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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oai:doaj.org-article:ebb5f6863a5041feb0e63b20d93b76582021-11-25T17:42:29ZGenomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data10.3390/genes121118302073-4425https://doaj.org/article/ebb5f6863a5041feb0e63b20d93b76582021-11-01T00:00:00Zhttps://www.mdpi.com/2073-4425/12/11/1830https://doaj.org/toc/2073-4425Lactation 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.Victor B. PedrosaFlavio S. SchenkelShi-Yi ChenHinayah R. OliveiraTheresa M. CaseyMelkaye G. MelkaLuiz F. BritoMDPI AGarticledairy cattleextended lactationgenetic variantsgenomewide association studyGWASQTLGeneticsQH426-470ENGenes, Vol 12, Iss 1830, p 1830 (2021) |
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| collection |
DOAJ |
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| topic |
dairy cattle extended lactation genetic variants genomewide association study GWAS QTL Genetics QH426-470 |
| spellingShingle |
dairy cattle extended lactation genetic variants genomewide association study GWAS QTL Genetics QH426-470 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 |
| 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. |
| format |
article |
| 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 |
| title |
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_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_sort |
genomewide association analyses of lactation persistency and milk production traits in holstein cattle based on imputed whole-genome sequence data |
| publisher |
MDPI AG |
| publishDate |
2021 |
| url |
https://doaj.org/article/ebb5f6863a5041feb0e63b20d93b7658 |
| work_keys_str_mv |
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| _version_ |
1718412137875898368 |