Abstract
Phosphodiesterase9A (PDE9A) is a cyclic guanosine monophosphate (cGMP)-specific enzyme widely expressed among the tissues, which is important in activating cGMP-dependent signaling pathways. In our previous genome-wide association study, a single nucleotide polymorphism (SNP) (BTA-55340-no-rsb) located in the intron 14 of PDE9A, was found to be significantly associated with protein yield. In addition, we found that PDE9A was highly expressed in mammary gland by analyzing its mRNA expression in different tissues. The objectives of this study were to identify genetic polymorphisms of PDE9A and to determine the effects of these variants on milk production traits in dairy cattle. DNA sequencing identified 11 single nucleotide polymorphisms (SNPs) and six SNPs in 5′ regulatory region were genotyped to test for the subsequent association analyses. After Bonferroni correction for multiple testing, all these identified SNPs were statistically significant for one or more milk production traits (p < 0.0001~0.0077). Interestingly, haplotype-based association analysis revealed similar effects on milk production traits (p < 0.01). In follow-up RNA expression analyses, two SNPs (c.-1376 G>A, c.-724 A>G) were involved in the regulation of gene expression. Consequently, our findings provide confirmatory evidences for associations of PDE9A variants with milk production traits and these identified SNPs may serve as genetic markers to accelerate Chinese Holstein breeding program.
Highlights
Milk production traits are the most economically important traits controlled by numerous genes and environmental factors in dairy cattle
The results suggested that the PDE9A gene was extremely conserved within mammalian species
We demonstrated that significant associations exist between PDE9A variants and milk production traits in Chinese Holstein cow26s5. 3T6o find more evidence for such associations, we compared our results with the known major gene and previously reported QTL and genome-wide association study (GWAS) data
Summary
Milk production traits are the most economically important traits controlled by numerous genes and environmental factors in dairy cattle. An improvement in milk production traits continues to be the most profitable breeding objective. Mutations can alter breeding values of economical traits in dairy cattle [1]. New molecular techniques focused on genome analysis have made it feasible to screen for mutations associated with complex traits by genome-wide association study (GWAS) [2]. Compared with traditional QTL (quantitative trait loci) mapping strategy, GWAS shows obvious advantages both in the power to detect harboring variants and in simplifying the discovery of causal variants [3]. GWAS have been widely recognized as an important strategy to explore genes associated with complex traits in many species. Using Illumina 50K chip, we identified 105 genome-wide significant SNPs associated with milk production traits in Chinese
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