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Hao X, Plastow G, Zhang C, Xu S, Hu Z, Yang T, Wang K, Yang H, Yin X, Liu S, Wang Z, Wang Z, Zhang S. Genome-wide association study identifies candidate genes for piglet splay leg syndrome in different populations. BMC Genet 2017; 18:64. [PMID: 28679362 PMCID: PMC5499021 DOI: 10.1186/s12863-017-0532-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/28/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Piglet splay leg syndrome (PSL) is one of the most frequent genetic defects, and can cause considerable economic loss in pig production. The present understanding of etiology and pathogenesis of PSL is poor. The current study focused on identifying loci associated with PSL through a genome-wide association study (GWAS) performed with the Illumina Porcine60 SNP Beadchip v2.0. The study was a case/control design with four pig populations (Duroc, Landrace, Yorkshire and one crossbred of Landrace × Yorkshire). RESULT After quality control of the genotyping data, 185 animals (73 cases, 112 controls) and 43,495 SNPs were retained for further analysis. Principal components (PCs) identified from the genomic kinship matrix were included in the statistical model for correcting the effect of population structure. Seven chromosome-wide significant SNPs were identified on Sus scrofa chromosome 1 (SSC1), SSC2 (2 SNPs), SSC7, SSC15 (2 SNPs) and SSC16 after strict Bonferroni correction. Four genes (HOMER1 and JMY on SSC2, ITGA1 on SSC16, and RAB32 on SSC1) related to muscle development, glycogen metabolism and mitochondrial dynamics were identified as potential candidate genes for PSL. CONCLUSIONS We identified seven chromosome-wide significant SNPs associated with PSL and four potential candidate genes for PSL. To our knowledge, this is the first pilot study aiming to identify the loci associated with PSL using GWAS. Further investigations and validations for those findings are encouraged.
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Affiliation(s)
- Xingjie Hao
- Key Lab of Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei 430070 China
- Livestock Gentec Center, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2C8 Canada
| | - Graham Plastow
- Livestock Gentec Center, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2C8 Canada
| | - Chunyan Zhang
- Livestock Gentec Center, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2C8 Canada
| | - Sutong Xu
- Key Lab of Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Zhiqiu Hu
- Livestock Gentec Center, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2C8 Canada
| | - Tianfu Yang
- Livestock Gentec Center, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2C8 Canada
| | - Kai Wang
- Key Lab of Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Huawei Yang
- Hubei Tianzhong Stock Corporation, Wuhan, Hubei China
| | - Xiaoxue Yin
- Hubei Tianzhong Stock Corporation, Wuhan, Hubei China
| | - Shili Liu
- Hubei Tianzhong Stock Corporation, Wuhan, Hubei China
| | - Zhenghua Wang
- Hubei Tianzhong Stock Corporation, Wuhan, Hubei China
| | - Zhiquan Wang
- Livestock Gentec Center, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2C8 Canada
| | - Shujun Zhang
- Key Lab of Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei 430070 China
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