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

Signer-Hasler, Heidi; Henkel, Jan; Bangerter, Erika; Bulut, Zafer; Consortium, The VarGoats; 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) Springer 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 forma‑tion 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 anno‑tated 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:	School of Agricultural, Forest and Food Sciences HAFL School of Agricultural, Forest and Food Sciences HAFL > Agriculture School of Agricultural, Forest and Food Sciences HAFL > Agriculture > Livestock and Horses
Name:	Signer-Hasler, Heidi0000-0001-5193-5306; Henkel, Jan; Bangerter, Erika; Bulut, Zafer; Consortium, The VarGoats; Drögemüller, Cord; Leeb, Tosso and Flury, Christine
Subjects:	S Agriculture > SF Animal culture
ISSN:	1297-9686
Publisher:	Springer
Language:	English
Submitter:	Heidi Signer-Hasler
Date Deposited:	23 Feb 2022 09:37
Last Modified:	27 Feb 2022 01:35
Publisher DOI:	10.1186/s12711-022-00695-w
ARBOR DOI:	10.24451/arbor.16525
URI:	https://arbor.bfh.ch/id/eprint/16525