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Background  Our previous RNA-sequencing study revealed that the  ATF3  and  CDKN1A  genes were remarkably differentially expressed between the mammary glands of lactating Holstein cows with extremely high and low milk protein and fat percentage so that both of them were considered as candidates for milk composition. Herein, we further verified whether these genes have genetic effects on milk production traits in a Chinese Holstein cow population.    Results  By re-sequencing the entire coding and regulatory regions, we identified four SNPs in 5’promoter region, two in exons, seven in 3′ un-translated region (UTR), and six in 3’flanking region of  ATF3  gene, and one SNP in exon 5, two in 3’UTR, and two in 3’flanking region of  CDKN1A  gene. Of these, only the SNP, c.271C > T (rs442346530), in exon 5 of  CDKN1A  gene was predicted to result in an amino acid replacement from arginine to tryptophan. Subsequent genotype-phenotype association analysis revealed that 19 SNPs in  ATF3  and 5 SNPs in  CDKN1A  were evidently associated with 305-days milk yield, fat yield, protein yield, or protein percentage ( P  = < 0.0001 ~ 0.0494). Whilst, no significant SNPs in  ATF3  gene were associated with fat percentage in both first and second lactations ( P  > 0.05), and only two SNPs of  CDKN1A  gene, c.271C > T ( P  = 0.0377) and c.*654C > T ( P  = 0.0144), were markedly associated with fat percentage in the first lactation. Further, linkage disequilibrium (LD) analyses were conducted among the identified SNPs in  ATF3  and/or  CDKN1A  genes to further confirm the association results. We also observed that the four SNPs, g.72834301C > A, g.72834229C > A, g.72833969A > G, and g.72833562G > T altered the specific transcription factor (TF) binding sites in  ATF3  promoter, and one SNP, c.271C > T, changed the CDKN1A protein secondary structure, suggesting they might be the promising potential functional mutations.    Conclusion  Our findings first profiled the genetic effects of  ATF3  and  CDKN1A  genes for milk production traits in dairy cattle and will be available for marker-assisted breeding in dairy cattle.    Electronic supplementary material  The online version of this article (doi:10.1186/s12863-017-0516-4) contains supplementary material, which is available to authorized users.

Determination of genetic effects of ATF3 and CDKN1A genes on milk yield and compositions in Chinese Holstein population