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Determination of Genetic Effects of LIPK and LIPJ Genes on Milk Fatty Acids in Dairy Cattle

1
Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, China
2
Beijing Dairy Cattle Center, Qinghe’nanzhen Deshengmenwai Street, Chaoyang District, Beijing 100192, China
3
Beijing General Station of Animal Husbandry, N0.96 Huizhongsi, Yayun Village, Chaoyang District, Beijing 100101, China
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Genes 2019, 10(2), 86; https://doi.org/10.3390/genes10020086
Received: 10 November 2018 / Revised: 13 January 2019 / Accepted: 14 January 2019 / Published: 28 January 2019
(This article belongs to the Section Animal Genetics and Genomics)
In our previous genome-wide association study (GWAS) on milk fatty acids (FAs) in Chinese Holstein, we discovered 83 genome-wide significant single nucleotide polymorphisms (SNPs) associated with milk FAs. Two of them were close to lipase family member K (LIPK) and lipase family member J (LIPJ), respectively. Hence, this study is a follow-up to verify whether the LIPK and LIPJ have significant genetic effects on milk FAs in dairy cattle. By re-sequencing the entire exons, and 3 kb of 5′ and 3′ flanking regions, two and seven SNPs were identified in LIPK and LIPJ, respectively, including a novel SNP, ss158213049726. With the Haploview 4.1 software, we found that five of the SNPs in LIPJ formed a haplotype block (D′ = 0.96 ~ 1.00). Single-locus association analyses revealed that each SNP in LIPK and LIPJ was significantly associated with at least one milk FA (p = < 1.00 × 10−4 ~ 4.88 × 10−2), and the haplotype-based association analyses showed significant genetic effects on nine milk FAs (p = < 1.00 × 10−4 ~ 3.98 × 10−2). Out of these SNPs, the missense mutation in LIPK gene, rs42774527, could change the protein secondary structure and function predicted by SOPMA, SIFT, and PROVEAN softwares. With the Genomatix software, we predicted that two SNPs, rs110322221 in LIPK and rs211373799 in LIPJ, altered the transcription factors binding sites (TFBSs), indicating their potential regulation on promoter activity of the genes. Furthermore, we found that both LIPK and LIPJ had relatively high expressions in the mammary gland. In conclusion, our research is the first to demonstrate that LIPK and LIPJ genes have significant associations with milk FAs, and the identified SNPs might be served as genetic markers to optimize breeding programs for milk FAs in dairy cattle. This research deserves in-depth verification. View Full-Text
Keywords: lipase family member K; lipase family member J; genetic effects; milk fatty acids; dairy cattle lipase family member K; lipase family member J; genetic effects; milk fatty acids; dairy cattle
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Shi, L.; Han, B.; Liu, L.; Lv, X.; Ma, Z.; Li, C.; Xu, L.; Li, Y.; Zhao, F.; Yang, Y.; Sun, D. Determination of Genetic Effects of LIPK and LIPJ Genes on Milk Fatty Acids in Dairy Cattle. Genes 2019, 10, 86.

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