Hao Xingjie, Plastow Graham, Zhang Chunyan, Xu Sutong, Hu Zhiqiu, Yang Tianfu, Wang Kai, Yang Huawei, Yin Xiaoxue, Liu Shili, Wang Zhenghua, Wang Zhiquan, Zhang Shujun
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.
BMC Genet. 2017 Jul 5;18(1):64. doi: 10.1186/s12863-017-0532-4.
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).
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.
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.
仔猪八字腿综合征（PSL）是最常见的遗传缺陷之一，会给养猪生产造成相当大的经济损失。目前对PSL病因和发病机制的了解较少。本研究通过使用Illumina Porcine60 SNP Beadchip v2.0进行全基因组关联研究（GWAS），重点确定与PSL相关的基因座。该研究采用病例/对照设计，涉及四个猪群（杜洛克猪、长白猪、大白猪以及一个长白猪×大白猪的杂交群体）。
对基因分型数据进行质量控制后，保留了185只动物（73例病例，112例对照）和43495个单核苷酸多态性（SNP）用于进一步分析。从基因组亲缘关系矩阵中确定的主成分（PC）被纳入统计模型，以校正群体结构的影响。经过严格的Bonferroni校正后，在猪1号染色体（SSC1）、SSC2（2个SNP）、SSC7、SSC15（2个SNP）和SSC16上鉴定出7个全染色体显著的SNP。与肌肉发育、糖原代谢和线粒体动力学相关的四个基因（SSC2上的HOMER1和JMY、SSC16上的ITGA1以及SSC1上的RAB32）被确定为PSL的潜在候选基因。
我们鉴定出7个与PSL相关的全染色体显著SNP以及4个PSL的潜在候选基因。据我们所知，这是第一项旨在使用GWAS鉴定与PSL相关基因座的初步研究。鼓励对这些发现进行进一步的调查和验证。
