Runs of homozygosity in Swiss goats reveal genetic changes associated with domestication and modern selection

Signer-Hasler, Heidi; Henkel, Jan; Bangerter, Erika; Bulut, Zafer; Drögemüller, Cord; Leeb, Tosso; Flury, Christine (2022). Runs of homozygosity in Swiss goats reveal genetic changes associated with domestication and modern selection. Genetics, selection, evolution, 54(1), p. 6. BioMed Central 10.1186/s12711-022-00695-w

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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.

Item Type:

Journal Article (Original Article)

Division/Institute:

09 Interdisciplinary Units > Next Generation Sequencing (NGS) Platform
05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH) > Institute of Genetics
05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH)

Graduate School:

Graduate School for Cellular and Biomedical Sciences (GCB)

UniBE Contributor:

Henkel, Jan Wolfgang, Drögemüller, Cord, Leeb, Tosso

Subjects:

500 Science > 590 Animals (Zoology)
600 Technology > 630 Agriculture
500 Science > 570 Life sciences; biology
600 Technology > 610 Medicine & health

ISSN:

1297-9686

Publisher:

BioMed Central

Language:

English

Submitter:

Cord Drögemüller

Date Deposited:

11 Feb 2022 16:36

Last Modified:

05 Dec 2022 16:05

Publisher DOI:

10.1186/s12711-022-00695-w

PubMed ID:

35073837

BORIS DOI:

10.48350/164803

URI:

https://boris.unibe.ch/id/eprint/164803

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