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Whole genome sequence and analysis of the Marwari horse breed and its genetic origin

BACKGROUND: The horse (Equus ferus caballus) is one of the earliest domesticated species and has played an important role in the development of human societies over the past 5,000 years. In this study, we characterized the genome of the Marwari horse, a rare breed with unique phenotypic characterist...

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Autores principales: Jun, JeHoon, Cho, Yun Sung, Hu, Haejin, Kim, Hak-Min, Jho, Sungwoong, Gadhvi, Priyvrat, Park, Kyung Mi, Lim, Jeongheui, Paek, Woon Kee, Han, Kyudong, Manica, Andrea, Edwards, Jeremy S, Bhak, Jong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4290615/
https://www.ncbi.nlm.nih.gov/pubmed/25521865
http://dx.doi.org/10.1186/1471-2164-15-S9-S4
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author Jun, JeHoon
Cho, Yun Sung
Hu, Haejin
Kim, Hak-Min
Jho, Sungwoong
Gadhvi, Priyvrat
Park, Kyung Mi
Lim, Jeongheui
Paek, Woon Kee
Han, Kyudong
Manica, Andrea
Edwards, Jeremy S
Bhak, Jong
author_facet Jun, JeHoon
Cho, Yun Sung
Hu, Haejin
Kim, Hak-Min
Jho, Sungwoong
Gadhvi, Priyvrat
Park, Kyung Mi
Lim, Jeongheui
Paek, Woon Kee
Han, Kyudong
Manica, Andrea
Edwards, Jeremy S
Bhak, Jong
author_sort Jun, JeHoon
collection PubMed
description BACKGROUND: The horse (Equus ferus caballus) is one of the earliest domesticated species and has played an important role in the development of human societies over the past 5,000 years. In this study, we characterized the genome of the Marwari horse, a rare breed with unique phenotypic characteristics, including inwardly turned ear tips. It is thought to have originated from the crossbreeding of local Indian ponies with Arabian horses beginning in the 12th century. RESULTS: We generated 101 Gb (~30 × coverage) of whole genome sequences from a Marwari horse using the Illumina HiSeq2000 sequencer. The sequences were mapped to the horse reference genome at a mapping rate of ~98% and with ~95% of the genome having at least 10 × coverage. A total of 5.9 million single nucleotide variations, 0.6 million small insertions or deletions, and 2,569 copy number variation blocks were identified. We confirmed a strong Arabian and Mongolian component in the Marwari genome. Novel variants from the Marwari sequences were annotated, and were found to be enriched in olfactory functions. Additionally, we suggest a potential functional genetic variant in the TSHZ1 gene (p.Ala344>Val) associated with the inward-turning ear tip shape of the Marwari horses. CONCLUSIONS: Here, we present an analysis of the Marwari horse genome. This is the first genomic data for an Asian breed, and is an invaluable resource for future studies of genetic variation associated with phenotypes and diseases in horses.
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spelling pubmed-42906152015-01-15 Whole genome sequence and analysis of the Marwari horse breed and its genetic origin Jun, JeHoon Cho, Yun Sung Hu, Haejin Kim, Hak-Min Jho, Sungwoong Gadhvi, Priyvrat Park, Kyung Mi Lim, Jeongheui Paek, Woon Kee Han, Kyudong Manica, Andrea Edwards, Jeremy S Bhak, Jong BMC Genomics Research BACKGROUND: The horse (Equus ferus caballus) is one of the earliest domesticated species and has played an important role in the development of human societies over the past 5,000 years. In this study, we characterized the genome of the Marwari horse, a rare breed with unique phenotypic characteristics, including inwardly turned ear tips. It is thought to have originated from the crossbreeding of local Indian ponies with Arabian horses beginning in the 12th century. RESULTS: We generated 101 Gb (~30 × coverage) of whole genome sequences from a Marwari horse using the Illumina HiSeq2000 sequencer. The sequences were mapped to the horse reference genome at a mapping rate of ~98% and with ~95% of the genome having at least 10 × coverage. A total of 5.9 million single nucleotide variations, 0.6 million small insertions or deletions, and 2,569 copy number variation blocks were identified. We confirmed a strong Arabian and Mongolian component in the Marwari genome. Novel variants from the Marwari sequences were annotated, and were found to be enriched in olfactory functions. Additionally, we suggest a potential functional genetic variant in the TSHZ1 gene (p.Ala344>Val) associated with the inward-turning ear tip shape of the Marwari horses. CONCLUSIONS: Here, we present an analysis of the Marwari horse genome. This is the first genomic data for an Asian breed, and is an invaluable resource for future studies of genetic variation associated with phenotypes and diseases in horses. BioMed Central 2014-12-08 /pmc/articles/PMC4290615/ /pubmed/25521865 http://dx.doi.org/10.1186/1471-2164-15-S9-S4 Text en Copyright © 2014 Jun et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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
Jun, JeHoon
Cho, Yun Sung
Hu, Haejin
Kim, Hak-Min
Jho, Sungwoong
Gadhvi, Priyvrat
Park, Kyung Mi
Lim, Jeongheui
Paek, Woon Kee
Han, Kyudong
Manica, Andrea
Edwards, Jeremy S
Bhak, Jong
Whole genome sequence and analysis of the Marwari horse breed and its genetic origin
title Whole genome sequence and analysis of the Marwari horse breed and its genetic origin
title_full Whole genome sequence and analysis of the Marwari horse breed and its genetic origin
title_fullStr Whole genome sequence and analysis of the Marwari horse breed and its genetic origin
title_full_unstemmed Whole genome sequence and analysis of the Marwari horse breed and its genetic origin
title_short Whole genome sequence and analysis of the Marwari horse breed and its genetic origin
title_sort whole genome sequence and analysis of the marwari horse breed and its genetic origin
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4290615/
https://www.ncbi.nlm.nih.gov/pubmed/25521865
http://dx.doi.org/10.1186/1471-2164-15-S9-S4
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