An imputation-based genome-wide association study on traits related to male reproduction in a White DurocxErhualian F-2 population

作者：Zhao, Xueyan; Zhao, Kewei; Ren, Jun; Zhang, Feng; Jiang, Chao; Hong, Yuan; Jiang, Kai; Yang, Qiang; Wang, Chengbin; Ding, Nengshui; Huang, Lusheng; Zhang, Zhiyan^*; Xing, Yuyun^*

来源：Animal Science Journal, 2016, 87(5): 646-654.

DOI：10.1111/asj.12468

• boar
• GWAS
• imputation
• reproduction traits

Boar reproductive traits are economically important for the pig industry. Here we conducted a genome-wide association study (GWAS) for 13 reproductive traits measured on 205 F-2 boars at day 300 using 60K single nucleotide polymorphism (SNP) data imputed from a reference panel of 1200 pigs in a White Duroc x Erhualian F-2 intercross population. We identified 10 significant loci for seven traits on eight pig chromosomes (SSC). Two loci surpassed the genome-wide significance level, including one for epididymal weight around 60.25 Mb on SSC7 and one for semen temperature around 43.69 Mb on SSC4. Four of the 10 significant loci that we identified were consistent with previously reported quantitative trait loci for boar reproduction traits. We highlighted several interesting candidate genes at these loci, including APN, TEP1, PARP2, SPINK1 and PDE1C. To evaluate the imputation accuracy, we further genotyped nine GWAS top SNPs using PCR restriction fragment length polymorphism or Sanger sequencing. We found an average of 91.44% of genotype concordance, 95.36% of allelic concordance and 0.85 of r(2) correlation between imputed and real genotype data. This indicates that our GWAS mapping results based on imputed SNP data are reliable, providing insights into the genetic basis of boar reproductive traits.

• 出版日期2016-5
• 单位江西农业大学