Genomic relatedness and diversity of Swedish native cattle breeds

Abstract

Background: Native cattle breeds are important genetic resources given their adaptation to the local environment in which they are bred. However, the widespread use of commercial cattle breeds has resulted in a marked reduction in population size of several native cattle breeds worldwide. Therefore, conservation management of native cattle breeds requires urgent attention to avoid their extinction. To this end, we genotyped nine Swedish native cattle breeds with genome-wide 150 K single nucleotide polymorphisms (SNPs) to investigate the level of genetic diversity and relatedness between these breeds.

Results: We used various SNP-based approaches on this dataset to connect the demographic history with the genetic diversity and population structure of these Swedish cattle breeds. Our results suggest that the Väne and Ringamåla breeds originating from southern Sweden have experienced population isolation and have a low genetic diversity, whereas the Fjäll breed has a large founder population and a relatively high genetic diversity. Based on the shared ancestry and the constructed phylogenetic trees, we identified two major clusters in Swedish native cattle. In the first cluster, which includes Swedish mountain cattle breeds, there was little differentiation among the Fjäll, Fjällnära, Swedish Polled, and Bohus Polled breeds. The second cluster consists of breeds from southern Sweden: Väne, Ringamåla and Swedish Red. Interestingly, we also identified sub-structuring in the Fjällnära breed, which indicates different breeding practices on the farms that maintain this breed.

Conclusions: This study represents the first comprehensive genome-wide analysis of the genetic relatedness and diversity in Swedish native cattle breeds. Our results show that different demographic patterns such as genetic isolation and cross-breeding have shaped the genomic diversity of Swedish native cattle breeds and that the Swedish mountain breeds have retained their authentic distinct gene pool without significant contribution from any of the other European cattle breeds that were included in this study.

Fig. 1

A map of Sweden indicating the approximate geographic origin of the analysed Swedish cattle breeds. Important locations where remaining animals of local breeds were found are marked (star = Fjällnära, diamond = Bohus Polled, triangle = Väne, square = Ringamåla). Some of the breeds originated from a wider geographic area: the Fjäll breed from northern Sweden, the Swedish Red Polled from middle Sweden, the Swedish Red from south middle to southern Sweden, and the Swedish Holstein-Friesian from southern Sweden. The Swedish Polled cattle shares ancestry with the Swedish Red Polled and Fjäll breeds

Fig. 2

a ROH profile of Swedish cattle breeds, where each circle represents an individual and b linkage disequilibrium decay in four Swedish cattle breeds for which the sample size was larger than 8

Fig. 3

Genetic relatedness among the Swedish cattle breeds using: a principal component analysis, b F_st-based phylogenetic tree, and c maximum likelihood based phylogenetic tree

Fig. 4

Model-based clustering of Swedish cattle breeds based on the estimated membership fraction of individuals

Fig. 5

fineSTRUCTURE-based phylogenetic tree. The intensity of colours indicates the number of shared haplotypic chunks. The asterisk (*) indicates low differentiation between Swedish Polled cattle and Fjäll cattle

Fig. 6

Genetic relationships between the Swedish cattle breeds and several European cattle breeds using: a principal component analysis and b model-based clustering of different European cattle breeds based on the estimated membership fraction of individuals