Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data
Lactation persistency and milk production are among the most economically important traits in the dairy industry. In this study, we explored the association of over 6.1 million imputed whole-genome sequence variants with lactation persistency (LP), milk yield (MILK), fat yield (FAT), fat percentage...
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MDPI AG
2021-11-01
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| author | Victor B. Pedrosa Flavio S. Schenkel Shi-Yi Chen Hinayah R. Oliveira Theresa M. Casey Melkaye G. Melka Luiz F. Brito |
| author_facet | Victor B. Pedrosa Flavio S. Schenkel Shi-Yi Chen Hinayah R. Oliveira Theresa M. Casey Melkaye G. Melka Luiz F. Brito |
| author_sort | Victor B. Pedrosa |
| collection | DOAJ |
| description | Lactation persistency and milk production are among the most economically important traits in the dairy industry. In this study, we explored the association of over 6.1 million imputed whole-genome sequence variants with lactation persistency (LP), milk yield (MILK), fat yield (FAT), fat percentage (FAT%), protein yield (PROT), and protein percentage (PROT%) in North American Holstein cattle. We identified 49, 3991, 2607, 4459, 805, and 5519 SNPs significantly associated with LP, MILK, FAT, FAT%, PROT, and PROT%, respectively. Various known associations were confirmed while several novel candidate genes were also revealed, including <i>ARHGAP35</i>, <i>NPAS1</i>, <i>TMEM160</i>, <i>ZC3H4</i>, <i>SAE1</i>, <i>ZMIZ1</i>, <i>PPIF</i>, <i>LDB2</i>, <i>ABI3</i>, <i>SERPINB6</i>, and <i>SERPINB9</i> for LP; <i>NIM1K</i>, <i>ZNF131</i>, <i>GABRG1</i>, <i>GABRA2</i>, <i>DCHS1</i>, and <i>SPIDR</i> for MILK; <i>NR6A1</i>, <i>OLFML2A</i>, <i>EXT2</i>, POL<i>D1</i>, <i>GOT1</i>, and <i>ETV6</i> for FAT; <i>DPP6</i>, <i>LRRC26</i>, and the KCN gene family for FAT%; <i>CDC14A</i>, <i>RTCA</i>, <i>HSTN</i>, and <i>ODAM</i> for PROT; and <i>HERC3</i>, <i>HERC5</i>, <i>LALBA</i>, <i>CCL28</i>, and <i>NEURL1</i> for PROT%. Most of these genes are involved in relevant gene ontology (GO) terms such as fatty acid homeostasis, transporter regulator activity, response to progesterone and estradiol, response to steroid hormones, and lactation. The significant genomic regions found contribute to a better understanding of the molecular mechanisms related to LP and milk production in North American Holstein cattle. |
| first_indexed | 2024-03-10T05:29:02Z |
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| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T05:29:02Z |
| publishDate | 2021-11-01 |
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| spelling | doaj.art-ebb5f6863a5041feb0e63b20d93b76582023-11-22T23:29:25ZengMDPI AGGenes2073-44252021-11-011211183010.3390/genes12111830Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence DataVictor B. Pedrosa0Flavio S. Schenkel1Shi-Yi Chen2Hinayah R. Oliveira3Theresa M. Casey4Melkaye G. Melka5Luiz F. Brito6Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USACentre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G2W1, CanadaDepartment of Animal Sciences, Purdue University, West Lafayette, IN 47907, USADepartment of Animal Sciences, Purdue University, West Lafayette, IN 47907, USADepartment of Animal Sciences, Purdue University, West Lafayette, IN 47907, USADepartment of Animal and Food Science, University of Wisconsin River Falls, River Falls, WI 54022, USADepartment of Animal Sciences, Purdue University, West Lafayette, IN 47907, USALactation persistency and milk production are among the most economically important traits in the dairy industry. In this study, we explored the association of over 6.1 million imputed whole-genome sequence variants with lactation persistency (LP), milk yield (MILK), fat yield (FAT), fat percentage (FAT%), protein yield (PROT), and protein percentage (PROT%) in North American Holstein cattle. We identified 49, 3991, 2607, 4459, 805, and 5519 SNPs significantly associated with LP, MILK, FAT, FAT%, PROT, and PROT%, respectively. Various known associations were confirmed while several novel candidate genes were also revealed, including <i>ARHGAP35</i>, <i>NPAS1</i>, <i>TMEM160</i>, <i>ZC3H4</i>, <i>SAE1</i>, <i>ZMIZ1</i>, <i>PPIF</i>, <i>LDB2</i>, <i>ABI3</i>, <i>SERPINB6</i>, and <i>SERPINB9</i> for LP; <i>NIM1K</i>, <i>ZNF131</i>, <i>GABRG1</i>, <i>GABRA2</i>, <i>DCHS1</i>, and <i>SPIDR</i> for MILK; <i>NR6A1</i>, <i>OLFML2A</i>, <i>EXT2</i>, POL<i>D1</i>, <i>GOT1</i>, and <i>ETV6</i> for FAT; <i>DPP6</i>, <i>LRRC26</i>, and the KCN gene family for FAT%; <i>CDC14A</i>, <i>RTCA</i>, <i>HSTN</i>, and <i>ODAM</i> for PROT; and <i>HERC3</i>, <i>HERC5</i>, <i>LALBA</i>, <i>CCL28</i>, and <i>NEURL1</i> for PROT%. Most of these genes are involved in relevant gene ontology (GO) terms such as fatty acid homeostasis, transporter regulator activity, response to progesterone and estradiol, response to steroid hormones, and lactation. The significant genomic regions found contribute to a better understanding of the molecular mechanisms related to LP and milk production in North American Holstein cattle.https://www.mdpi.com/2073-4425/12/11/1830dairy cattleextended lactationgenetic variantsgenomewide association studyGWASQTL |
| spellingShingle | Victor B. Pedrosa Flavio S. Schenkel Shi-Yi Chen Hinayah R. Oliveira Theresa M. Casey Melkaye G. Melka Luiz F. Brito Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data Genes dairy cattle extended lactation genetic variants genomewide association study GWAS QTL |
| title | Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data |
| title_full | Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data |
| title_fullStr | Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data |
| title_full_unstemmed | Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data |
| title_short | Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data |
| title_sort | genomewide association analyses of lactation persistency and milk production traits in holstein cattle based on imputed whole genome sequence data |
| topic | dairy cattle extended lactation genetic variants genomewide association study GWAS QTL |
| url | https://www.mdpi.com/2073-4425/12/11/1830 |
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