Genetic Variation and the Distribution of Variant Types in the Horse

Genetic variation is a key contributor to health and disease. Understanding the link between an individual’s genotype and the corresponding phenotype is a major goal of medical genetics. Whole genome sequencing (WGS) within and across populations enables highly efficient variant discovery and elucid...

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Autores principales:	S. A. Durward-Akhurst, R. J. Schaefer, B. Grantham, W. K. Carey, J. R. Mickelson, M. E. McCue
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	genetic variation whole genome sequence variant discovery equine breed differences genetics Genetics QH426-470
Acceso en línea:	https://doaj.org/article/00b6cd5791364baa8128ea438ea8a068
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spelling	oai:doaj.org-article:00b6cd5791364baa8128ea438ea8a0682021-12-02T09:28:19ZGenetic Variation and the Distribution of Variant Types in the Horse1664-802110.3389/fgene.2021.758366https://doaj.org/article/00b6cd5791364baa8128ea438ea8a0682021-12-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fgene.2021.758366/fullhttps://doaj.org/toc/1664-8021Genetic variation is a key contributor to health and disease. Understanding the link between an individual’s genotype and the corresponding phenotype is a major goal of medical genetics. Whole genome sequencing (WGS) within and across populations enables highly efficient variant discovery and elucidation of the molecular nature of virtually all genetic variation. Here, we report the largest catalog of genetic variation for the horse, a species of importance as a model for human athletic and performance related traits, using WGS of 534 horses. We show the extent of agreement between two commonly used variant callers. In data from ten target breeds that represent major breed clusters in the domestic horse, we demonstrate the distribution of variants, their allele frequencies across breeds, and identify variants that are unique to a single breed. We investigate variants with no homozygotes that may be potential embryonic lethal variants, as well as variants present in all individuals that likely represent regions of the genome with errors, poor annotation or where the reference genome carries a variant. Finally, we show regions of the genome that have higher or lower levels of genetic variation compared to the genome average. This catalog can be used for variant prioritization for important equine diseases and traits, and to provide key information about regions of the genome where the assembly and/or annotation need to be improved.S. A. Durward-AkhurstR. J. SchaeferB. GranthamW. K. CareyJ. R. MickelsonM. E. McCueFrontiers Media S.A.articlegenetic variationwhole genome sequencevariant discoveryequinebreed differencesgeneticsGeneticsQH426-470ENFrontiers in Genetics, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	genetic variation whole genome sequence variant discovery equine breed differences genetics Genetics QH426-470
spellingShingle	genetic variation whole genome sequence variant discovery equine breed differences genetics Genetics QH426-470 S. A. Durward-Akhurst R. J. Schaefer B. Grantham W. K. Carey J. R. Mickelson M. E. McCue Genetic Variation and the Distribution of Variant Types in the Horse
description	Genetic variation is a key contributor to health and disease. Understanding the link between an individual’s genotype and the corresponding phenotype is a major goal of medical genetics. Whole genome sequencing (WGS) within and across populations enables highly efficient variant discovery and elucidation of the molecular nature of virtually all genetic variation. Here, we report the largest catalog of genetic variation for the horse, a species of importance as a model for human athletic and performance related traits, using WGS of 534 horses. We show the extent of agreement between two commonly used variant callers. In data from ten target breeds that represent major breed clusters in the domestic horse, we demonstrate the distribution of variants, their allele frequencies across breeds, and identify variants that are unique to a single breed. We investigate variants with no homozygotes that may be potential embryonic lethal variants, as well as variants present in all individuals that likely represent regions of the genome with errors, poor annotation or where the reference genome carries a variant. Finally, we show regions of the genome that have higher or lower levels of genetic variation compared to the genome average. This catalog can be used for variant prioritization for important equine diseases and traits, and to provide key information about regions of the genome where the assembly and/or annotation need to be improved.
format	article
author	S. A. Durward-Akhurst R. J. Schaefer B. Grantham W. K. Carey J. R. Mickelson M. E. McCue
author_facet	S. A. Durward-Akhurst R. J. Schaefer B. Grantham W. K. Carey J. R. Mickelson M. E. McCue
author_sort	S. A. Durward-Akhurst
title	Genetic Variation and the Distribution of Variant Types in the Horse
title_short	Genetic Variation and the Distribution of Variant Types in the Horse
title_full	Genetic Variation and the Distribution of Variant Types in the Horse
title_fullStr	Genetic Variation and the Distribution of Variant Types in the Horse
title_full_unstemmed	Genetic Variation and the Distribution of Variant Types in the Horse
title_sort	genetic variation and the distribution of variant types in the horse
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/00b6cd5791364baa8128ea438ea8a068
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Genetic Variation and the Distribution of Variant Types in the Horse

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