Whole-Genome Sequencing Data Reveal New Loci Affecting Milk Production in German Black Pied Cattle (DSN)
German Black Pied (DSN) is considered an ancestral population of the Holstein breed. The goal of the current study was to fine-map genomic loci for milk production traits and to provide sequence variants for selection. We studied genome-wide associations for milk-production traits in 2160 DSN cows....
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MDPI AG
2023-02-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/3/581 |
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| author | Paula Korkuć Guilherme B. Neumann Deike Hesse Danny Arends Monika Reißmann Siham Rahmatalla Katharina May Manuel J. Wolf Sven König Gudrun A. Brockmann |
| author_facet | Paula Korkuć Guilherme B. Neumann Deike Hesse Danny Arends Monika Reißmann Siham Rahmatalla Katharina May Manuel J. Wolf Sven König Gudrun A. Brockmann |
| author_sort | Paula Korkuć |
| collection | DOAJ |
| description | German Black Pied (DSN) is considered an ancestral population of the Holstein breed. The goal of the current study was to fine-map genomic loci for milk production traits and to provide sequence variants for selection. We studied genome-wide associations for milk-production traits in 2160 DSN cows. Using 11.7 million variants from whole-genome sequencing of 304 representative DSN cattle, we identified 1980 associated variants (−log<sub>10</sub>(<i>p</i>) ≥ 7.1) in 13 genomic loci on 9 chromosomes. The highest significance was found for the <i>MGST1</i> region affecting milk fat content (−log<sub>10</sub>(<i>p</i>) = 11.93, MAF = 0.23, substitution effect of the minor allele (ß<sub>MA</sub>) = −0.151%). Different from Holstein, <i>DGAT1</i> was fixed (0.97) for the alanine protein variant for high milk and protein yield. A key gene affecting protein content was <i>CSN1S1</i> (−log<sub>10</sub>(<i>p</i>) = 8.47, MAF = 049, ß<sub>MA</sub> = −0.055%) and the <i>GNG2</i> region (−log<sub>10</sub>(<i>p</i>) = 10.48, MAF = 0.34, ß<sub>MA</sub> = 0.054%). Additionally, we suggest the importance of <i>FGF12</i> for protein and fat yield, <i>HTR3C</i> for milk yield, <i>TLE4</i> for milk and protein yield, and <i>TNKS</i> for milk and fat yield. Selection for favored alleles can improve milk yield and composition. With respect to maintaining the dual-purpose type of DSN, unfavored linkage to genes affecting muscularity has to be investigated carefully, before the milk-associated variants can be applied for selection in the small population. |
| first_indexed | 2024-03-11T06:29:50Z |
| format | Article |
| id | doaj.art-3162fbbac33f4acb83b11169eaf5a079 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T06:29:50Z |
| publishDate | 2023-02-01 |
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| record_format | Article |
| series | Genes |
| spelling | doaj.art-3162fbbac33f4acb83b11169eaf5a0792023-11-17T11:16:35ZengMDPI AGGenes2073-44252023-02-0114358110.3390/genes14030581Whole-Genome Sequencing Data Reveal New Loci Affecting Milk Production in German Black Pied Cattle (DSN)Paula Korkuć0Guilherme B. Neumann1Deike Hesse2Danny Arends3Monika Reißmann4Siham Rahmatalla5Katharina May6Manuel J. Wolf7Sven König8Gudrun A. Brockmann9Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Animal Breeding and Molecular Genetics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, GermanyAlbrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Animal Breeding and Molecular Genetics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, GermanyAlbrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Animal Breeding and Molecular Genetics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, GermanyDepartment of Applied Sciences, Northumbria University, Ellison PI, Newcastle upon Tyne NE1 8ST, UKAlbrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Animal Breeding and Molecular Genetics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, GermanyAlbrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Animal Breeding and Molecular Genetics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, GermanyInstitute of Animal Breeding and Genetics, Justus-Liebig-Universität Gießen, Ludwigstr. 21, 35390 Gießen, GermanyInstitute of Animal Breeding and Genetics, Justus-Liebig-Universität Gießen, Ludwigstr. 21, 35390 Gießen, GermanyInstitute of Animal Breeding and Genetics, Justus-Liebig-Universität Gießen, Ludwigstr. 21, 35390 Gießen, GermanyAlbrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Animal Breeding and Molecular Genetics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, GermanyGerman Black Pied (DSN) is considered an ancestral population of the Holstein breed. The goal of the current study was to fine-map genomic loci for milk production traits and to provide sequence variants for selection. We studied genome-wide associations for milk-production traits in 2160 DSN cows. Using 11.7 million variants from whole-genome sequencing of 304 representative DSN cattle, we identified 1980 associated variants (−log<sub>10</sub>(<i>p</i>) ≥ 7.1) in 13 genomic loci on 9 chromosomes. The highest significance was found for the <i>MGST1</i> region affecting milk fat content (−log<sub>10</sub>(<i>p</i>) = 11.93, MAF = 0.23, substitution effect of the minor allele (ß<sub>MA</sub>) = −0.151%). Different from Holstein, <i>DGAT1</i> was fixed (0.97) for the alanine protein variant for high milk and protein yield. A key gene affecting protein content was <i>CSN1S1</i> (−log<sub>10</sub>(<i>p</i>) = 8.47, MAF = 049, ß<sub>MA</sub> = −0.055%) and the <i>GNG2</i> region (−log<sub>10</sub>(<i>p</i>) = 10.48, MAF = 0.34, ß<sub>MA</sub> = 0.054%). Additionally, we suggest the importance of <i>FGF12</i> for protein and fat yield, <i>HTR3C</i> for milk yield, <i>TLE4</i> for milk and protein yield, and <i>TNKS</i> for milk and fat yield. Selection for favored alleles can improve milk yield and composition. With respect to maintaining the dual-purpose type of DSN, unfavored linkage to genes affecting muscularity has to be investigated carefully, before the milk-associated variants can be applied for selection in the small population.https://www.mdpi.com/2073-4425/14/3/581GWAS<i>MGST1</i>alpha S1-caseinserotonin receptorlactationmilk yield |
| spellingShingle | Paula Korkuć Guilherme B. Neumann Deike Hesse Danny Arends Monika Reißmann Siham Rahmatalla Katharina May Manuel J. Wolf Sven König Gudrun A. Brockmann Whole-Genome Sequencing Data Reveal New Loci Affecting Milk Production in German Black Pied Cattle (DSN) Genes GWAS <i>MGST1</i> alpha S1-casein serotonin receptor lactation milk yield |
| title | Whole-Genome Sequencing Data Reveal New Loci Affecting Milk Production in German Black Pied Cattle (DSN) |
| title_full | Whole-Genome Sequencing Data Reveal New Loci Affecting Milk Production in German Black Pied Cattle (DSN) |
| title_fullStr | Whole-Genome Sequencing Data Reveal New Loci Affecting Milk Production in German Black Pied Cattle (DSN) |
| title_full_unstemmed | Whole-Genome Sequencing Data Reveal New Loci Affecting Milk Production in German Black Pied Cattle (DSN) |
| title_short | Whole-Genome Sequencing Data Reveal New Loci Affecting Milk Production in German Black Pied Cattle (DSN) |
| title_sort | whole genome sequencing data reveal new loci affecting milk production in german black pied cattle dsn |
| topic | GWAS <i>MGST1</i> alpha S1-casein serotonin receptor lactation milk yield |
| url | https://www.mdpi.com/2073-4425/14/3/581 |
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