Collaborative Cross mice and their power to map host susceptibility to Aspergillus fumigatus infection

Abstract

The Collaborative Cross (CC) is a genetic reference panel of recombinant inbred lines of mice, designed for the dissection of complex traits and gene networks. Each line is independently descended from eight genetically diverse founder strains such that the genomes of the CC lines, once fully inbred, are fine-grained homozygous mosaics of the founder haplotypes. We present an analysis of 120 CC lines, from a cohort of the CC bred at Tel Aviv University in collaboration with the University of Oxford, which at the time of this study were between the sixth and 12th generations of inbreeding and substantially homozygous at 170,000 SNPs. We show how CC genomes decompose into mosaics, and we identify loci that carry a deficiency or excess of a founder, many being deficient for the wild-derived strains WSB/EiJ and PWK/PhJ. We phenotyped 371 mice from 66 CC lines for a susceptibility to Aspergillus fumigatus infection. The survival time after infection varied significantly between CC lines. Quantitative trait locus (QTL) mapping identified genome-wide significant QTLs on chromosomes 2, 3, 8, 10 (two QTLs), 15, and 18. Simulations show that QTL mapping resolution (the median distance between the QTL peak and true location) varied between 0.47 and 1.18 Mb. Most of the QTLs involved contrasts between wild-derived founder strains and therefore would not segregate between classical inbred strains. Use of variation data from the genomes of the CC founder strains refined these QTLs further and suggested several candidate genes. These results support the use of the CC for dissecting complex traits.

Figure 1.

Reconstructions of the genomes of representative CC lines IL-18 and IL-507 from the hidden Markov model (HMM) implemented by HAPPY. The x-axis shows the 19 autosomes. Each reconstruction is represented by two panels. The top panel y-axis shows the eight CC founders, and the probability of descent from a founder at a locus is represented by the shade of gray, with white = 0 and black = 1. Regions where a single haplotype predominates appear as dark horizontal bands; loci with residual heterozygosity or where the founder haplotypes are indistinguishable are gray. The lower panel indicates local heterozygosity (red).

Figure 2.

Representative mean survival time in days post-infection with Aspergillus fumigatus, of standard inbred lines (black) and of CC lines (gray), with standard errors indicated.

Figure 3.

(A) Survival curves of selected CC lines following infection with Aspergillus fumigatus. (B) log[−log(D(t))] versus log(time) for all CC animals.

Figure 4.

Genome scan of susceptibility to Aspergillus fumigatus in 66 CC lines. The x-axis is genome location; the y-axis is the logP of the test of association between locus and survival time. Genome-wide thresholds of association at E < 0.5, E < 0.1, and E < 0.05 expectation levels are indicated by the horizontal gray lines at logP = 3.97, 5.26, and 5.64, respectively (i.e., the threshold P means that in a fraction P of permutations the genome-wide maximum logP exceeded the threshold).

Figure 5.

Simulation-based empirical distribution of mapping resolution for QTL Asprl1. The x-axis is the distance of the maximum logP in the region from the simulated locus. The y-axis is the fraction of 100,000 simulations. Note that the x-axis labeling is offset to the left side of each bar, so the central highest peak is in reality centered at zero.

Figure 6.

Estimated effects on survival time after Aspergillus fumigatus infection, for the eight CC founder strains for each of the Asprl QTLs. Effects are shown as deviations relative to WSB/EiJ, which is assigned the trait effect of 0. The x-axis of each plot shows the founder strains; the y-axis shows the estimated parameter for the haplotype of the CC founder s.

Figure 7.

Merge analysis of sequence variants around the QTL Asprl1 on chr 8, for susceptibility to Aspergillus fumigatus infection in the CC. The x-axis is genome location; the y-axis is the logP of the test of association between locus and survival time. The continuous black line is the genome scan in Figure 4. The blue and red dots are the results of merge analysis tests of sequence variants segregating in the eight founders of the CC. For clarity, the great majority of variants with merge logP < 1 are not shown. Biallelic SNPs are in blue; variants with more than two alleles (caused when alleles are unknown in one or more founders, which are then treated as private alleles) are red. Image is taken from the genome scan viewer (http://mus.well.ox.ac.uk/gscan_flot/).