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An Epigenetic Aging Clock for Cattle Using Portable Sequencing Technology
Extensively grazed cattle are often mustered only once a year. Therefore, birthdates are typically unknown or inaccurate. Birthdates would be useful for deriving important traits (growth rate; calving interval), breed registrations, and making management decisions. Epigenetic clocks use methylation...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8637324/ https://www.ncbi.nlm.nih.gov/pubmed/34868240 http://dx.doi.org/10.3389/fgene.2021.760450 |
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author | Hayes, Ben J. Nguyen, Loan T. Forutan, Mehrnush Engle, Bailey N. Lamb, Harrison J. Copley, James P. Randhawa, Imtiaz A. S. Ross, Elizabeth M. |
author_facet | Hayes, Ben J. Nguyen, Loan T. Forutan, Mehrnush Engle, Bailey N. Lamb, Harrison J. Copley, James P. Randhawa, Imtiaz A. S. Ross, Elizabeth M. |
author_sort | Hayes, Ben J. |
collection | PubMed |
description | Extensively grazed cattle are often mustered only once a year. Therefore, birthdates are typically unknown or inaccurate. Birthdates would be useful for deriving important traits (growth rate; calving interval), breed registrations, and making management decisions. Epigenetic clocks use methylation of DNA to predict an individual’s age. An epigenetic clock for cattle could provide a solution to the challenges of industry birthdate recording. Here we derived the first epigenetic clock for tropically adapted cattle using portable sequencing devices from tail hair, a tissue which is widely used in industry for genotyping. Cattle (n = 66) with ages ranging from 0.35 to 15.7 years were sequenced using Oxford Nanopore Technologies MinION and methylation was called at CpG sites across the genome. Sites were then filtered and used to calculate a covariance relationship matrix based on methylation state. Best linear unbiased prediction was used with 10-fold cross validation to predict age. A second methylation relationship matrix was also calculated that contained sites associated with genes used in the dog and human epigenetic clocks. The correlation between predicted age and actual age was 0.71 for all sites and 0.60 for dog and human gene epigenetic clock sites. The mean absolute deviation was 1.4 years for animals aged less than 3 years of age, and 1.5 years for animals aged 3–10 years. This is the first reported epigenetic clock using industry relevant samples in cattle. |
format | Online Article Text |
id | pubmed-8637324 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-86373242021-12-03 An Epigenetic Aging Clock for Cattle Using Portable Sequencing Technology Hayes, Ben J. Nguyen, Loan T. Forutan, Mehrnush Engle, Bailey N. Lamb, Harrison J. Copley, James P. Randhawa, Imtiaz A. S. Ross, Elizabeth M. Front Genet Genetics Extensively grazed cattle are often mustered only once a year. Therefore, birthdates are typically unknown or inaccurate. Birthdates would be useful for deriving important traits (growth rate; calving interval), breed registrations, and making management decisions. Epigenetic clocks use methylation of DNA to predict an individual’s age. An epigenetic clock for cattle could provide a solution to the challenges of industry birthdate recording. Here we derived the first epigenetic clock for tropically adapted cattle using portable sequencing devices from tail hair, a tissue which is widely used in industry for genotyping. Cattle (n = 66) with ages ranging from 0.35 to 15.7 years were sequenced using Oxford Nanopore Technologies MinION and methylation was called at CpG sites across the genome. Sites were then filtered and used to calculate a covariance relationship matrix based on methylation state. Best linear unbiased prediction was used with 10-fold cross validation to predict age. A second methylation relationship matrix was also calculated that contained sites associated with genes used in the dog and human epigenetic clocks. The correlation between predicted age and actual age was 0.71 for all sites and 0.60 for dog and human gene epigenetic clock sites. The mean absolute deviation was 1.4 years for animals aged less than 3 years of age, and 1.5 years for animals aged 3–10 years. This is the first reported epigenetic clock using industry relevant samples in cattle. Frontiers Media S.A. 2021-11-18 /pmc/articles/PMC8637324/ /pubmed/34868240 http://dx.doi.org/10.3389/fgene.2021.760450 Text en Copyright © 2021 Hayes, Nguyen, Forutan, Engle, Lamb, Copley, Randhawa and Ross. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Hayes, Ben J. Nguyen, Loan T. Forutan, Mehrnush Engle, Bailey N. Lamb, Harrison J. Copley, James P. Randhawa, Imtiaz A. S. Ross, Elizabeth M. An Epigenetic Aging Clock for Cattle Using Portable Sequencing Technology |
title | An Epigenetic Aging Clock for Cattle Using Portable Sequencing Technology |
title_full | An Epigenetic Aging Clock for Cattle Using Portable Sequencing Technology |
title_fullStr | An Epigenetic Aging Clock for Cattle Using Portable Sequencing Technology |
title_full_unstemmed | An Epigenetic Aging Clock for Cattle Using Portable Sequencing Technology |
title_short | An Epigenetic Aging Clock for Cattle Using Portable Sequencing Technology |
title_sort | epigenetic aging clock for cattle using portable sequencing technology |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8637324/ https://www.ncbi.nlm.nih.gov/pubmed/34868240 http://dx.doi.org/10.3389/fgene.2021.760450 |
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