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Genome sequencing and protein domain annotations of Korean Hanwoo cattle identify Hanwoo-specific immunity-related and other novel genes

BACKGROUND: Identification of genetic mechanisms and idiosyncrasies at the breed-level can provide valuable information for potential use in evolutionary studies, medical applications, and breeding of selective traits. Here, we analyzed genomic data collected from 136 Korean Native cattle, known as...

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Autores principales: Caetano-Anolles, Kelsey, Kim, Kwondo, Kwak, Woori, Sung, Samsun, Kim, Heebal, Choi, Bong-Hwan, Lim, Dajeong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5975384/
https://www.ncbi.nlm.nih.gov/pubmed/29843617
http://dx.doi.org/10.1186/s12863-018-0623-x
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author Caetano-Anolles, Kelsey
Kim, Kwondo
Kwak, Woori
Sung, Samsun
Kim, Heebal
Choi, Bong-Hwan
Lim, Dajeong
author_facet Caetano-Anolles, Kelsey
Kim, Kwondo
Kwak, Woori
Sung, Samsun
Kim, Heebal
Choi, Bong-Hwan
Lim, Dajeong
author_sort Caetano-Anolles, Kelsey
collection PubMed
description BACKGROUND: Identification of genetic mechanisms and idiosyncrasies at the breed-level can provide valuable information for potential use in evolutionary studies, medical applications, and breeding of selective traits. Here, we analyzed genomic data collected from 136 Korean Native cattle, known as Hanwoo, using advanced statistical methods. RESULTS: Results revealed Hanwoo-specific protein domains which were largely characterized by immunoglobulin function. Furthermore, domain interactions of novel Hanwoo-specific genes reveal additional links to immunity. Novel Hanwoo-specific genes linked to muscle and other functions were identified, including protein domains with functions related to energy, fat storage, and muscle function that may provide insight into the mechanisms behind Hanwoo cattle’s uniquely high percentage of intramuscular fat and fat marbling. CONCLUSION: The identification of Hanwoo-specific genes linked to immunity are potentially useful for future medical research and selective breeding. The significant genomic variations identified here can crucially identify genetic novelties that are arising from useful adaptations. These results will allow future researchers to compare and classify breeds, identify important genetic markers, and develop breeding strategies to further improve significant traits. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12863-018-0623-x) contains supplementary material, which is available to authorized users.
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spelling pubmed-59753842018-05-31 Genome sequencing and protein domain annotations of Korean Hanwoo cattle identify Hanwoo-specific immunity-related and other novel genes Caetano-Anolles, Kelsey Kim, Kwondo Kwak, Woori Sung, Samsun Kim, Heebal Choi, Bong-Hwan Lim, Dajeong BMC Genet Research Article BACKGROUND: Identification of genetic mechanisms and idiosyncrasies at the breed-level can provide valuable information for potential use in evolutionary studies, medical applications, and breeding of selective traits. Here, we analyzed genomic data collected from 136 Korean Native cattle, known as Hanwoo, using advanced statistical methods. RESULTS: Results revealed Hanwoo-specific protein domains which were largely characterized by immunoglobulin function. Furthermore, domain interactions of novel Hanwoo-specific genes reveal additional links to immunity. Novel Hanwoo-specific genes linked to muscle and other functions were identified, including protein domains with functions related to energy, fat storage, and muscle function that may provide insight into the mechanisms behind Hanwoo cattle’s uniquely high percentage of intramuscular fat and fat marbling. CONCLUSION: The identification of Hanwoo-specific genes linked to immunity are potentially useful for future medical research and selective breeding. The significant genomic variations identified here can crucially identify genetic novelties that are arising from useful adaptations. These results will allow future researchers to compare and classify breeds, identify important genetic markers, and develop breeding strategies to further improve significant traits. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12863-018-0623-x) contains supplementary material, which is available to authorized users. BioMed Central 2018-05-29 /pmc/articles/PMC5975384/ /pubmed/29843617 http://dx.doi.org/10.1186/s12863-018-0623-x Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Caetano-Anolles, Kelsey
Kim, Kwondo
Kwak, Woori
Sung, Samsun
Kim, Heebal
Choi, Bong-Hwan
Lim, Dajeong
Genome sequencing and protein domain annotations of Korean Hanwoo cattle identify Hanwoo-specific immunity-related and other novel genes
title Genome sequencing and protein domain annotations of Korean Hanwoo cattle identify Hanwoo-specific immunity-related and other novel genes
title_full Genome sequencing and protein domain annotations of Korean Hanwoo cattle identify Hanwoo-specific immunity-related and other novel genes
title_fullStr Genome sequencing and protein domain annotations of Korean Hanwoo cattle identify Hanwoo-specific immunity-related and other novel genes
title_full_unstemmed Genome sequencing and protein domain annotations of Korean Hanwoo cattle identify Hanwoo-specific immunity-related and other novel genes
title_short Genome sequencing and protein domain annotations of Korean Hanwoo cattle identify Hanwoo-specific immunity-related and other novel genes
title_sort genome sequencing and protein domain annotations of korean hanwoo cattle identify hanwoo-specific immunity-related and other novel genes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5975384/
https://www.ncbi.nlm.nih.gov/pubmed/29843617
http://dx.doi.org/10.1186/s12863-018-0623-x
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