with the development of high‑throughput sequencing, rna sequencing has been widely
used in the identification of candidate genes for complex traits in livestock, and the functional genes
and mutations with large genetic effects on milk production traits can provide molecular informa‑
tion for marker‑assisted selection to increase the selection accuracy and accelerate genetic gain in
dairy cattle. our previous study on the liver transcriptome of holstein cows found that acyl‑coa
dehydrogenase (acadvl) and interferon regulatory factor 6 (irf6) are differentially expressed be‑
tween dry and peak lactation periods, as well as that they are involved in lipid metabolism and the
proliferation and differentiation of mammary epithelial cells. thus, the two genes were considered
candidates for milk traits. hence, this study further collected 1186 holstein cows from 110 sire fami‑
lies to investigate their genetic associations with milk yield and composition traits. by resequencing
the entire exons and 2000 bp of the 5′ and 3′ flanking regions of the two genes, we identified eight
snps in acadvl and eight snps in irf6. subsequent single‑locus association analyses showed that
the eight snps in acadvl were all significantly associated with milk fat yield, fat percentage, and
protein yield (p values ≤ 0.0001–0.0414), and the eight snps in irf6 were associated with milk, fat,
and protein yields in the first or second lactation (p values ≤ 0.0001–0.0467). using haploview 4.2,
one haplotype block with eight of the snps in acadvl (d’ = 0.99–1.00) and two haplotype blocks in
irf6 with three of the snps in each were observed (d’ = 0.98–1.00). similarly, the haplotype combina‑
tions of acadvl were significantly associated with milk yield, fat percentage, fat yield, and protein
yield in the two lactations (p values ≤ 0.0001–0.0125), and those of irf6 were associated with five
milk traits (p values ≤ 0.0001–0.0263). furthermore, with the jaspar software, it was predicted that
the snps 19:g.26933503t>c in acadvl and 16:g.73501985g>a in irf6 changed the transcription
factor binding sites of zeb1, plagl2, and rhoxf1, implying their impacts on the expressions of
the corresponding genes. our findings demonstrated that the acadvl and irf6 genes have signif‑
icant genetic effects on milk yield and composition traits, and the valuable snps might be used as
genetic markers for genomic selection programs in dairy cattle.