title: A post-GWAS replication study confirming the PTK2 gene associated with milk production traits in Chinese Holstein.
abstract: Our initial genome-wide association study (GWAS) demonstrated that two SNPs (ARS-BFGL-NGS-33248, UA-IFASA-9288) within the protein tyrosine kinase 2 (PTK2) gene were significantly associated with milk production traits in Chinese Holstein dairy cattle. To further validate if the statistical evidence provided in GWAS were true-positive findings, a replication study was performed herein through genotype-phenotype associations. The two tested SNPs were found to show significant associations with milk production traits, which confirmed the associations observed in the original study. Specifically, SNPs lying in the PTK2 gene were also detected by sequencing 14 unrelated sires in Chinese Holsteins and a total of thirty-three novel SNPs were identified. Thirteen out of these identified SNPs were genotyped and tested for association with milk production traits in an independent resource population. After Bonferroni correction for multiple testing, twelve SNPs were statistically significant for more than two milk production traits. Analyses of pairwise D' measures of linkage disequilibrium (LD) between all SNPs were also explored. Two haplotype blocks were inferred and the association study at haplotype level revealed similar effects on milk production traits. In addition, the RNA expression analyses revealed that a non-synonymous coding SNP (g.4061098T>G) was involved in the regulation of gene expression. Thus the findings presented here provide strong evidence for associations of PTK2 variants with dairy production traits and may be applied in Chinese Holstein breeding program.
authors.affiliation: Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
authors.forename: Haifei
authors.initials: H
authors.lastname: Wang
authors.affiliation: Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
authors.forename: Li
authors.initials: L
authors.lastname: Jiang
authors.affiliation: Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
authors.forename: Xuan
authors.initials: X
authors.lastname: Liu
authors.affiliation: Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Yang
authors.affiliation: Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
authors.forename: Julong
authors.initials: J
authors.lastname: Wei
authors.affiliation: Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
authors.forename: Jingen
authors.initials: J
authors.lastname: Xu
authors.affiliation: Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
authors.forename: Qin
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
authors.forename: Jian-Feng
authors.initials: JF
authors.lastname: Liu
mesh_terms: D000483:Alleles; D000818:Animals; D002417:Cattle; D005260:Female; D015870:Gene Expression; D005787:Gene Frequency; D023061:Gene Order; D056726:Genetic Association Studies; D055106:Genome-Wide Association Study; D005838:Genotype; D015810:Linkage Disequilibrium; D008892:Milk; D009690:Nucleic Acid Conformation; D020641:Polymorphism, Single Nucleotide; D011505:Protein-Tyrosine Kinases / Q000235:genetics* / Q000378:metabolism; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable
chemical_list: D011505:Protein-Tyrosine Kinases