Scientia Agricultura Sinica ›› 2014, Vol. 47 ›› Issue (14): 2872-2880.doi: 10.3864/j.issn.0578-1752.2014.14.017

• ANIMAL SCIENCE·VETERINARY SCIENCERE·SOURCE INSECT • Previous Articles     Next Articles

Genome-Wide Association Study Reveals Candidate Susceptibility Loci for Pig Scrotal Hernia Using Both F2 Intercross and Outbred Populations

 SU  Ying-1, RUAN  Guo-Rong-2, LONG  Yi-1, YANG  Bin-1, ZHANG  Zhi-Yan-1, DENG  Wei-Yun-1, WU  Li-Hua-1, 吕Xian-Shan-1 , AI  Hua-Shui-1, XIAO  Shi-Jun-1, REN  Jun-1, HUANG  Lu-Sheng-1, DING  Neng-Shui-1   

  1. 1、Candidate of National Key Laboratory for Animal Biotechnology, Jiangxi Agricultural University, Nanchang 330045;
    2、Fujian Vocational College of Agriculture, Fuzhou 350119
  • Received:2013-12-03 Online:2014-07-15 Published:2014-05-07

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Abstract: 【Objective】Isolation of susceptible loci and positional candidate genes associated with pig scrotal hernia through case-control genome-wide association study (GWAS) based on haplotypes in a F2 White Duroc × Erhualian intercross and it’s replication in outbred trio families.【Method】Phenotypic data and Illumina porcine 60K SNP genotypes were collected from 1020 individuals in the White Duroc × Erhualian intercross (containing 19 affected pigs) and outbred trio families (containing 237 scrotal hernia pigs). Quality control was carried out using PLINK v1.07 for each population， separately. Samples of low (<90%) call rate were removed. SNP markers were removed if they had genotype-missing rates ＞0.1, or Hardy-Weinberg P≤10-3(based on Chi-squared test) or minor allele frequencies (MAF) ＜0.05, and SNPs on sex chromosomes or with unknown positions were also excluded. PHASEBOOK package was used to infer haplotypes from the genotyped individuals and to assign them to K ancestral haplotype clusters by hidden monto carlo markov models. The software GLASCOW based on generalized linear mixed models was used to carry out GWAS for pig scrotal hernia in the F2 intercross by the ancestral haplotype and significant SNPs were chosen to perform transmission disequilibrium test (TDT) based on both single SNP markers and haplotypes in the outbred population (containing 237 affected pigs) by Haploview. 【Result】After quality control, all samples in F2 population and 724 samples in outbred populations passed the filter and a final set of 38 033 SNPs and 96 SNPs were selected for GWAS and TDT analysis. In total, 108 SNPs with Bonferroni chromosome-wise significance (P＜2.63×10-5) were identified to be associated with scrotal hernia in F2 intercross, and located on SSC2, SSC8 and SSC17, respectively. The most promising SNP was located on SSC17. Five significant SNPs, located in on nearby IQGAP2，CHMP4B，SERINC3，ZNF334 genes, were replicated (located on SSC2 and SSC17) in outbred trio families by TDT analysis. TDT analysis based on haplotype revealed that two haplotypes contribute to risk of scrotal hernia, one of which was overlapped with two significant SNP on SSC17 in the TDT analysis based on single marker. IQGAP2 and CHMP4B genes close to the SNPs most associated with pig scrotal hernia were selected as positional candidate genes according to its biological and physiological functions.【Conclusion】A GWAS with small samples was conducted and variation and replication test was performed in a larger populations, which revealed 5 susceptible loci for pig scrotal hernia both in the F2 intercross and the outbred populations. IQGAP2 and CHMP4B may play a role in the risk of scrotal hernia, and deeper analysis should be carried out in the future study.

Key words: pig , genome-wide association study , transmission disequilibrium test , scrotal hernia , susceptibility gene

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