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Genome-Wide Detection of Copy Number Variations Associated with Miniature Features in Horses

Copy number variations (CNVs) are crucial structural genomic variants affecting complex traits in humans and livestock animals. The current study was designed to conduct a comprehensive comparative copy number variation analysis among three breeds, Debao (DB), Baise (BS), and Warmblood (WB), with a...

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Autores principales: Choudhury, Md. Panir, Wang, Zihao, Zhu, Min, Teng, Shaohua, Yan, Jing, Cao, Shuwei, Yi, Guoqiang, Liu, Yuwen, Liao, Yuying, Tang, Zhonglin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10606273/
https://www.ncbi.nlm.nih.gov/pubmed/37895283
http://dx.doi.org/10.3390/genes14101934
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author Choudhury, Md. Panir
Wang, Zihao
Zhu, Min
Teng, Shaohua
Yan, Jing
Cao, Shuwei
Yi, Guoqiang
Liu, Yuwen
Liao, Yuying
Tang, Zhonglin
author_facet Choudhury, Md. Panir
Wang, Zihao
Zhu, Min
Teng, Shaohua
Yan, Jing
Cao, Shuwei
Yi, Guoqiang
Liu, Yuwen
Liao, Yuying
Tang, Zhonglin
author_sort Choudhury, Md. Panir
collection PubMed
description Copy number variations (CNVs) are crucial structural genomic variants affecting complex traits in humans and livestock animals. The current study was designed to conduct a comprehensive comparative copy number variation analysis among three breeds, Debao (DB), Baise (BS), and Warmblood (WB), with a specific focus on identifying genomic regions associated with miniature features in horses. Using whole-genome next-generation resequencing data, we identified 18,974 CNVs across 31 autosomes. Among the breeds, we found 4279 breed-specific CNV regions (CNVRs). Baise, Debao, and Warmblood displayed 2978, 986, and 895 distinct CNVRs, respectively, with 202 CNVRs shared across all three breeds. After removing duplicates, we obtained 1545 CNVRs from 26 horse genomes. Functional annotation reveals enrichment in biological functions, including antigen processing, cell metabolism, olfactory conduction, and nervous system development. Debao horses have 970 genes overlapping with CNVRs, possibly causing their small size and mountainous adaptations. We also found that the genes GHR, SOX9, and SOX11 may be responsible for the miniature features of the Debao horse by analyzing their overlapping CNVRs. Overall, this study offers valuable insights into the widespread presence of CNVs in the horse genome. The findings contribute to mapping horse CNVs and advance research on unique miniature traits observed in the Debao horse.
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spelling pubmed-106062732023-10-28 Genome-Wide Detection of Copy Number Variations Associated with Miniature Features in Horses Choudhury, Md. Panir Wang, Zihao Zhu, Min Teng, Shaohua Yan, Jing Cao, Shuwei Yi, Guoqiang Liu, Yuwen Liao, Yuying Tang, Zhonglin Genes (Basel) Article Copy number variations (CNVs) are crucial structural genomic variants affecting complex traits in humans and livestock animals. The current study was designed to conduct a comprehensive comparative copy number variation analysis among three breeds, Debao (DB), Baise (BS), and Warmblood (WB), with a specific focus on identifying genomic regions associated with miniature features in horses. Using whole-genome next-generation resequencing data, we identified 18,974 CNVs across 31 autosomes. Among the breeds, we found 4279 breed-specific CNV regions (CNVRs). Baise, Debao, and Warmblood displayed 2978, 986, and 895 distinct CNVRs, respectively, with 202 CNVRs shared across all three breeds. After removing duplicates, we obtained 1545 CNVRs from 26 horse genomes. Functional annotation reveals enrichment in biological functions, including antigen processing, cell metabolism, olfactory conduction, and nervous system development. Debao horses have 970 genes overlapping with CNVRs, possibly causing their small size and mountainous adaptations. We also found that the genes GHR, SOX9, and SOX11 may be responsible for the miniature features of the Debao horse by analyzing their overlapping CNVRs. Overall, this study offers valuable insights into the widespread presence of CNVs in the horse genome. The findings contribute to mapping horse CNVs and advance research on unique miniature traits observed in the Debao horse. MDPI 2023-10-13 /pmc/articles/PMC10606273/ /pubmed/37895283 http://dx.doi.org/10.3390/genes14101934 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Choudhury, Md. Panir
Wang, Zihao
Zhu, Min
Teng, Shaohua
Yan, Jing
Cao, Shuwei
Yi, Guoqiang
Liu, Yuwen
Liao, Yuying
Tang, Zhonglin
Genome-Wide Detection of Copy Number Variations Associated with Miniature Features in Horses
title Genome-Wide Detection of Copy Number Variations Associated with Miniature Features in Horses
title_full Genome-Wide Detection of Copy Number Variations Associated with Miniature Features in Horses
title_fullStr Genome-Wide Detection of Copy Number Variations Associated with Miniature Features in Horses
title_full_unstemmed Genome-Wide Detection of Copy Number Variations Associated with Miniature Features in Horses
title_short Genome-Wide Detection of Copy Number Variations Associated with Miniature Features in Horses
title_sort genome-wide detection of copy number variations associated with miniature features in horses
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10606273/
https://www.ncbi.nlm.nih.gov/pubmed/37895283
http://dx.doi.org/10.3390/genes14101934
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