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This study reports runs of homozygosity (ROH) and heterozygosity (ROHet) distributed in a large population of Holstein cattle on the basis of two microarrays of medium (50k; 2163 animals; 54 609 SNPs) and high single nucleotide polymorphism (SNP) density (HD; 600 animals; 777 692 SNPs). To assess the inbreeding values of Holstein cattle, the ROH-based genomic inbreeding coefficient (FROH) was calculated. The comparison of SNP panels suggested that FROH values above 4 Mb should be considered for panels of medium densities as a relatively reliable measure of inbreeding. Moreover, ROH hotspots and coldspots were identified and compared between the HD and 50k SNP panels and were carefully examined for association with production and functional traits. The obtained results pinpointed genomic regions presumably under selection pressure in Holstein cattle. The regions overlapped with a large number of genes, including <italic>GHR</italic>, <italic>GBF1</italic>, <italic>SUMF1</italic>, <italic>CCL28</italic>, <italic>NIM1K</italic>, <italic>U6</italic>, <italic>BTRC</italic> and <italic>FABP1,</italic> many of which are involved in important Holstein cattle characteristics. We also found that some ROH hotspots and coldspots identified with the HD panel were not detected with the 50k panel, mainly because of insufficient SNP density in certain genomic regions. This suggests that using medium-density panels might not be the best choice when precise identification of ROH patterns is the main goal. In summary, in this work, we confirmed that a high-density SNP panel compared to a medium-density SNP panel allows for more precise identification of ROH patterns, especially in the case of short ROH that could be associated with ancestral inbreeding.
</abstract>

This study reports runs of homozygosity (ROH) and heterozygosity (ROHet) distributed in a large population of Holstein cattle on the basis of two microarrays of medium (50k; 2163 animals; 54 609 SNPs) and high single nucleotide polymorphism (SNP) density (HD; 600 animals; 777 692 SNPs). To assess the inbreeding values of Holstein cattle, the ROH-based genomic inbreeding coefficient (FROH) was calculated. The comparison of SNP panels suggested that FROH values above 4 Mb should be considered for panels of medium densities as a relatively reliable measure of inbreeding. Moreover, ROH hotspots and coldspots were identified and compared between the HD and 50k SNP panels and were carefully examined for association with production and functional traits. The obtained results pinpointed genomic regions presumably under selection pressure in Holstein cattle. The regions overlapped with a large number of genes, including GHR, GBF1, SUMF1, CCL28, NIM1K, U6, BTRC and FABP1, many of which are involved in important Holstein cattle characteristics. We also found that some ROH hotspots and coldspots identified with the HD panel were not detected with the 50k panel, mainly because of insufficient SNP density in certain genomic regions. This suggests that using medium-density panels might not be the best choice when precise identification of ROH patterns is the main goal. In summary, in this work, we confirmed that a high-density SNP panel compared to a medium-density SNP panel allows for more precise identification of ROH patterns, especially in the case of short ROH that could be associated with ancestral inbreeding.

Comprehensive analysis of runs of homozygosity and heterozygosity in Holstein cattle on the basis of medium and high density SNP panels and large population sample

Annals of Animal Science

This work is licensed under the Creative Commons Attribution 4.0 International License.

This study reports runs of homozygosity (ROH) and heterozygosity (ROHet) distributed in a large population of Holstein cattle on the basis of two microarrays...

Comprehensive analysis of runs of homozygosity and heterozygosity in Holstein cattle on the basis of medium and high density SNP panels and large population sample

Published Online: Apr 23, 2024

Page range: 431 - 444

Received: Aug 01, 2023

Accepted: Oct 04, 2023

DOI: https://doi.org/10.2478/aoas-2023-0100

Keywords
runs of homozygosity, microarray, Holstein cattle, inbreeding

© 2024 Tomasz Szmatoła et al., published by Sciendo

This work is licensed under the Creative Commons Attribution 4.0 International License.

Comprehensive analysis of runs of homozygosity and heterozygosity in Holstein cattle on the basis of medium and high density SNP panels and large population sample

Published Online: Apr 23, 2024

Page range: 431 - 444

Received: Aug 01, 2023

Accepted: Oct 04, 2023

DOI: https://doi.org/10.2478/aoas-2023-0100

Keywordsruns of homozygosity, microarray, Holstein cattle, inbreeding

© 2024 Tomasz Szmatoła et al., published by Sciendo

This work is licensed under the Creative Commons Attribution 4.0 International License.

Keywords
runs of homozygosity, microarray, Holstein cattle, inbreeding