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Multi-strategy genome-wide association studies identify the DCAF16-NCAPG region as a susceptibility locus for average daily gain in cattle

Average daily gain (ADG) is the most economically important trait in beef cattle industry. Using genome-wide association study (GWAS) approaches, previous studies have identified several causal variants within the PLAG1, NCAPG and LCORL genes for ADG in cattle. Multi-strategy GWASs were implemented...

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Autores principales: Zhang, Wengang, Li, Junya, Guo, Yong, Zhang, Lupei, Xu, Lingyang, Gao, Xue, Zhu, Bo, Gao, Huijiang, Ni, Hemin, Chen, Yan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5125095/
https://www.ncbi.nlm.nih.gov/pubmed/27892541
http://dx.doi.org/10.1038/srep38073
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author Zhang, Wengang
Li, Junya
Guo, Yong
Zhang, Lupei
Xu, Lingyang
Gao, Xue
Zhu, Bo
Gao, Huijiang
Ni, Hemin
Chen, Yan
author_facet Zhang, Wengang
Li, Junya
Guo, Yong
Zhang, Lupei
Xu, Lingyang
Gao, Xue
Zhu, Bo
Gao, Huijiang
Ni, Hemin
Chen, Yan
author_sort Zhang, Wengang
collection PubMed
description Average daily gain (ADG) is the most economically important trait in beef cattle industry. Using genome-wide association study (GWAS) approaches, previous studies have identified several causal variants within the PLAG1, NCAPG and LCORL genes for ADG in cattle. Multi-strategy GWASs were implemented in this study to improve detection and to explore the causal genes and regions. In this study, we conducted GWASs based on the genotypes of 1,173 Simmental cattle. In the SNP-based GWAS, the most significant SNPs (rs109303784 and rs110058857, P = 1.78 × 10(−7)) were identified in the NCAPG intron on BTA6 and explained 4.01% of the phenotypic variance, and the independent and significant SNP (rs110406669, P = 5.18 × 10(−6)) explained 3.32% of the phenotypic variance. Similarly, in the haplotype-based GWAS, the most significant haplotype block, Hap-6-N1416 (P = 2.56 × 10(−8)), spanned 12.7 kb on BTA6 and explained 4.85% of the phenotypic variance. Also, in the gene-based GWAS, seven significant genes were obtained which included DCAF16 and NCAPG. Moreover, analysis of the transcript levels confirmed that transcripts abundance of NCAPG (P = 0.046) and DCAF16 (P = 0.046) were significantly correlated with the ADG trait. Overall, our results from the multi-strategy GWASs revealed the DCAF16-NCAPG region to be a susceptibility locus for ADG in cattle.
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spelling pubmed-51250952016-12-08 Multi-strategy genome-wide association studies identify the DCAF16-NCAPG region as a susceptibility locus for average daily gain in cattle Zhang, Wengang Li, Junya Guo, Yong Zhang, Lupei Xu, Lingyang Gao, Xue Zhu, Bo Gao, Huijiang Ni, Hemin Chen, Yan Sci Rep Article Average daily gain (ADG) is the most economically important trait in beef cattle industry. Using genome-wide association study (GWAS) approaches, previous studies have identified several causal variants within the PLAG1, NCAPG and LCORL genes for ADG in cattle. Multi-strategy GWASs were implemented in this study to improve detection and to explore the causal genes and regions. In this study, we conducted GWASs based on the genotypes of 1,173 Simmental cattle. In the SNP-based GWAS, the most significant SNPs (rs109303784 and rs110058857, P = 1.78 × 10(−7)) were identified in the NCAPG intron on BTA6 and explained 4.01% of the phenotypic variance, and the independent and significant SNP (rs110406669, P = 5.18 × 10(−6)) explained 3.32% of the phenotypic variance. Similarly, in the haplotype-based GWAS, the most significant haplotype block, Hap-6-N1416 (P = 2.56 × 10(−8)), spanned 12.7 kb on BTA6 and explained 4.85% of the phenotypic variance. Also, in the gene-based GWAS, seven significant genes were obtained which included DCAF16 and NCAPG. Moreover, analysis of the transcript levels confirmed that transcripts abundance of NCAPG (P = 0.046) and DCAF16 (P = 0.046) were significantly correlated with the ADG trait. Overall, our results from the multi-strategy GWASs revealed the DCAF16-NCAPG region to be a susceptibility locus for ADG in cattle. Nature Publishing Group 2016-11-28 /pmc/articles/PMC5125095/ /pubmed/27892541 http://dx.doi.org/10.1038/srep38073 Text en Copyright © 2016, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Zhang, Wengang
Li, Junya
Guo, Yong
Zhang, Lupei
Xu, Lingyang
Gao, Xue
Zhu, Bo
Gao, Huijiang
Ni, Hemin
Chen, Yan
Multi-strategy genome-wide association studies identify the DCAF16-NCAPG region as a susceptibility locus for average daily gain in cattle
title Multi-strategy genome-wide association studies identify the DCAF16-NCAPG region as a susceptibility locus for average daily gain in cattle
title_full Multi-strategy genome-wide association studies identify the DCAF16-NCAPG region as a susceptibility locus for average daily gain in cattle
title_fullStr Multi-strategy genome-wide association studies identify the DCAF16-NCAPG region as a susceptibility locus for average daily gain in cattle
title_full_unstemmed Multi-strategy genome-wide association studies identify the DCAF16-NCAPG region as a susceptibility locus for average daily gain in cattle
title_short Multi-strategy genome-wide association studies identify the DCAF16-NCAPG region as a susceptibility locus for average daily gain in cattle
title_sort multi-strategy genome-wide association studies identify the dcaf16-ncapg region as a susceptibility locus for average daily gain in cattle
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5125095/
https://www.ncbi.nlm.nih.gov/pubmed/27892541
http://dx.doi.org/10.1038/srep38073
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