Genetic analysis of complex traits in the emerging Collaborative Cross

Abstract

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.

Figure 1.

Genetic properties of the Pre-CC panel. (A) Eight founder's inbred strains were bred according to the original funnel design (Churchill et al. 2004). The G₂:F₁ generation has contributions from all eight founders. Siblings are mated in this and all subsequent generations until the lines are isogenic. (B) An example of a pre-CC genome from a single G₂:F₇ animal. Ancestry was inferred by comparing pre-CC and founder genotypes using an HMM. (C) Founder contributions to any particular line (columns) vary from 1.3% to 30.7%. (D) Each of the eight founders contributes between 11.4% and 13.5% to 184 lines from the exercise behavior and metabolism phenotyping arm.

Figure 2.

Allele frequencies. Genome-wide founder allele frequencies range from 4.1% to 27.3%. The color corresponding to each founder strain is the same as in Figure 1D.

Figure 3.

White head-spot genome scan. (A) Marker-based (light gray) and eight-allele (black) models implicate an allele on Chr 10. (B) Superimposing WSB/EiJ homozygous regions from white head-spotted samples reveals two candidate regions from 88.6 to 94.3 Mb and from 96.4 to 101.3 Mb.

Figure 4.

Baseline body weight genome scan. (A) Eight-allele model (black) indicates a QTL on Chr 4, named here Bwq14, and several suggestive peaks. No peaks reach significance using the marker-based method (light gray). (B) Allele effects plot for Bwq14 suggest a shared NZO/HlLtJ and C57BL/6J allele at this locus is associated with an increase in body weight (dark-gray and light-blue lines). The color corresponding to each founder strain is the same as in Figure 1D. (C) A region of sequence identity between NZO/HlLtJ and C57BL/6J (black bars) reduces the candidate region to 4.69 Mb.

Figure 5.

Expression QTL from liver. (A) A total of 7235 eQTLs were detected for 6327 genes. Genes, arranged in order of genomic position along the y-axis, are associated with genetic variation plotted by genomic position on the x-axis. The prominent diagonal band indicates local eQTLs. (B) Local eQTL peaks generally fell within 1 Mb of the gene's genomic location, with the most significant eQTLs also being the most accurate.