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. 2022 Jan 29;12(3):329.
doi: 10.3390/ani12030329.

Selection and Drift: A Comparison between Historic and Recent Dutch Friesian Cattle and Recent Holstein Friesian Using WGS Data

Ina Hulsegge  1   2 , Kor Oldenbroek  1   2 , Aniek Bouwman  1 , Roel Veerkamp  1 , Jack Windig  1   2
Affiliations

Selection and Drift: A Comparison between Historic and Recent Dutch Friesian Cattle and Recent Holstein Friesian Using WGS Data

Ina Hulsegge et al. Animals (Basel). .

Abstract

Over the last century, genetic diversity in many cattle breeds has been affected by the replacement of traditional local breeds with just a few milk-producing breeds. In the Netherlands, the local Dutch Friesian breed (DF) has gradually been replaced by the Holstein Friesian breed (HF). The objective of this study is to investigate genomewide genetic diversity between a group of historically and recently used DF bulls and a group of recently used HF bulls. Genetic material of 12 historic (hDF), 12 recent DF bulls (rDF), and 12 recent HF bulls (rHF) in the Netherlands was sequenced. Based on the genomic information, different parameters-e.g., allele frequencies, inbreeding coefficient, and runs of homozygosity (ROH)-were calculated. Our findings showed that a large amount of diversity is shared between the three groups, but each of them has a unique genetic identity (12% of the single nucleotide polymorphisms were group-specific). The rDF is slightly more diverged from rHF than hDF. The inbreeding coefficient based on runs of homozygosity (Froh) was higher for rDF (0.24) than for hDF (0.17) or rHF (0.13). Our results also displayed the presence of several genomic regions that differentiated between the groups. In addition, thirteen, forty-five, and six ROH islands were identified in hDF, rDF, and rHF, respectively. The genetic diversity of the DF breed reduced over time, but this did not lead to higher inbreeding levels-especially, inbreeding due to recent ancestors was not increased.

Keywords: Dutch Friesian; Holstein Friesian; WGS; cattle breeds; genetic diversity.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Venn diagram showing percentage of shared and group-specific variants in each group.
Figure 2
Figure 2
Genetic relationships based on PCA between the three groups.
Figure 3
Figure 3
The mean and standard deviation of the average length of runs of homozygosity (ROH) (A) and mean number of ROH within each ROH length class (B).
Figure 4
Figure 4
Manhattan plots of Z-transformed fixation index (ZFst) across all autosomes. The ZFst values were calculated for each sliding 40-kb window with steps of 20 kb across all autosomes. The solid red line indicates ZFst values > 8; differentiated genomic regions (ZFst values > 8 and the number of SNPs in the region > 5) are highlight green.
Figure 4
Figure 4
Manhattan plots of Z-transformed fixation index (ZFst) across all autosomes. The ZFst values were calculated for each sliding 40-kb window with steps of 20 kb across all autosomes. The solid red line indicates ZFst values > 8; differentiated genomic regions (ZFst values > 8 and the number of SNPs in the region > 5) are highlight green.
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