Genome-Wide Identification of Candidate Genes for Milk Production Traits in Korean Holstein Cattle
We performed a genome-wide association study and fine mapping using two methods (single marker regression: frequentist approach and Bayesian C (BayesC): fitting selected single nucleotide polymorphisms (SNPs) in a Bayesian framework) through three high-density SNP chip platforms to analyze milk prod...
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MDPI AG
2021-05-01
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| author | Sangwook Kim Byeonghwi Lim Joohyeon Cho Seokhyun Lee Chang-Gwon Dang Jung-Hwan Jeon Jun-Mo Kim Jungjae Lee |
| author_facet | Sangwook Kim Byeonghwi Lim Joohyeon Cho Seokhyun Lee Chang-Gwon Dang Jung-Hwan Jeon Jun-Mo Kim Jungjae Lee |
| author_sort | Sangwook Kim |
| collection | DOAJ |
| description | We performed a genome-wide association study and fine mapping using two methods (single marker regression: frequentist approach and Bayesian C (BayesC): fitting selected single nucleotide polymorphisms (SNPs) in a Bayesian framework) through three high-density SNP chip platforms to analyze milk production phenotypes in Korean Holstein cattle (<i>n</i> = 2780). We identified four significant SNPs for each phenotype in the single marker regression model: AX-311625843 and AX-115099068 on <i>Bos taurus</i> autosome (BTA) 14 for milk yield (MY) and adjusted 305-d fat yield (FY), respectively, AX-428357234 on BTA 18 for adjusted 305-d protein yield (PY), and AX-185120896 on BTA 5 for somatic cell score (SCS). Using the BayesC model, we discovered significant 1-Mb window regions that harbored over 0.5% of the additive genetic variance effects for four milk production phenotypes. The concordant significant SNPs and 1-Mb window regions were characterized into quantitative trait loci (QTL). Among the QTL regions, we focused on a well-known gene (diacylglycerol O-acyltransferase 1 (<i>DGAT1</i>)) and newly identified genes (phosphodiesterase 4B (<i>PDE4B</i>), and anoctamin 2 (<i>ANO2</i>)) for MY and FY, and observed that <i>DGAT1</i> is involved in glycerolipid metabolism, fat digestion and absorption, metabolic pathways, and retinol metabolism, and <i>PDE4B</i> is involved in cAMP signaling. Our findings suggest that the candidate genes in QTL are strongly related to physiological mechanisms related to the fat production and consequent total MY in Korean Holstein cattle. |
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| last_indexed | 2024-03-10T11:27:06Z |
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| series | Animals |
| spelling | doaj.art-b60b5238e8074d179c731f4150e266872023-11-21T19:37:01ZengMDPI AGAnimals2076-26152021-05-01115139210.3390/ani11051392Genome-Wide Identification of Candidate Genes for Milk Production Traits in Korean Holstein CattleSangwook Kim0Byeonghwi Lim1Joohyeon Cho2Seokhyun Lee3Chang-Gwon Dang4Jung-Hwan Jeon5Jun-Mo Kim6Jungjae Lee7Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Gyeonggi-do, KoreaDepartment of Animal Science and Technology, Chung-Ang University, Anseong 17546, Gyeonggi-do, KoreaDairy Cattle Genetic Improvement Center, Nonghyup, Goyang 10292, Gyeonggi-do, KoreaDairy Cattle Genetic Improvement Center, Nonghyup, Goyang 10292, Gyeonggi-do, KoreaAnimal Genetics and Breeding Division, National Institute of Animal Science, RDA, Cheonan 31000, Chungcheongnam-do, KoreaAnimal Welfare Research Team, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, KoreaDepartment of Animal Science and Technology, Chung-Ang University, Anseong 17546, Gyeonggi-do, KoreaDepartment of Animal Science and Technology, Chung-Ang University, Anseong 17546, Gyeonggi-do, KoreaWe performed a genome-wide association study and fine mapping using two methods (single marker regression: frequentist approach and Bayesian C (BayesC): fitting selected single nucleotide polymorphisms (SNPs) in a Bayesian framework) through three high-density SNP chip platforms to analyze milk production phenotypes in Korean Holstein cattle (<i>n</i> = 2780). We identified four significant SNPs for each phenotype in the single marker regression model: AX-311625843 and AX-115099068 on <i>Bos taurus</i> autosome (BTA) 14 for milk yield (MY) and adjusted 305-d fat yield (FY), respectively, AX-428357234 on BTA 18 for adjusted 305-d protein yield (PY), and AX-185120896 on BTA 5 for somatic cell score (SCS). Using the BayesC model, we discovered significant 1-Mb window regions that harbored over 0.5% of the additive genetic variance effects for four milk production phenotypes. The concordant significant SNPs and 1-Mb window regions were characterized into quantitative trait loci (QTL). Among the QTL regions, we focused on a well-known gene (diacylglycerol O-acyltransferase 1 (<i>DGAT1</i>)) and newly identified genes (phosphodiesterase 4B (<i>PDE4B</i>), and anoctamin 2 (<i>ANO2</i>)) for MY and FY, and observed that <i>DGAT1</i> is involved in glycerolipid metabolism, fat digestion and absorption, metabolic pathways, and retinol metabolism, and <i>PDE4B</i> is involved in cAMP signaling. Our findings suggest that the candidate genes in QTL are strongly related to physiological mechanisms related to the fat production and consequent total MY in Korean Holstein cattle.https://www.mdpi.com/2076-2615/11/5/1392milk productionHolstein cattlegenome-wide association studiesfine mappinggenomic selection |
| spellingShingle | Sangwook Kim Byeonghwi Lim Joohyeon Cho Seokhyun Lee Chang-Gwon Dang Jung-Hwan Jeon Jun-Mo Kim Jungjae Lee Genome-Wide Identification of Candidate Genes for Milk Production Traits in Korean Holstein Cattle Animals milk production Holstein cattle genome-wide association studies fine mapping genomic selection |
| title | Genome-Wide Identification of Candidate Genes for Milk Production Traits in Korean Holstein Cattle |
| title_full | Genome-Wide Identification of Candidate Genes for Milk Production Traits in Korean Holstein Cattle |
| title_fullStr | Genome-Wide Identification of Candidate Genes for Milk Production Traits in Korean Holstein Cattle |
| title_full_unstemmed | Genome-Wide Identification of Candidate Genes for Milk Production Traits in Korean Holstein Cattle |
| title_short | Genome-Wide Identification of Candidate Genes for Milk Production Traits in Korean Holstein Cattle |
| title_sort | genome wide identification of candidate genes for milk production traits in korean holstein cattle |
| topic | milk production Holstein cattle genome-wide association studies fine mapping genomic selection |
| url | https://www.mdpi.com/2076-2615/11/5/1392 |
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