Background
Our initial genome-wide association study (GWAS) identified 20 promising candidate genes for milk fatty acid (FA) traits in a Chinese Holstein population, including
PRLR
,
MOGAT1, MINPP1
and
CHUK
genes. In this study, we performed whether they had significant genetic effects on milk FA traits in Chinese Holstein.
Results
We re-sequenced the entire exons and 3000 bp of the 5′ and 3′ flanking regions, and identified 11 single nucleotide polymorphisms (SNPs), containing four in
PRLR
, two in
MOGAT1
, two in
MINPP1
, and three in
CHUK
. The SNP-based association analyses showed that all the 11 SNPs were significantly associated with at least one milk FA trait (
P
= 0.0456 ~ < 0.0001), and none of them had association with C11:0, C13:0, C15:0 and C16:0 (
P
> 0.05). By the linkage disequilibrium (LD) analyses, we found two, one, one, and one haplotype blocks in
PRLR
,
MOGAT1
,
MINPP1
, and
CHUK
, respectively, and each haplotype block was significantly associated with at least one milk FA trait (
P
= 0.0456 ~ < 0.0001). Further, g.38949011G > A in
PRLR
, and g.111599360A > G and g.111601747 T > A in
MOGAT1
were predicted to alter the transcription factor binding sites (TFBSs). A missense mutation, g.39115344G > A, could change the PRLR protein structure. The g.20966385C > G of
CHUK
varied the binding sequences for microRNAs. Therefore, we deduced the five SNPs as the potential functional mutations.
Conclusion
In summary, we first detected the genetic effects of
PRLR
,
MOGAT1, MINPP1
and
CHUK
genes on milk FA traits, and researched the potential functional mutations. These data provided the basis for further investigation on function validation of the four genes in Chinese Holstein.
Electronic supplementary material
The online version of this article (10.1186/s12863-019-0769-1) contains supplementary material, which is available to authorized users.