Wang, Lupei Zhang, Xue Gao, Yan Chen, Junya Li, HongYan Ren, Huijiang Gao
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/fc1257f9fc0040f29dfcae02008eb079
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spelling	oai:doaj.org-article:fc1257f9fc0040f29dfcae02008eb0792021-11-25T05:55:53ZGenome-wide association studies using haplotypes and individual SNPs in Simmental cattle.1932-620310.1371/journal.pone.0109330https://doaj.org/article/fc1257f9fc0040f29dfcae02008eb0792014-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0109330https://doaj.org/toc/1932-6203Recent advances in high-throughput genotyping technologies have provided the opportunity to map genes using associations between complex traits and markers. Genome-wide association studies (GWAS) based on either a single marker or haplotype have identified genetic variants and underlying genetic mechanisms of quantitative traits. Prompted by the achievements of studies examining economic traits in cattle and to verify the consistency of these two methods using real data, the current study was conducted to construct the haplotype structure in the bovine genome and to detect relevant genes genuinely affecting a carcass trait and a meat quality trait. Using the Illumina BovineHD BeadChip, 942 young bulls with genotyping data were introduced as a reference population to identify the genes in the beef cattle genome significantly associated with foreshank weight and triglyceride levels. In total, 92,553 haplotype blocks were detected in the genome. The regions of high linkage disequilibrium extended up to approximately 200 kb, and the size of haplotype blocks ranged from 22 bp to 199,266 bp. Additionally, the individual SNP analysis and the haplotype-based analysis detected similar regions and common SNPs for these two representative traits. A total of 12 and 7 SNPs in the bovine genome were significantly associated with foreshank weight and triglyceride levels, respectively. By comparison, 4 and 5 haplotype blocks containing the majority of significant SNPs were strongly associated with foreshank weight and triglyceride levels, respectively. In addition, 36 SNPs with high linkage disequilibrium were detected in the GNAQ gene, a potential hotspot that may play a crucial role for regulating carcass trait components.Yang WuHuizhong FanYanhui WangLupei ZhangXue GaoYan ChenJunya LiHongYan RenHuijiang GaoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 10, p e109330 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yang Wu Huizhong Fan Yanhui Wang Lupei Zhang Xue Gao Yan Chen Junya Li HongYan Ren Huijiang Gao Genome-wide association studies using haplotypes and individual SNPs in Simmental cattle.
description	Recent advances in high-throughput genotyping technologies have provided the opportunity to map genes using associations between complex traits and markers. Genome-wide association studies (GWAS) based on either a single marker or haplotype have identified genetic variants and underlying genetic mechanisms of quantitative traits. Prompted by the achievements of studies examining economic traits in cattle and to verify the consistency of these two methods using real data, the current study was conducted to construct the haplotype structure in the bovine genome and to detect relevant genes genuinely affecting a carcass trait and a meat quality trait. Using the Illumina BovineHD BeadChip, 942 young bulls with genotyping data were introduced as a reference population to identify the genes in the beef cattle genome significantly associated with foreshank weight and triglyceride levels. In total, 92,553 haplotype blocks were detected in the genome. The regions of high linkage disequilibrium extended up to approximately 200 kb, and the size of haplotype blocks ranged from 22 bp to 199,266 bp. Additionally, the individual SNP analysis and the haplotype-based analysis detected similar regions and common SNPs for these two representative traits. A total of 12 and 7 SNPs in the bovine genome were significantly associated with foreshank weight and triglyceride levels, respectively. By comparison, 4 and 5 haplotype blocks containing the majority of significant SNPs were strongly associated with foreshank weight and triglyceride levels, respectively. In addition, 36 SNPs with high linkage disequilibrium were detected in the GNAQ gene, a potential hotspot that may play a crucial role for regulating carcass trait components.
format	article
author	Yang Wu Huizhong Fan Yanhui Wang Lupei Zhang Xue Gao Yan Chen Junya Li HongYan Ren Huijiang Gao
author_facet	Yang Wu Huizhong Fan Yanhui Wang Lupei Zhang Xue Gao Yan Chen Junya Li HongYan Ren Huijiang Gao
author_sort	Yang Wu
title	Genome-wide association studies using haplotypes and individual SNPs in Simmental cattle.
title_short	Genome-wide association studies using haplotypes and individual SNPs in Simmental cattle.
title_full	Genome-wide association studies using haplotypes and individual SNPs in Simmental cattle.
title_fullStr	Genome-wide association studies using haplotypes and individual SNPs in Simmental cattle.
title_full_unstemmed	Genome-wide association studies using haplotypes and individual SNPs in Simmental cattle.
title_sort	genome-wide association studies using haplotypes and individual snps in simmental cattle.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/fc1257f9fc0040f29dfcae02008eb079
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Genome-wide association studies using haplotypes and individual SNPs in Simmental cattle.

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