Selection and Drift: A Comparison between Historic and Recent Dutch Friesian Cattle and Recent Holstein Friesian Using WGS Data
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 In the Netherlands, the local Dutch Friesian breed (DF) has gradually been replaced by the Holstein Friesian breed (HF).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 objectiv...
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MDPI AG
2022-01-01
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| Online Access: | https://www.mdpi.com/2076-2615/12/3/329 |
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| author | Ina Hulsegge Kor Oldenbroek Aniek Bouwman Roel Veerkamp Jack Windig |
| author_facet | Ina Hulsegge Kor Oldenbroek Aniek Bouwman Roel Veerkamp Jack Windig |
| author_sort | Ina Hulsegge |
| collection | DOAJ |
| description | 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 In the Netherlands, the local Dutch Friesian breed (DF) has gradually been replaced by the Holstein Friesian breed (HF).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. |
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| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-10T00:18:13Z |
| publishDate | 2022-01-01 |
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| series | Animals |
| spelling | doaj.art-bc98d9599c484ff789a8f021b6aadde32023-11-23T15:48:02ZengMDPI AGAnimals2076-26152022-01-0112332910.3390/ani12030329Selection and Drift: A Comparison between Historic and Recent Dutch Friesian Cattle and Recent Holstein Friesian Using WGS DataIna Hulsegge0Kor Oldenbroek1Aniek Bouwman2Roel Veerkamp3Jack Windig4Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH Wageningen, The NetherlandsAnimal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH Wageningen, The NetherlandsAnimal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH Wageningen, The NetherlandsAnimal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH Wageningen, The NetherlandsAnimal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH Wageningen, The NetherlandsOver 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.https://www.mdpi.com/2076-2615/12/3/329genetic diversityDutch FriesianHolstein Friesiancattle breedsWGS |
| spellingShingle | Ina Hulsegge Kor Oldenbroek Aniek Bouwman Roel Veerkamp Jack Windig Selection and Drift: A Comparison between Historic and Recent Dutch Friesian Cattle and Recent Holstein Friesian Using WGS Data Animals genetic diversity Dutch Friesian Holstein Friesian cattle breeds WGS |
| title | Selection and Drift: A Comparison between Historic and Recent Dutch Friesian Cattle and Recent Holstein Friesian Using WGS Data |
| title_full | Selection and Drift: A Comparison between Historic and Recent Dutch Friesian Cattle and Recent Holstein Friesian Using WGS Data |
| title_fullStr | Selection and Drift: A Comparison between Historic and Recent Dutch Friesian Cattle and Recent Holstein Friesian Using WGS Data |
| title_full_unstemmed | Selection and Drift: A Comparison between Historic and Recent Dutch Friesian Cattle and Recent Holstein Friesian Using WGS Data |
| title_short | Selection and Drift: A Comparison between Historic and Recent Dutch Friesian Cattle and Recent Holstein Friesian Using WGS Data |
| title_sort | selection and drift a comparison between historic and recent dutch friesian cattle and recent holstein friesian using wgs data |
| topic | genetic diversity Dutch Friesian Holstein Friesian cattle breeds WGS |
| url | https://www.mdpi.com/2076-2615/12/3/329 |
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