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...

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Autores principales:	Ben J. Hayes, Loan T. Nguyen, Mehrnush Forutan, Bailey N. Engle, Harrison J. Lamb, James P. Copley, Imtiaz A. S. Randhawa, Elizabeth M. Ross
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	cattle epigenetic clock long-read sequencing age prediction DNA methylation Genetics QH426-470
Acceso en línea:	https://doaj.org/article/0f484110e9f44122b905429887db98d6
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spelling	oai:doaj.org-article:0f484110e9f44122b905429887db98d62021-11-18T09:05:02ZAn Epigenetic Aging Clock for Cattle Using Portable Sequencing Technology1664-802110.3389/fgene.2021.760450https://doaj.org/article/0f484110e9f44122b905429887db98d62021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fgene.2021.760450/fullhttps://doaj.org/toc/1664-8021Extensively 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.Ben J. HayesLoan T. NguyenMehrnush ForutanBailey N. EngleHarrison J. LambJames P. CopleyImtiaz A. S. RandhawaElizabeth M. RossFrontiers Media S.A.articlecattleepigenetic clocklong-read sequencingage predictionDNA methylationGeneticsQH426-470ENFrontiers in Genetics, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	cattle epigenetic clock long-read sequencing age prediction DNA methylation Genetics QH426-470
spellingShingle	cattle epigenetic clock long-read sequencing age prediction DNA methylation Genetics QH426-470 Ben J. Hayes Loan T. Nguyen Mehrnush Forutan Bailey N. Engle Harrison J. Lamb James P. Copley Imtiaz A. S. Randhawa Elizabeth M. Ross An Epigenetic Aging Clock for Cattle Using Portable Sequencing Technology
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	article
author	Ben J. Hayes Loan T. Nguyen Mehrnush Forutan Bailey N. Engle Harrison J. Lamb James P. Copley Imtiaz A. S. Randhawa Elizabeth M. Ross
author_facet	Ben J. Hayes Loan T. Nguyen Mehrnush Forutan Bailey N. Engle Harrison J. Lamb James P. Copley Imtiaz A. S. Randhawa Elizabeth M. Ross
author_sort	Ben J. Hayes
title	An Epigenetic Aging Clock for Cattle Using Portable Sequencing Technology
title_short	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_sort	epigenetic aging clock for cattle using portable sequencing technology
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/0f484110e9f44122b905429887db98d6
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An Epigenetic Aging Clock for Cattle Using Portable Sequencing Technology

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