Bayesian Diallel Analysis Reveals Mx1-Dependent and Mx1-Independent Effects on Response to Influenza A Virus in Mice

Abstract

Influenza A virus (IAV) is a respiratory pathogen that causes substantial morbidity and mortality during both seasonal and pandemic outbreaks. Infection outcomes in unexposed populations are affected by host genetics, but the host genetic architecture is not well understood. Here, we obtain a broad view of how heritable factors affect a mouse model of response to IAV infection using an 8 × 8 diallel of the eight inbred founder strains of the Collaborative Cross (CC). Expanding on a prior statistical framework for modeling treatment response in diallels, we explore how a range of heritable effects modify acute host response to IAV through 4 d postinfection. Heritable effects in aggregate explained ∼57% of the variance in IAV-induced weight loss. Much of this was attributable to a pattern of additive effects that became more prominent through day 4 postinfection and was consistent with previous reports of antiinfluenza myxovirus resistance 1 (Mx1) polymorphisms segregating between these strains; these additive effects largely recapitulated haplotype effects observed at the Mx1 locus in a previous study of the incipient CC, and are also replicated here in a CC recombinant intercross population. Genetic dominance of protective Mx1 haplotypes was observed to differ by subspecies of origin: relative to the domesticus null Mx1 allele, musculus acts dominantly whereas castaneus acts additively. After controlling for Mx1, heritable effects, though less distinct, accounted for ∼34% of the phenotypic variance. Implications for future mapping studies are discussed.

Keywords: Bayesian mixed model; MPP; causal effect; multiparental populations; multiple imputation; treatment response.

Figure 1

Phenotype and treatment-response classes for analysis of IAV infection in the diallel. Each filled square represents a weight or weight-change phenotype that is modeled independently. The gray square represents the starting body weight in all animals, prior to treatment, at D0 (analyzed with model 1 in Table 2). Light blue squares represent animals that were mock treated and red squares represent animals infected with IAV, with daily weights for each taken from D1 to D4 p.i. (and these were analyzed with model 2 in Table 2). Purple squares represent infection response, the primary quantity of interest, estimated using match quartets of one mock to three infected mice (analyzed with models 3 and 4 in Table 2). Labels within each square indicate phenotypes analyzed, where weight = preinfection body weight, pct = p.i. percent change in starting D0 weight (post), and “delta” = infection response, as described in the Statistical Models and Methods section. The coloring increases in saturation from D1 to D4 for the influenza and matched quartet groups to indicate an overall increasing amount of p.i. weight loss over time.

Figure 2

Diagram of breeding strategy for diallel, pre-CC, and CC-RIX. (A) The diallel cross produces inbred (n = 8) and F1 (n = 54 lines) genotypes from an 8 × 8 cross of inbred strains. (B) The pre-CC is comprised of incompletely inbred (n = 155 lines) genotypes from 155 inbreeding funnels. (C) The CC-RIX produces F1 hybrid lines (n = 105 lines) from a sparse, round robin-like cross of 65 inbred CC strains.

Figure 3

Influenza-induced weight loss in an 8 × 8 diallel cross of mice, through 4 d p.i. Mean weight change, as % D0 weight, is shown at (A) D1, (B) D2, (C) D3, and (D) D4 p.i. with 500 pfu IAV (PR8) in male and female inbreds and F1 hybrids of CC founder strains (n = 774 for D1 and D2, n = 382 for D3, and n = 381 for D4). Results from mock-infected mice not shown. Squares with a gray “X” indicate matings that do not produce offspring.

Figure 4

Diallel effects on host weight IAV-infection response, before and after accounting for Mx1 haplotypes. (A) Effect estimates for additive, maternal, inbred, and epistatic effects, including sex-specific effects, are presented as HPD intervals across 163 individual effects categories for IAV-induced weight change at D4 p.i. (phenotype D4delta). HPDs are given for each parameter, including 95% (thin line) and 50% (thick line) intervals, and median (white break) and mean (black vertical line). Parameters are labeled according to the methods. Symmetric epistatic, asymmetric epistatic, and sex-specific parameters are indicated by “v:”, “w:”, and “f:”, respectively. The overall treatment effect (data not shown), θ, is −8.85% (−9.92, −7.78%). (B and C) TReVarPs, a generalization of heritability for diallel effects classes, at D4 are shown for three fixed (overall) effects, five random effects classes, and five corresponding sex-specific random effects classes (posterior median and 95% HPD intervals) before (B) and (C) after accounting for diplotypes at the host influenza resistance locus, Mx1. (D and E) TReVarPs before and after Mx1 for all four p.i. time points.

Figure 5

Time course of subspecies-specific Mx1 haplotype effects on IAV-induced weight change in the diallel. (A) Predictive means of Mx1 diplotype effects across 4 d p.i., modeled simultaneously with other diallel effects and covariates. (B) HPD intervals of Mx1 diplotype effects on weight change on D4 p.i. Increased resistance is indicated by values further to the right. Dashed lines highlight the mode of interaction between Mx1 haplotypes: the green line shows the additive effect of crossing castaneus with domesticus, the blue line shows the dominant effect of crossing musculus with domesticus, and the orange line shows the negligible effect of castaneus crossed with musculus.

Figure 6

Posterior density of the dominance index on (A) D3 and (B) D4. (C) Posterior density of the dominance difference index, i.e., the difference between the dominance indices of castaneus and musculus, across all 4 d.

Figure 7

Additive CC-strain haplotype effects on IAV-induced weight loss across three CC-related populations. (A) Additive effects from the CC founder diallel of mice infected with IAV (PR8) or mock (n_flu = 393, n_mock = 131) at D4 p.i. (from Figure 1). (B) Additive strain haplotype effects at the Mx1 locus for female pre-CC mice (n = 155) infected with IAV (PR8) at D4 p.i. (C) Additive strain haplotype effects at Mx1 for female CC-RIX mice (n = 1402) infected with IAV (CA04) at D7 p.i. Estimates are shown as HPD intervals as described in Figure 1, with blue lines connecting posterior means. Parameter scales are given as additional IAV-induced weight loss per dose of strain in % of (A) D0, and (B and C) normalized effect size.