Genomic regions underlying positive selection in local, Alpine cattle breeds

Signer-Hasler, Heidi (author), Casanova, Lucas (author), Barenco, Alex (author), Maître, Blaise (author), Bagnato, Alessandro (author), Vevey, Mario (author), Berger, Beate (author), Simčič, Mojca (author), Boichon, Denis (author), Capitan, Aurélien (author), Medjugorac, Ivica (author), Bennewitz, Jörn (author), Mészáros, Gábor (author), Sölkner, Johann (author), Drögemüller, Cord (author), Flury, Christine (author)

We used genome-wide SNP data from 18 local cattle breeds from six countries of the Alpine region to characterize population structure and identify genomic regions underlying positive selection. The geographically close breeds Evolèner, Eringer, Valdostana Pezzata Nera, and Valdostana Castana were found to differ from all other Alpine breeds. In addition, three breeds, Simmental, and Original Braunvieh from Switzerland and Pinzgauer from Austria built three separate clusters. Of the 18 breeds studied, the intra-alpine Swiss breed Evolèner had the highest average inbreeding based on runs of homozygosity (FROH) and the highest average genomic relationship within the breed. In contrast, Slovenian Cika cattle had the lowest average genomic inbreeding and the lowest average genomic relationship within the breed. We found selection signatures on chromosome 6 near known genes such as KIT and LCORL explaining variation in coat color and body size in cattle. The most prominent selection signatures were similar regardless of marker density and the breeds in the data set. In addition, using available high-density SNP data from 14 of the breeds we identified 47 genome regions as ROH islands. The proportion of homozygous animals was higher in all studied animals of local breeds than in Holstein and Brown Swiss cattle, the two most important commercial breeds in the Alpine region. We report ROH islands near genes related to thermoregulation, coat color, production, and stature. The results of this study serve as a basis for the search for causal variants underlying adaptation to the alpine environment and other specific characteristics selected during the evolution of local Alpine cattle breeds.

• Language: English
• Keywords: diversity, selection signature, runs of homozygosity, cattle
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Publication status: Published
• Publication version: Version of Record
• Year: 2023
• Number of pages: Str. 239-253
• Numbering: Vol. 54, iss. 3, art. 13295
• PID: 20.500.12556/RUL-146996
• UDC: 636.2:575
• ISSN on article: 1365-2052
• DOI: 10.1111/age.13295
• COBISS.SI-ID: 141111043
• Publication date in RUL: 19.06.2023

Record is a part of a journal

• Title: Animal genetics
• Shortened title: Anim. genet.
• Publisher: Wiley
• ISSN: 1365-2052
• COBISS.SI-ID: 2344072

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: govedo, lokalne pasme, Alpe, genetika, genomika

Projects

• Funder: Other - Other funder or multiple funders
• Funding programme: The Swiss Federal Office of Agriculture (FOAG)