Genetic analysis of complex traits in the emerging Collaborative Cross
Open accessAbstract
The Collaborative Cross (CC) is a mouse recombinant inbred strain panel that is being developed as a resource for mammalian systems genetics. Here we describe an experiment that uses partially inbred CC lines to evaluate the genetic properties and utility of this emerging resource. Genome-wide analysis of the incipient strains reveals high genetic diversity, balanced allele frequencies, and dense, evenly distributed recombination sites—all ideal qualities for a systems genetics resource. We map discrete, complex, and biomolecular traits and contrast two quantitative trait locus (QTL) mapping approaches. Analysis based on inferred haplotypes improves power, reduces false discovery, and provides information to identify and prioritize candidate genes that is unique to multifounder crosses like the CC. The number of expression QTLs discovered here exceeds all previous efforts at eQTL mapping in mice, and we map local eQTL at 1-Mb resolution. We demonstrate that the genetic diversity of the CC, which derives from random mixing of eight founder strains, results in high phenotypic diversity and enhances our ability to map causative loci underlying complex disease-related traits.
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Previous eQTL studies in genetically diverse populations suggest that the most significant eQTL tend to be local.
“Previous eQTL studies in genetically diverse populations suggest that the most significant eQTL tend to be local (Rockman and Kruglyak 2006; Pickrell et al. 2010; Aylor et al. 2011; Lappalainen et al. 2013).”
From RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations (2014) · cites this paper as Aylor et al. 2011
Transgressive segregation in mapping populations of mice and flies from eight founder strains provides strong empirical support for common polygenes.
“the phenomenon of transgressive segregation in mapping populations of mice and flies established from eight founder strains provides strong empirical support for the existence of common polygenes94–96.”
From Rare and common variants: twenty arguments (2012) · cites this paper as [94]
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References 42 · Cited by 328
- Authors
- Aylor, D. L., Valdar, W., Foulds-Mathes, W., Buus, R. J., Verdugo, R. A., Baric, R. S., Ferris, M. T., Frelinger, J. A., Heise, M., Frieman, M. B., Gralinski, L. E., Bell, T. A., Didion, J. D., Hua, K., Nehrenberg, D. L., Powell, C. L., Steigerwalt, J., Xie, Y., Kelada, S. N. P., Collins, F. S., Yang, I. V., Schwartz, D. A., Branstetter, L. A., Chesler, E. J., Miller, D. R., Spence, J., Liu, E. Y., McMillan, L., Sarkar, A., Wang, J., Wang, W., Zhang, Q., Broman, K. W., Korstanje, R., Durrant, C., Mott, R., Iraqi, F. A., Pomp, D., Threadgill, D., Pardo-Manuel de Villena, F., & Churchill, G. A.
- Affiliations
- University of North Carolina at Chapel Hill (US)
- Jackson Laboratory (US)
- North Carolina State University (US)
- National Institutes of Health (US)
- National Jewish Health (US)
- Oak Ridge National Laboratory (US)
- University of Wisconsin–Madison (US)
- Centre for Human Genetics (GB)
- Tel Aviv University (IL)
- ORCID
- Aylor, David L.
- Valdar, William
- Buus, Ryan J.
- Verdugo, Ricardo A.
- Baric, Ralph S.
- Ferris, Martin T.
- Gralinski, Lisa E.
- Bell, Timothy A.
- Xie, Yuying
- Kelada, Samir N.P.
- Collins, Francis S.
- Yang, Ivana V.
- Schwartz, David A.
- Chesler, Elissa J.
- Miller, Darla R.
- Spence, Jason
- Liu, Eric Yi
- McMillan, Leonard
- Sarkar, Abhishek
- Broman, Karl W.
- Korstanje, Ron
- Durrant, Caroline
- Mott, Richard
- Pomp, Daniel
- Threadgill, David
- Churchill, Gary A.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2011-03-15
- Volume
- 21
- Issue
- 8
- Pages
- 1213-1222
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC3149489
- OpenAlex
- W4300097765
- Cited by
- 328
- References
- 42
- Citations by year
- 2026: 3 · 2025: 4 · 2024: 12 · 2023: 7 · 2022: 16 · 2021: 17 · 2020: 21 · 2019: 25 · 2018: 23 · 2017: 24 · 2016: 20 · 2015: 21 · 2014: 32 · 2013: 27 · 2012: 52
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Carolina Digital Repository (University of North Carolina at Chapel Hill) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion)
- HighWire Press Open Archive (submittedVersion)
- UNC Libraries
- Funders
- U.S. Department of Energy (AC05-00OR22725, DE--AC05--00OR22725, DE-AC05?, DE-AC05-00OR22725 with UT-Battelle, under Contract DE-AC05-00OR22725, 00OR22725)
- Ellison Medical Foundation (AG-IA-0202-05)
- Battelle (DE-AC05- 00OR22725, DE-AC05)
- Wellcome Trust (090532)
- UT-Battelle (DE-AC05, DEAC05-00OR22725, Contract DE-AC05-00OR22725, AC05-00OR22725)
- National Institutes of Health (DE-AC05-00OR22725, GM074244, DK-056350)
- National Institute of Mental Health (MH090338, P50MH090338, T32MH076694)
- National Cancer Institute (U01CA105417, U01CA134240)
- National Institute of General Medical Sciences (GM067553, P50GM076468, GM074244, GM076468, T32GM007092, T32GM067553, R01GM070683, GM 070683, R01GM074244, T32 GM07092, F32GM090667)
- National Institute of Allergy and Infectious Diseases (U54AI081680)
- National Institute of Diabetes and Digestive and Kidney Diseases (DK-076050, R01DK076050, DK-056350, P30DK056350)
- School of Medicine, University of North Carolina at Chapel Hill
- 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
- Collaborative Cross, systems genetics, genetic diversity, allele frequency, recombination mapping, quantitative trait loci, haplotype inference, candidate gene prioritization, phenotypic diversity
- MeSH terms
- Animals, Crosses, Genetic, Female, Haplotypes, Male, Phenotype, Gene Expression, Genome, Quantitative Trait Loci, Mice, Genetic Association Studies
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