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Whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice
BACKGROUND: The laboratory mouse was domesticated from the wild house mouse. Understanding the genetics underlying domestication in laboratory mice, especially in the widely used classical inbred mice, is vital for studies using mouse models. However, the genetic mechanism of laboratory mouse domest...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9511766/ https://www.ncbi.nlm.nih.gov/pubmed/36163035 http://dx.doi.org/10.1186/s13059-022-02772-1 |
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author | Liu, Ming Yu, Caixia Zhang, Zhichao Song, Mingjing Sun, Xiuping Piálek, Jaroslav Jacob, Jens Lu, Jiqi Cong, Lin Zhang, Hongmao Wang, Yong Li, Guoliang Feng, Zhiyong Du, Zhenglin Wang, Meng Wan, Xinru Wang, Dawei Wang, Yan-Ling Li, Hongjun Wang, Zuoxin Zhang, Bing Zhang, Zhibin |
author_facet | Liu, Ming Yu, Caixia Zhang, Zhichao Song, Mingjing Sun, Xiuping Piálek, Jaroslav Jacob, Jens Lu, Jiqi Cong, Lin Zhang, Hongmao Wang, Yong Li, Guoliang Feng, Zhiyong Du, Zhenglin Wang, Meng Wan, Xinru Wang, Dawei Wang, Yan-Ling Li, Hongjun Wang, Zuoxin Zhang, Bing Zhang, Zhibin |
author_sort | Liu, Ming |
collection | PubMed |
description | BACKGROUND: The laboratory mouse was domesticated from the wild house mouse. Understanding the genetics underlying domestication in laboratory mice, especially in the widely used classical inbred mice, is vital for studies using mouse models. However, the genetic mechanism of laboratory mouse domestication remains unknown due to lack of adequate genomic sequences of wild mice. RESULTS: We analyze the genetic relationships by whole-genome resequencing of 36 wild mice and 36 inbred strains. All classical inbred mice cluster together distinctly from wild and wild-derived inbred mice. Using nucleotide diversity analysis, Fst, and XP-CLR, we identify 339 positively selected genes that are closely associated with nervous system function. Approximately one third of these positively selected genes are highly expressed in brain tissues, and genetic mouse models of 125 genes in the positively selected genes exhibit abnormal behavioral or nervous system phenotypes. These positively selected genes show a higher ratio of differential expression between wild and classical inbred mice compared with all genes, especially in the hippocampus and frontal lobe. Using a mutant mouse model, we find that the SNP rs27900929 (T>C) in gene Astn2 significantly reduces the tameness of mice and modifies the ratio of the two Astn2 (a/b) isoforms. CONCLUSION: Our study indicates that classical inbred mice experienced high selection pressure during domestication under laboratory conditions. The analysis shows the positively selected genes are closely associated with behavior and the nervous system in mice. Tameness may be related to the Astn2 mutation and regulated by the ratio of the two Astn2 (a/b) isoforms. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02772-1. |
format | Online Article Text |
id | pubmed-9511766 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-95117662022-09-27 Whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice Liu, Ming Yu, Caixia Zhang, Zhichao Song, Mingjing Sun, Xiuping Piálek, Jaroslav Jacob, Jens Lu, Jiqi Cong, Lin Zhang, Hongmao Wang, Yong Li, Guoliang Feng, Zhiyong Du, Zhenglin Wang, Meng Wan, Xinru Wang, Dawei Wang, Yan-Ling Li, Hongjun Wang, Zuoxin Zhang, Bing Zhang, Zhibin Genome Biol Research BACKGROUND: The laboratory mouse was domesticated from the wild house mouse. Understanding the genetics underlying domestication in laboratory mice, especially in the widely used classical inbred mice, is vital for studies using mouse models. However, the genetic mechanism of laboratory mouse domestication remains unknown due to lack of adequate genomic sequences of wild mice. RESULTS: We analyze the genetic relationships by whole-genome resequencing of 36 wild mice and 36 inbred strains. All classical inbred mice cluster together distinctly from wild and wild-derived inbred mice. Using nucleotide diversity analysis, Fst, and XP-CLR, we identify 339 positively selected genes that are closely associated with nervous system function. Approximately one third of these positively selected genes are highly expressed in brain tissues, and genetic mouse models of 125 genes in the positively selected genes exhibit abnormal behavioral or nervous system phenotypes. These positively selected genes show a higher ratio of differential expression between wild and classical inbred mice compared with all genes, especially in the hippocampus and frontal lobe. Using a mutant mouse model, we find that the SNP rs27900929 (T>C) in gene Astn2 significantly reduces the tameness of mice and modifies the ratio of the two Astn2 (a/b) isoforms. CONCLUSION: Our study indicates that classical inbred mice experienced high selection pressure during domestication under laboratory conditions. The analysis shows the positively selected genes are closely associated with behavior and the nervous system in mice. Tameness may be related to the Astn2 mutation and regulated by the ratio of the two Astn2 (a/b) isoforms. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02772-1. BioMed Central 2022-09-26 /pmc/articles/PMC9511766/ /pubmed/36163035 http://dx.doi.org/10.1186/s13059-022-02772-1 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Liu, Ming Yu, Caixia Zhang, Zhichao Song, Mingjing Sun, Xiuping Piálek, Jaroslav Jacob, Jens Lu, Jiqi Cong, Lin Zhang, Hongmao Wang, Yong Li, Guoliang Feng, Zhiyong Du, Zhenglin Wang, Meng Wan, Xinru Wang, Dawei Wang, Yan-Ling Li, Hongjun Wang, Zuoxin Zhang, Bing Zhang, Zhibin Whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice |
title | Whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice |
title_full | Whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice |
title_fullStr | Whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice |
title_full_unstemmed | Whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice |
title_short | Whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice |
title_sort | whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9511766/ https://www.ncbi.nlm.nih.gov/pubmed/36163035 http://dx.doi.org/10.1186/s13059-022-02772-1 |
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