{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,2]],"date-time":"2025-11-02T10:39:09Z","timestamp":1762079949216,"version":"build-2065373602"},"reference-count":50,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2022,12,16]],"date-time":"2022-12-16T00:00:00Z","timestamp":1671148800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"S&amp;T Program of Hebei","award":["22326321D","2022KJCXZX-LYS-19","2021","2021YFF1000700","IRT_15R62"],"award-info":[{"award-number":["22326321D","2022KJCXZX-LYS-19","2021","2021YFF1000700","IRT_15R62"]}]},{"name":"HAAFS Science and Technology Innovation Special Project","award":["22326321D","2022KJCXZX-LYS-19","2021","2021YFF1000700","IRT_15R62"],"award-info":[{"award-number":["22326321D","2022KJCXZX-LYS-19","2021","2021YFF1000700","IRT_15R62"]}]},{"name":"Inner Mongolia and Hohhot Science and Technology Plan","award":["22326321D","2022KJCXZX-LYS-19","2021","2021YFF1000700","IRT_15R62"],"award-info":[{"award-number":["22326321D","2022KJCXZX-LYS-19","2021","2021YFF1000700","IRT_15R62"]}]},{"name":"National Key Research and Development Program of China","award":["22326321D","2022KJCXZX-LYS-19","2021","2021YFF1000700","IRT_15R62"],"award-info":[{"award-number":["22326321D","2022KJCXZX-LYS-19","2021","2021YFF1000700","IRT_15R62"]}]},{"name":"Program for Changjiang Scholars and Innovative Research Team in University","award":["22326321D","2022KJCXZX-LYS-19","2021","2021YFF1000700","IRT_15R62"],"award-info":[{"award-number":["22326321D","2022KJCXZX-LYS-19","2021","2021YFF1000700","IRT_15R62"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>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 information 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 between 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 families to investigate their genetic associations with milk yield and composition traits. By resequencing the entire exons and 2000 bp of the 5\u2032 and 3\u2032 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 \u2264 0.0001\u20130.0414), and the eight SNPs in IRF6 were associated with milk, fat, and protein yields in the first or second lactation (p values \u2264 0.0001\u20130.0467). Using Haploview 4.2, one haplotype block with eight of the SNPs in ACADVL (D\u2019 = 0.99\u20131.00) and two haplotype blocks in IRF6 with three of the SNPs in each were observed (D\u2019 = 0.98\u20131.00). Similarly, the haplotype combinations of ACADVL were significantly associated with milk yield, fat percentage, fat yield, and protein yield in the two lactations (p values \u2264 0.0001\u20130.0125), and those of IRF6 were associated with five milk traits (p values \u2264 0.0001\u20130.0263). Furthermore, with the JASPAR software, it was predicted that the SNPs 19:g.26933503T&gt;C in ACADVL and 16:g.73501985G&gt;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 significant 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.<\/jats:p>","DOI":"10.3390\/genes13122393","type":"journal-article","created":{"date-parts":[[2022,12,19]],"date-time":"2022-12-19T06:58:29Z","timestamp":1671433109000},"page":"2393","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Identification of Genetic Effects of ACADVL and IRF6 Genes with Milk Production Traits of Holstein Cattle in China"],"prefix":"10.3390","volume":"13","author":[{"given":"Peng","family":"Peng","sequence":"first","affiliation":[{"name":"Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"},{"name":"Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanan","family":"Liu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Weijie","family":"Zheng","sequence":"additional","affiliation":[{"name":"Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bo","family":"Han","sequence":"additional","affiliation":[{"name":"Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kun","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7512-5946","authenticated-orcid":false,"given":"Dongxiao","family":"Sun","sequence":"additional","affiliation":[{"name":"Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"},{"name":"National Dairy Innovation Center, Hohhot 010000, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,12,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"3011","DOI":"10.1093\/jn\/134.11.3011","article-title":"Protein source, quantity, and time of consumption determine the effect of proteins on short-term food intake in young men","volume":"134","author":"Anderson","year":"2004","journal-title":"J. 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