Genome-wide association study identifies candidate genes for piglet splay leg syndrome in different populations

BMC Genetics

Research Article

Zhenghua Wang¹  Shili Liu¹  Huawei Yang¹  Xiaoxue Yin¹  Kai Wang²  Shujun Zhang²  Sutong Xu²  Xingjie Hao³  Graham Plastow⁴  Zhiqiu Hu⁴  Chunyan Zhang⁴  Tianfu Yang⁴  Zhiquan Wang⁴ 

[1] Hubei Tianzhong Stock Corporation, Wuhan, Hubei, China;Key Lab of Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, Hubei, China;Key Lab of Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, Hubei, China;Livestock Gentec Center, Department of Agricultural, Food and Nutritional Science, University of Alberta, T6G 2C8, Edmonton, AB, Canada;Livestock Gentec Center, Department of Agricultural, Food and Nutritional Science, University of Alberta, T6G 2C8, Edmonton, AB, Canada;

关键词: Genome-wide association study (GWAS);    Pig;    Splay leg;    Principal component analysis (PCA);    Muscle;   

DOI  :  10.1186/s12863-017-0532-4

 received in 2017-02-21, accepted in 2017-06-28,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundPiglet 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).ResultAfter 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.ConclusionsWe 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.

【 授权许可】

CC BY   
© The Author(s). 2017