Abstract
Simple SummaryOver the last century, genetic diversity in the cattle species has been affected by the replacement of many local, dual-purpose breeds with a few specialized, high-output dairy breeds. This replacement caused a sharp decline in the population size of local breeds. In the Netherlands, the local Dutch Friesian breed has gradually been replaced by the Holstein Friesian. This resulted in a rapid decrease in numbers of the Dutch Friesian breed with an associated risk of loss of genetic diversity due to drift. The objective of this study is to investigate genomewide genetic diversity between a group of historic and recent Dutch Friesian bulls and a group of recently used Holstein Friesian bulls. Our findings showed that a large amount of diversity is shared between the three groups, but each of them has some unique genetic identity (12% of the single nucleotide polymorphism were group-specific). The genetic diversity of the Dutch Friesians reduced over time, but this did not lead to higher inbreeding levels—especially, inbreeding due to recent ancestors has not increased. Genetically, the recent Dutch Friesians were slightly more different from Holstein Friesians than the historic Dutch Friesians. Our results also highlighted the presence of several genomic regions that differentiated between the groups.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 In the Netherlands, the local Dutch Friesian breed (DF) has gradually been replaced by the Holstein Friesian breed (HF).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.
Highlights
Over the last century, genetic diversity in many European national cattle populations has been affected by replacement of traditional local breeds with just a few specialized milk producing breeds, e.g., the Holstein Friesian, Brown Swiss, and Jersey
Among the set of 10,780,681 single nucleotide polymorphism (SNP), 11.98% were identified as putatively group-specific (Figure 1), indicating that the genotype of one of the alleles was present in only one of the three groups
(6.69%), while recent DF bulls (rDF) displayed the lowest number of group-specific SNPs (2.14%)
Summary
Genetic diversity in many European national cattle populations has been affected by replacement of traditional local breeds with just a few specialized milk producing breeds, e.g., the Holstein Friesian, Brown Swiss, and Jersey. The predominant use of these breeds caused a sharp decline in the population size of local dual-purpose breeds [1,2]. Moscarelli et al [3] reported the presence of several genomic regions that vary between original and modern Brown cattle populations, in line with their different breeding histories. Selection and genetic drift will both have contributed to the genetic differentiation between original and modern breeds. Local breeds might represent an important genetic resource to facilitate animal breeding when changes occur in production systems and market requirements
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