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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.

Polymorphisms and genetic effects of PRLR, MOGAT1, MINPP1 and CHUK genes on milk fatty acid traits in Chinese Holstein