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Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays
BACKGROUND: Beak deformity, typically expressed as the crossing of upper and lower mandibles, is found in several indigenous chicken breeds, including the Beijing-You chickens studied here. Beak deformity severely impairs the birds’ growth and welfare. Although previous studies shed some light on th...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022433/ https://www.ncbi.nlm.nih.gov/pubmed/29954329 http://dx.doi.org/10.1186/s12864-018-4882-8 |
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author | Bai, Hao Sun, Yanyan Liu, Nian Xue, Fuguang Li, Yunlei Xu, Songshan Ye, Jianhua Zhang, Lei Chen, Yu Chen, Jilan |
author_facet | Bai, Hao Sun, Yanyan Liu, Nian Xue, Fuguang Li, Yunlei Xu, Songshan Ye, Jianhua Zhang, Lei Chen, Yu Chen, Jilan |
author_sort | Bai, Hao |
collection | PubMed |
description | BACKGROUND: Beak deformity, typically expressed as the crossing of upper and lower mandibles, is found in several indigenous chicken breeds, including the Beijing-You chickens studied here. Beak deformity severely impairs the birds’ growth and welfare. Although previous studies shed some light on the genetic regulation of this complex trait, the genetic basis of this malformation remains incompletely understood. RESULTS: In this study, single SNP- and pathway-based genome-wide association studies (GWASs) were performed using ROADTRIPS and SNP ratio test (SRT), respectively. A total of 48 birds with deformed beaks (case) and 48 normal birds (control) were genotyped using Affymetrix 600 K HD genotyping arrays. As a result, 95 individuals and 429,539 SNPs were obtained after quality control. The P-value was corrected by a Bonferroni adjustment based on linkage disequilibrium pruning. The single SNP-based association study identified one associated SNP with 5% genome-wide significance and seven suggestively associated SNPs. Four high-confidence genes, LOC421892, TDRD3, RET, and STMN1, were identified as the most promising candidate genes underlying this complex trait in view of their positions, functions, and overlaps with previous studies. The pathway-based association study highlighted the association of six pathways with beak deformity, including the calcium signaling pathway. CONCLUSIONS: Potentially useful candidate genes and pathways for beak deformity were identified, which should be the subject of further functional characterization. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4882-8) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6022433 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-60224332018-07-09 Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays Bai, Hao Sun, Yanyan Liu, Nian Xue, Fuguang Li, Yunlei Xu, Songshan Ye, Jianhua Zhang, Lei Chen, Yu Chen, Jilan BMC Genomics Research Article BACKGROUND: Beak deformity, typically expressed as the crossing of upper and lower mandibles, is found in several indigenous chicken breeds, including the Beijing-You chickens studied here. Beak deformity severely impairs the birds’ growth and welfare. Although previous studies shed some light on the genetic regulation of this complex trait, the genetic basis of this malformation remains incompletely understood. RESULTS: In this study, single SNP- and pathway-based genome-wide association studies (GWASs) were performed using ROADTRIPS and SNP ratio test (SRT), respectively. A total of 48 birds with deformed beaks (case) and 48 normal birds (control) were genotyped using Affymetrix 600 K HD genotyping arrays. As a result, 95 individuals and 429,539 SNPs were obtained after quality control. The P-value was corrected by a Bonferroni adjustment based on linkage disequilibrium pruning. The single SNP-based association study identified one associated SNP with 5% genome-wide significance and seven suggestively associated SNPs. Four high-confidence genes, LOC421892, TDRD3, RET, and STMN1, were identified as the most promising candidate genes underlying this complex trait in view of their positions, functions, and overlaps with previous studies. The pathway-based association study highlighted the association of six pathways with beak deformity, including the calcium signaling pathway. CONCLUSIONS: Potentially useful candidate genes and pathways for beak deformity were identified, which should be the subject of further functional characterization. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4882-8) contains supplementary material, which is available to authorized users. BioMed Central 2018-06-28 /pmc/articles/PMC6022433/ /pubmed/29954329 http://dx.doi.org/10.1186/s12864-018-4882-8 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Bai, Hao Sun, Yanyan Liu, Nian Xue, Fuguang Li, Yunlei Xu, Songshan Ye, Jianhua Zhang, Lei Chen, Yu Chen, Jilan Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays |
title | Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays |
title_full | Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays |
title_fullStr | Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays |
title_full_unstemmed | Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays |
title_short | Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays |
title_sort | single snp- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600k snp arrays |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022433/ https://www.ncbi.nlm.nih.gov/pubmed/29954329 http://dx.doi.org/10.1186/s12864-018-4882-8 |
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