Rare and common variant discovery by whole-genome sequencing of 101 Thoroughbred racehorses

Abstract The Thoroughbred breed was formed by crossing Oriental horse breeds and British native horses and is currently used in horseracing worldwide. In this study, we constructed a single-nucleotide variant (SNV) database using data from 101 Thoroughbred racehorses. Whole genome sequencing (WGS) r...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Teruaki Tozaki, Aoi Ohnuma, Mio Kikuchi, Taichiro Ishige, Hironaga Kakoi, Kei-ichi Hirota, Kanichi Kusano, Shun-ichi Nagata
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d5c2c82800b540f586fca57203d22338
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:d5c2c82800b540f586fca57203d22338
record_format	dspace
spelling	oai:doaj.org-article:d5c2c82800b540f586fca57203d223382021-12-02T17:06:10ZRare and common variant discovery by whole-genome sequencing of 101 Thoroughbred racehorses10.1038/s41598-021-95669-12045-2322https://doaj.org/article/d5c2c82800b540f586fca57203d223382021-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-95669-1https://doaj.org/toc/2045-2322Abstract The Thoroughbred breed was formed by crossing Oriental horse breeds and British native horses and is currently used in horseracing worldwide. In this study, we constructed a single-nucleotide variant (SNV) database using data from 101 Thoroughbred racehorses. Whole genome sequencing (WGS) revealed 11,570,312 and 602,756 SNVs in autosomal (1–31) and X chromosomes, respectively, yielding a total of 12,173,068 SNVs. About 6.9% of identified SNVs were rare variants observed only in one allele in 101 horses. The number of SNVs detected in individual horses ranged from 4.8 to 5.3 million. Individual horses had a maximum of 25,554 rare variants; several of these were functional variants, such as non-synonymous substitutions, start-gained, start-lost, stop-gained, and stop-lost variants. Therefore, these rare variants may affect differences in traits and phenotypes among individuals. When observing the distribution of rare variants among horses, one breeding stallion had a smaller number of rare variants compared to other horses, suggesting that the frequency of rare variants in the Japanese Thoroughbred population increases through breeding. In addition, our variant database may provide useful basic information for industrial applications, such as the detection of genetically modified racehorses in gene-doping control and pedigree-registration of racehorses using SNVs as markers.Teruaki TozakiAoi OhnumaMio KikuchiTaichiro IshigeHironaga KakoiKei-ichi HirotaKanichi KusanoShun-ichi NagataNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Teruaki Tozaki Aoi Ohnuma Mio Kikuchi Taichiro Ishige Hironaga Kakoi Kei-ichi Hirota Kanichi Kusano Shun-ichi Nagata Rare and common variant discovery by whole-genome sequencing of 101 Thoroughbred racehorses
description	Abstract The Thoroughbred breed was formed by crossing Oriental horse breeds and British native horses and is currently used in horseracing worldwide. In this study, we constructed a single-nucleotide variant (SNV) database using data from 101 Thoroughbred racehorses. Whole genome sequencing (WGS) revealed 11,570,312 and 602,756 SNVs in autosomal (1–31) and X chromosomes, respectively, yielding a total of 12,173,068 SNVs. About 6.9% of identified SNVs were rare variants observed only in one allele in 101 horses. The number of SNVs detected in individual horses ranged from 4.8 to 5.3 million. Individual horses had a maximum of 25,554 rare variants; several of these were functional variants, such as non-synonymous substitutions, start-gained, start-lost, stop-gained, and stop-lost variants. Therefore, these rare variants may affect differences in traits and phenotypes among individuals. When observing the distribution of rare variants among horses, one breeding stallion had a smaller number of rare variants compared to other horses, suggesting that the frequency of rare variants in the Japanese Thoroughbred population increases through breeding. In addition, our variant database may provide useful basic information for industrial applications, such as the detection of genetically modified racehorses in gene-doping control and pedigree-registration of racehorses using SNVs as markers.
format	article
author	Teruaki Tozaki Aoi Ohnuma Mio Kikuchi Taichiro Ishige Hironaga Kakoi Kei-ichi Hirota Kanichi Kusano Shun-ichi Nagata
author_facet	Teruaki Tozaki Aoi Ohnuma Mio Kikuchi Taichiro Ishige Hironaga Kakoi Kei-ichi Hirota Kanichi Kusano Shun-ichi Nagata
author_sort	Teruaki Tozaki
title	Rare and common variant discovery by whole-genome sequencing of 101 Thoroughbred racehorses
title_short	Rare and common variant discovery by whole-genome sequencing of 101 Thoroughbred racehorses
title_full	Rare and common variant discovery by whole-genome sequencing of 101 Thoroughbred racehorses
title_fullStr	Rare and common variant discovery by whole-genome sequencing of 101 Thoroughbred racehorses
title_full_unstemmed	Rare and common variant discovery by whole-genome sequencing of 101 Thoroughbred racehorses
title_sort	rare and common variant discovery by whole-genome sequencing of 101 thoroughbred racehorses
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/d5c2c82800b540f586fca57203d22338
work_keys_str_mv	AT teruakitozaki rareandcommonvariantdiscoverybywholegenomesequencingof101thoroughbredracehorses AT aoiohnuma rareandcommonvariantdiscoverybywholegenomesequencingof101thoroughbredracehorses AT miokikuchi rareandcommonvariantdiscoverybywholegenomesequencingof101thoroughbredracehorses AT taichiroishige rareandcommonvariantdiscoverybywholegenomesequencingof101thoroughbredracehorses AT hironagakakoi rareandcommonvariantdiscoverybywholegenomesequencingof101thoroughbredracehorses AT keiichihirota rareandcommonvariantdiscoverybywholegenomesequencingof101thoroughbredracehorses AT kanichikusano rareandcommonvariantdiscoverybywholegenomesequencingof101thoroughbredracehorses AT shunichinagata rareandcommonvariantdiscoverybywholegenomesequencingof101thoroughbredracehorses
_version_	1718381702011682816

Rare and common variant discovery by whole-genome sequencing of 101 Thoroughbred racehorses

Ejemplares similares