Mouse genomic variation and its effect on phenotypes and gene regulation.
Open accessAbstract
We report genome sequences of 17 inbred strains of laboratory mice and identify almost ten times more variants than previously known. We use these genomes to explore the phylogenetic history of the laboratory mouse and to examine the functional consequences of allele-specific variation on transcript abundance, revealing that at least 12% of transcripts show a significant tissue-specific expression bias. By identifying candidate functional variants at 718 quantitative trait loci we show that the molecular nature of functional variants and their position relative to genes vary according to the effect size of the locus. These sequences provide a starting point for a new era in the functional analysis of a key model organism. The laboratory mouse has become the workhorse of biomedical research. The draft sequence of the mouse reference genome was published in 2002, but some forms of variation are still poorly documented. Two papers in this issue go a long way towards filling the gaps. The generation and analysis of sequence from 17 key mouse genomes, including most of the commonly used inbred strains and their progenitors, reveal extensive genetic variation and provide insights into the molecular nature of functional variants as well as the phylogenetic history of the lab mouse. The data will be an important resource for a new era of functional analysis. The second paper describes the landscape of structural variants in the genomes of 13 classical and four wild-derived inbred mouse strains, mapping many of them to base-pair resolution. Despite their prevalence, structural variants are shown to have a relatively small impact on phenotypic variation.
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Until now, most gene expression studies of different mouse strains have used the BL6 reference genome despite millions of known genetic variations between strains.
“Until now, most gene expression studies of different mouse strains have used the BL6 reference genome despite millions of known genetic variations between strains.14,15”
From High-quality mouse reference genomes reveal the structural complexity of the murine protein-coding landscape (2026) · cites this paper as [15]
The Abstract identifies C57BL/6J as the mouse reference genome, and Data generation and variant discovery (page not provided) reports millions of variants across strains. Neither passage establishes that most gene-expression studies of different strains used that reference genome; the paper describes its own analysis, not the prevalence of that practice. (LLM, conf=0.82)
Experimental — accuracy not yet measuredA requirement for N-masking is that SNP positions are known, for example via a public resource like the Mouse Genomes Project.
“A requirement for N-masking is that SNP positions are known, e.g. via a public resource like the Mouse Genomes Project which provides high quality variant calls for a large number of mouse strains 8”
From SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes (2016) · cites this paper as [8]
The DO founder strain genomes were assembled by alignment of short DNA sequence reads to the mouse reference genome as a first step in identifying SNPs, indels, and structural variants.
“These genomes were assembled by alignment of short DNA sequence reads to the mouse reference genome as a first step in identifying SNPs, indels, and structural variants (Keane et al. 2011).”
From RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations (2014) · cites this paper as Keane et al. 2011
Compared to previous de novo mouse strain genomes and variation catalogs, these long-read genome assemblies show significant improvement in the most complex regions, such as MHC, defensin, TCR, and Ly49 loci.
“Compared to previous de novo mouse strain genomes and variation catalogs,14,15,18 these long-read genome assemblies show significant improvement in the most complex regions, such as MHC, defensin, T cell receptor (TCR), and Ly49 loci.”
From High-quality mouse reference genomes reveal the structural complexity of the murine protein-coding landscape (2026) · cites this paper as [15]
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“Compared to previous de novo mouse strain genomes and variation catalogs, 14,15,18 these long-read genome assemblies show significant improvement in the most complex regions, such as MHC, defensin, T cell receptor (TCR), and Ly49 loci.”
Self-citation
- Authors
- Keane, T. M., Goodstadt, L., Danecek, P., White, M. A., Wong, K., Yalcin, B., Heger, A., Agam, A., Slater, G., Goodson, M., Furlotte, N. A., Eskin, E., Nellåker, C., Whitley, H., Cleak, J., Janowitz, D., Hernandez-Pliego, P., Edwards, A., Belgard, T. G., Oliver, P. L., McIntyre, R. E., Bhomra, A., Nicod, J., Gan, X., Yuan, W., van der Weyden, L., Steward, C. A., Bala, S., Stalker, J., Mott, R., Durbin, R., Jackson, I. J., Czechanski, A., Guerra-Assunção, J. A., Donahue, L. R., Reinholdt, L. G., Payseur, B. A., Ponting, C. P., Birney, E., Flint, J., & Adams, D. J.
- Affiliations
- Wellcome Sanger Institute (GB)
- Centre for Human Genetics (GB)
- University of Wisconsin–Madison (US)
- University of Oxford (GB)
- University of California, Los Angeles (US)
- MRC Human Genetics Unit (GB)
- Jackson Laboratory (US)
- European Bioinformatics Institute (GB)
- Corresponding author
- Adams, David J.
- ORCID
- Keane, Thomas M.
- Danecek, Petr
- Wong, Kim
- Yalcin, Binnaz
- Heger, Andreas
- Slater, Guy
- Furlotte, Nicholas A.
- Eskin, Eleazar
- Nellåker, Christoffer
- Whitley, Helen
- Janowitz, Deborah
- Belgard, T. Grant
- Oliver, Peter L.
- McIntyre, Rebecca E.
- Bhomra, Amarjit
- Nicod, Jérôme
- Gan, Xiangchao
- Steward, Charles A.
- Mott, Richard
- Durbin, Richard
- Jackson, Ian J.
- Czechanski, Anne
- Reinholdt, Laura G.
- Payseur, Bret A.
- Ponting, Chris P.
- Birney, Ewan
- Adams, David J.
- Venue
- Nature
- Published
- 2011-09
- Volume
- 477
- Issue
- 7364
- Pages
- 289-294
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3276836
- OpenAlex
- W2005501593
- Cited by
- 1,580
- References
- 3
- Citations by year
- 2026: 39 · 2025: 74 · 2024: 100 · 2023: 77 · 2022: 118 · 2021: 130 · 2020: 130 · 2019: 103 · 2018: 104 · 2017: 114 · 2016: 118 · 2015: 122 · 2014: 106 · 2013: 126 · 2012: 102
- FWCI
- 69.44
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- HAL (submittedVersion, other-oa)
- RePEc: Research Papers in Economics (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion, cc-by-nc-sa)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
- Funders
- National Science Foundation (0918000)
- Juvenile Diabetes Research Foundation International
- Wellcome Trust (079912, 085906/Z/08/Z, 083573, 077192, 082356, 090532, 083573/Z/07/Z, 085906, 083573/Z/07)
- Immune Tolerance Network
- Cancer Research UK (A6997)
- National Institutes of Health (n01ai15416-28-0-11)
- Medical Research Council (MC_EX_G0802457)
- Biotechnology and Biological Sciences Research Council (BB/F022697/1)
- National Heart, Lung, and Blood Institute (K25HL080079)
- National Human Genome Research Institute (T32HG002536)
- National Institute of Allergy and Infectious Diseases (N01-AI-015416)
- National Institute of Diabetes and Digestive and Kidney Diseases
- U.S. National Library of Medicine (T15LM007359)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- inbred mouse strains, mRNA levels, quantitative trait loci, functional variants, structural variants, wild-derived mouse strains, phenotypic variability, gene expression regulation
- MeSH terms
- Alleles, Animals, Animals, Laboratory, Gene Expression Regulation, Mice, Inbred C57BL, Mice, Inbred Strains, Phenotype, Phylogeny, Genetic Variation, Genome, Genomics, Quantitative Trait Loci, Mice
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