title: An imputation-based genome-wide association study on traits related to male reproduction in a White Duroc × Erhualian F2 population.
abstract: 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 F2 boars at day 300 using 60 K single nucleotide polymorphism (SNP) data imputed from a reference panel of 1200 pigs in a White Duroc × Erhualian F2 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.
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Xueyan
authors.initials: X
authors.lastname: Zhao
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Kewei
authors.initials: K
authors.lastname: Zhao
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Ren
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Zhang
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Jiang
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Hong
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Kai
authors.initials: K
authors.lastname: Jiang
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Yang
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Chengbin
authors.initials: C
authors.lastname: Wang
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Nengshui
authors.initials: N
authors.lastname: Ding
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Lusheng
authors.initials: L
authors.lastname: Huang
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Zhiyan
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
authors.forename: Yuyun
authors.initials: Y
authors.lastname: Xing
mesh_terms: D000818:Animals; D002352:Carrier Proteins; D055106:Genome-Wide Association Study; D005838:Genotype; D006824:Hybridization, Genetic / Q000235:genetics*; D008297:Male; D011065:Poly(ADP-ribose) Polymerases; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D019655:Quantitative Trait, Heritable; D016601:RNA-Binding Proteins; D012098:Reproduction / Q000235:genetics*; D013552:Swine / Q000235:genetics* / Q000502:physiology*; D014359:Trypsin Inhibitor, Kazal Pancreatic
chemical_list: D002352:Carrier Proteins; D016601:RNA-Binding Proteins; C486642:SPINK1 protein, human; C104342:TEP1 protein, human; D014359:Trypsin Inhibitor, Kazal Pancreatic; C483041:PARP2 protein, human; D011065:Poly(ADP-ribose) Polymerases
keywords: GWAS; boar; imputation; reproduction traits