Genomic regions underlying positive selection in local, Alpine cattle breeds

Abstract

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 (F ROH ) 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.

Genetic legacy and adaptive signatures: investigating the history, diversity, and selection signatures in Rendena cattle resilient to eighteenth century rinderpest epidemics

“…The large number of immune response genes under selection may be the result of the Rendena having survived a series of historical epidemics that affected the Alps over several centuries. This hypothesis finds a further confirmation in the signatures of selection related to disease resistance and immunity that were found in other breeds from the Alpine arc [ 58 , 66 , 67 ].…”

MOCOS‐associated renal syndrome in a Brown Swiss cattle

“…Alternatively, it may indicate a very ancient origin of the derived allele, before the formation of these modern breeds. These breeds originate from the same geographical area and share a significant genetic relationship 12,13 . Interestingly, some carriers of the MOCOS variant have also been observed in the founding breed of Brown Swiss cattle that originated in North America from animals bred in Switzerland, the so‐called Original Braunvieh population.…”

“…These breeds originate from the same geographical area and share a significant genetic relationship. 12,13 Interestingly, some carriers of the MOCOS variant have also been observed in the founding breed of Brown Swiss cattle that originated in North America from animals bred in Switzerland, the so-called Original Braunvieh population. The Original Braunvieh breed is the ancestor of the modern global Brown Swiss population, which was created in the USA from animals purchased in Switzerland between 1869 and 1910.…”