Runs of homozygosity in Swiss goats reveal genetic changes associated with domestication and modern selection
Abstract Background The domestication of goat (Capra hircus) started 11,000 years ago in the fertile crescent. Breed formation in the nineteenth century, establishment of herd books, and selection for specific traits resulted in 10 modern goat breeds in Switzerland. We analyzed whole-genome sequenci...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | deu |
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BMC
2022-01-01
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| Series: | Genetics Selection Evolution |
| Online Access: | https://doi.org/10.1186/s12711-022-00695-w |
| _version_ | 1819280485022433280 |
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| author | Heidi Signer-Hasler Jan Henkel Erika Bangerter Zafer Bulut The VarGoats Consortium Cord Drögemüller Tosso Leeb Christine Flury |
| author_facet | Heidi Signer-Hasler Jan Henkel Erika Bangerter Zafer Bulut The VarGoats Consortium Cord Drögemüller Tosso Leeb Christine Flury |
| author_sort | Heidi Signer-Hasler |
| collection | DOAJ |
| description | Abstract Background The domestication of goat (Capra hircus) started 11,000 years ago in the fertile crescent. Breed formation in the nineteenth century, establishment of herd books, and selection for specific traits resulted in 10 modern goat breeds in Switzerland. We analyzed whole-genome sequencing (WGS) data from 217 modern goats and nine wild Bezoar goats (Capra aegagrus). After quality control, 27,728,288 biallelic single nucleotide variants (SNVs) were used for the identification of runs of homozygosity (ROH) and the detection of ROH islands. Results Across the 226 caprine genomes from 11 populations, we detected 344 ROH islands that harbor 1220 annotated genes. We compared the ROH islands between the modern breeds and the Bezoar goats. As a proof of principle, we confirmed a signature of selection, which contains the ASIP gene that controls several breed-specific coat color patterns. In two other ROH islands, we identified two missense variants, STC1:p.Lys139Arg and TSHR:p.Ala239Thr, which might represent causative functional variants for domestication signatures. Conclusions We have shown that the information from ROH islands using WGS data is suitable for the analysis of signatures of selection and allowed the detection of protein coding variants that may have conferred beneficial phenotypes during goat domestication. We hypothesize that the TSHR:p.Ala239Thr variant may have played a role in changing the seasonality of reproduction in modern domesticated goats. The exact functional significance of the STC1:p.Lys139Arg variant remains unclear and requires further investigation. Nonetheless, STC1 might represent a new domestication gene affecting relevant traits such as body size and/or milk yield in goats. |
| first_indexed | 2024-12-24T00:44:32Z |
| format | Article |
| id | doaj.art-9907fff68af74612a1f5d55ac6ed6b5c |
| institution | Directory Open Access Journal |
| issn | 1297-9686 |
| language | deu |
| last_indexed | 2024-12-24T00:44:32Z |
| publishDate | 2022-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj.art-9907fff68af74612a1f5d55ac6ed6b5c2022-12-21T17:23:51ZdeuBMCGenetics Selection Evolution1297-96862022-01-0154111110.1186/s12711-022-00695-wRuns of homozygosity in Swiss goats reveal genetic changes associated with domestication and modern selectionHeidi Signer-Hasler0Jan Henkel1Erika Bangerter2Zafer Bulut3The VarGoats ConsortiumCord Drögemüller4Tosso Leeb5Christine Flury6School of Agricultural, Forest and Food Sciences, Bern University of Applied SciencesInstitute of Genetics, Vetsuisse Faculty, University of BernSwiss Goat Breeding Association SZZVDepartment of Biochemistry, Faculty of Veterinary Medicine, Selcuk UniversityInstitute of Genetics, Vetsuisse Faculty, University of BernInstitute of Genetics, Vetsuisse Faculty, University of BernSchool of Agricultural, Forest and Food Sciences, Bern University of Applied SciencesAbstract Background The domestication of goat (Capra hircus) started 11,000 years ago in the fertile crescent. Breed formation in the nineteenth century, establishment of herd books, and selection for specific traits resulted in 10 modern goat breeds in Switzerland. We analyzed whole-genome sequencing (WGS) data from 217 modern goats and nine wild Bezoar goats (Capra aegagrus). After quality control, 27,728,288 biallelic single nucleotide variants (SNVs) were used for the identification of runs of homozygosity (ROH) and the detection of ROH islands. Results Across the 226 caprine genomes from 11 populations, we detected 344 ROH islands that harbor 1220 annotated genes. We compared the ROH islands between the modern breeds and the Bezoar goats. As a proof of principle, we confirmed a signature of selection, which contains the ASIP gene that controls several breed-specific coat color patterns. In two other ROH islands, we identified two missense variants, STC1:p.Lys139Arg and TSHR:p.Ala239Thr, which might represent causative functional variants for domestication signatures. Conclusions We have shown that the information from ROH islands using WGS data is suitable for the analysis of signatures of selection and allowed the detection of protein coding variants that may have conferred beneficial phenotypes during goat domestication. We hypothesize that the TSHR:p.Ala239Thr variant may have played a role in changing the seasonality of reproduction in modern domesticated goats. The exact functional significance of the STC1:p.Lys139Arg variant remains unclear and requires further investigation. Nonetheless, STC1 might represent a new domestication gene affecting relevant traits such as body size and/or milk yield in goats.https://doi.org/10.1186/s12711-022-00695-w |
| spellingShingle | Heidi Signer-Hasler Jan Henkel Erika Bangerter Zafer Bulut The VarGoats Consortium Cord Drögemüller Tosso Leeb Christine Flury Runs of homozygosity in Swiss goats reveal genetic changes associated with domestication and modern selection Genetics Selection Evolution |
| title | Runs of homozygosity in Swiss goats reveal genetic changes associated with domestication and modern selection |
| title_full | Runs of homozygosity in Swiss goats reveal genetic changes associated with domestication and modern selection |
| title_fullStr | Runs of homozygosity in Swiss goats reveal genetic changes associated with domestication and modern selection |
| title_full_unstemmed | Runs of homozygosity in Swiss goats reveal genetic changes associated with domestication and modern selection |
| title_short | Runs of homozygosity in Swiss goats reveal genetic changes associated with domestication and modern selection |
| title_sort | runs of homozygosity in swiss goats reveal genetic changes associated with domestication and modern selection |
| url | https://doi.org/10.1186/s12711-022-00695-w |
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