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Identification of unique ROH regions with unfavorable effects on production and fertility traits in Canadian Holsteins

BACKGROUND: The advent of genomic information and the reduction in the cost of genotyping have led to the use of genomic information to estimate genomic inbreeding as an alternative to pedigree inbreeding. Using genomic measures, effects of genomic inbreeding on production and fertility traits have...

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Autores principales: Makanjuola, Bayode O., Maltecca, Christian, Miglior, Filippo, Marras, Gabriele, Abdalla, Emhimad A., Schenkel, Flavio S., Baes, Christine F.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8406729/
https://www.ncbi.nlm.nih.gov/pubmed/34461820
http://dx.doi.org/10.1186/s12711-021-00660-z
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author Makanjuola, Bayode O.
Maltecca, Christian
Miglior, Filippo
Marras, Gabriele
Abdalla, Emhimad A.
Schenkel, Flavio S.
Baes, Christine F.
author_facet Makanjuola, Bayode O.
Maltecca, Christian
Miglior, Filippo
Marras, Gabriele
Abdalla, Emhimad A.
Schenkel, Flavio S.
Baes, Christine F.
author_sort Makanjuola, Bayode O.
collection PubMed
description BACKGROUND: The advent of genomic information and the reduction in the cost of genotyping have led to the use of genomic information to estimate genomic inbreeding as an alternative to pedigree inbreeding. Using genomic measures, effects of genomic inbreeding on production and fertility traits have been observed. However, there have been limited studies on the specific genomic regions causing the observed negative association with the trait of interest. Our aim was to identify unique run of homozygosity (ROH) genotypes present within a given genomic window that display negative associations with production and fertility traits and to quantify the effects of these identified ROH genotypes. METHODS: In total, 50,575 genotypes based on a 50K single nucleotide polymorphism (SNP) array and 259,871 pedigree records were available. Of these 50,575 genotypes, 46,430 cows with phenotypic records for production and fertility traits and having a first calving date between 2008 and 2018 were available. Unique ROH genotypes identified using a sliding-window approach were fitted into an animal mixed model as fixed effects to determine their effect on production and fertility traits. RESULTS: In total, 133 and 34 unique ROH genotypes with unfavorable effects were identified for production and fertility traits, respectively, at a 1% genome-wise false discovery rate. Most of these ROH regions were located on bovine chromosomes 8, 13, 14 and 19 for both production and fertility traits. For production traits, the average of all the unfavorably identified unique ROH genotypes effects were estimated to decrease milk yield by 247.30 kg, fat yield by 11.46 kg and protein yield by 8.11 kg. Similarly, for fertility traits, an average 4.81-day extension in first service to conception, a 0.16 increase in number of services, and a − 0.07 incidence in 56-day non-return rate were observed. Furthermore, a ROH region located on bovine chromosome 19 was identified that, when homozygous, had a negative effect on production traits. Signatures of selection proximate to this region have implicated GH1 as a potential candidate gene, which encodes the growth hormone that binds the growth hormone receptor. This observed negative effect could be a consequence of unfavorable alleles in linkage disequilibrium with favorable alleles. CONCLUSIONS: ROH genotypes with unfavorable effects on production and fertility traits were identified within and across multiple traits on most chromosomes. These identified ROH genotypes could be included in mate selection programs to minimize their frequency in future generations. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12711-021-00660-z.
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spelling pubmed-84067292021-08-31 Identification of unique ROH regions with unfavorable effects on production and fertility traits in Canadian Holsteins Makanjuola, Bayode O. Maltecca, Christian Miglior, Filippo Marras, Gabriele Abdalla, Emhimad A. Schenkel, Flavio S. Baes, Christine F. Genet Sel Evol Research Article BACKGROUND: The advent of genomic information and the reduction in the cost of genotyping have led to the use of genomic information to estimate genomic inbreeding as an alternative to pedigree inbreeding. Using genomic measures, effects of genomic inbreeding on production and fertility traits have been observed. However, there have been limited studies on the specific genomic regions causing the observed negative association with the trait of interest. Our aim was to identify unique run of homozygosity (ROH) genotypes present within a given genomic window that display negative associations with production and fertility traits and to quantify the effects of these identified ROH genotypes. METHODS: In total, 50,575 genotypes based on a 50K single nucleotide polymorphism (SNP) array and 259,871 pedigree records were available. Of these 50,575 genotypes, 46,430 cows with phenotypic records for production and fertility traits and having a first calving date between 2008 and 2018 were available. Unique ROH genotypes identified using a sliding-window approach were fitted into an animal mixed model as fixed effects to determine their effect on production and fertility traits. RESULTS: In total, 133 and 34 unique ROH genotypes with unfavorable effects were identified for production and fertility traits, respectively, at a 1% genome-wise false discovery rate. Most of these ROH regions were located on bovine chromosomes 8, 13, 14 and 19 for both production and fertility traits. For production traits, the average of all the unfavorably identified unique ROH genotypes effects were estimated to decrease milk yield by 247.30 kg, fat yield by 11.46 kg and protein yield by 8.11 kg. Similarly, for fertility traits, an average 4.81-day extension in first service to conception, a 0.16 increase in number of services, and a − 0.07 incidence in 56-day non-return rate were observed. Furthermore, a ROH region located on bovine chromosome 19 was identified that, when homozygous, had a negative effect on production traits. Signatures of selection proximate to this region have implicated GH1 as a potential candidate gene, which encodes the growth hormone that binds the growth hormone receptor. This observed negative effect could be a consequence of unfavorable alleles in linkage disequilibrium with favorable alleles. CONCLUSIONS: ROH genotypes with unfavorable effects on production and fertility traits were identified within and across multiple traits on most chromosomes. These identified ROH genotypes could be included in mate selection programs to minimize their frequency in future generations. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12711-021-00660-z. BioMed Central 2021-08-30 /pmc/articles/PMC8406729/ /pubmed/34461820 http://dx.doi.org/10.1186/s12711-021-00660-z Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
Makanjuola, Bayode O.
Maltecca, Christian
Miglior, Filippo
Marras, Gabriele
Abdalla, Emhimad A.
Schenkel, Flavio S.
Baes, Christine F.
Identification of unique ROH regions with unfavorable effects on production and fertility traits in Canadian Holsteins
title Identification of unique ROH regions with unfavorable effects on production and fertility traits in Canadian Holsteins
title_full Identification of unique ROH regions with unfavorable effects on production and fertility traits in Canadian Holsteins
title_fullStr Identification of unique ROH regions with unfavorable effects on production and fertility traits in Canadian Holsteins
title_full_unstemmed Identification of unique ROH regions with unfavorable effects on production and fertility traits in Canadian Holsteins
title_short Identification of unique ROH regions with unfavorable effects on production and fertility traits in Canadian Holsteins
title_sort identification of unique roh regions with unfavorable effects on production and fertility traits in canadian holsteins
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8406729/
https://www.ncbi.nlm.nih.gov/pubmed/34461820
http://dx.doi.org/10.1186/s12711-021-00660-z
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