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Genetic diversity, tissue-specific expression, and functional analysis of the ATP7A gene in sheep

In humans, variation of the ATP7A gene may cause cranial exostosis, which is similar to “human horn,” but the function of the ATP7A gene in sheep is still unknown. Tissue expression patterns and potential functional loci analysis of the ATP7A gene could help understand its function in sheep horn. In...

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Autores principales: Li, Hao, Du, Xiaolong, Li, Xinyue, Feng, Pingjie, Chu, Mingxing, Jin, Yi, Pan, Zhangyuan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10547898/
https://www.ncbi.nlm.nih.gov/pubmed/37799137
http://dx.doi.org/10.3389/fgene.2023.1239979
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author Li, Hao
Du, Xiaolong
Li, Xinyue
Feng, Pingjie
Chu, Mingxing
Jin, Yi
Pan, Zhangyuan
author_facet Li, Hao
Du, Xiaolong
Li, Xinyue
Feng, Pingjie
Chu, Mingxing
Jin, Yi
Pan, Zhangyuan
author_sort Li, Hao
collection PubMed
description In humans, variation of the ATP7A gene may cause cranial exostosis, which is similar to “human horn,” but the function of the ATP7A gene in sheep is still unknown. Tissue expression patterns and potential functional loci analysis of the ATP7A gene could help understand its function in sheep horn. In this study, we first identified tissue, sex, breed, and species-specific expression of the ATP7A gene in sheep based on the RNA-sequencing (RNA-seq) data. Second, the potential functional sites of the ATP7A gene were analyzed by using the whole genome sequencing (WGS) data of 99 sheep from 10 breeds. Last, the allele-specific expression of the ATP7A gene was explored. Our result showed the ATP7A gene has significantly higher expression in the big horn than in the small horn, and the ATP7A gene has high expression in the horn and skin, suggesting that this gene may be related to the horn. The PCA results show that the region around the ATP7A can distinguish horned and hornless groups to some extent, further indicating that the ATP7A may be related to horns. When compared with other species, we find seven ruminate specific amino acid sites of the ATP7A protein, which can be important to the ruminate horn. By analyzing WGS, we found 6 SNP sites with significant differences in frequency in horned and hornless populations, and most of these variants are present in the intron. But we still find some potential functional sites, including three missenses, three synonymous mutations, and four Indels. Finally, by combining the RNA-seq and WGS functional loci results, we find three mutations that showed allele-specific expression between big and small horns. This study shows that the ATP7A gene in sheep may be related to horn size, and several potential functional sites we identified here can be useful molecular markers for sheep horn breeding.
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spelling pubmed-105478982023-10-05 Genetic diversity, tissue-specific expression, and functional analysis of the ATP7A gene in sheep Li, Hao Du, Xiaolong Li, Xinyue Feng, Pingjie Chu, Mingxing Jin, Yi Pan, Zhangyuan Front Genet Genetics In humans, variation of the ATP7A gene may cause cranial exostosis, which is similar to “human horn,” but the function of the ATP7A gene in sheep is still unknown. Tissue expression patterns and potential functional loci analysis of the ATP7A gene could help understand its function in sheep horn. In this study, we first identified tissue, sex, breed, and species-specific expression of the ATP7A gene in sheep based on the RNA-sequencing (RNA-seq) data. Second, the potential functional sites of the ATP7A gene were analyzed by using the whole genome sequencing (WGS) data of 99 sheep from 10 breeds. Last, the allele-specific expression of the ATP7A gene was explored. Our result showed the ATP7A gene has significantly higher expression in the big horn than in the small horn, and the ATP7A gene has high expression in the horn and skin, suggesting that this gene may be related to the horn. The PCA results show that the region around the ATP7A can distinguish horned and hornless groups to some extent, further indicating that the ATP7A may be related to horns. When compared with other species, we find seven ruminate specific amino acid sites of the ATP7A protein, which can be important to the ruminate horn. By analyzing WGS, we found 6 SNP sites with significant differences in frequency in horned and hornless populations, and most of these variants are present in the intron. But we still find some potential functional sites, including three missenses, three synonymous mutations, and four Indels. Finally, by combining the RNA-seq and WGS functional loci results, we find three mutations that showed allele-specific expression between big and small horns. This study shows that the ATP7A gene in sheep may be related to horn size, and several potential functional sites we identified here can be useful molecular markers for sheep horn breeding. Frontiers Media S.A. 2023-09-20 /pmc/articles/PMC10547898/ /pubmed/37799137 http://dx.doi.org/10.3389/fgene.2023.1239979 Text en Copyright © 2023 Li, Du, Li, Feng, Chu, Jin and Pan. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Li, Hao
Du, Xiaolong
Li, Xinyue
Feng, Pingjie
Chu, Mingxing
Jin, Yi
Pan, Zhangyuan
Genetic diversity, tissue-specific expression, and functional analysis of the ATP7A gene in sheep
title Genetic diversity, tissue-specific expression, and functional analysis of the ATP7A gene in sheep
title_full Genetic diversity, tissue-specific expression, and functional analysis of the ATP7A gene in sheep
title_fullStr Genetic diversity, tissue-specific expression, and functional analysis of the ATP7A gene in sheep
title_full_unstemmed Genetic diversity, tissue-specific expression, and functional analysis of the ATP7A gene in sheep
title_short Genetic diversity, tissue-specific expression, and functional analysis of the ATP7A gene in sheep
title_sort genetic diversity, tissue-specific expression, and functional analysis of the atp7a gene in sheep
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10547898/
https://www.ncbi.nlm.nih.gov/pubmed/37799137
http://dx.doi.org/10.3389/fgene.2023.1239979
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