Genome-wide association studies reveal a simple genetic basis of resistance to naturally coevolving viruses in Drosophila melanogaster

Abstract

Variation in susceptibility to infectious disease often has a substantial genetic component in animal and plant populations. We have used genome-wide association studies (GWAS) in Drosophila melanogaster to identify the genetic basis of variation in susceptibility to viral infection. We found that there is substantially more genetic variation in susceptibility to two viruses that naturally infect D. melanogaster (DCV and DMelSV) than to two viruses isolated from other insects (FHV and DAffSV). Furthermore, this increased variation is caused by a small number of common polymorphisms that have a major effect on resistance and can individually explain up to 47% of the heritability in disease susceptibility. For two of these polymorphisms, it has previously been shown that they have been driven to a high frequency by natural selection. An advantage of GWAS in Drosophila is that the results can be confirmed experimentally. We verified that a gene called pastrel--which was previously not known to have an antiviral function--is associated with DCV-resistance by knocking down its expression by RNAi. Our data suggest that selection for resistance to infectious disease can increase genetic variation by increasing the frequency of major-effect alleles, and this has resulted in a simple genetic basis to variation in virus resistance.

Figure 1. Quantile–quantile plots of P-values.

The black dots represent the observed P-values against the P-values that are expected under the null hypothesis (that there are no true associations with resistance to four viruses), and the straight line is the distribution expected if the observed values equal the expected values. The red points show the P-values after the effect of the polymorphisms in pastrel (DCV), ref(2)P (DMelSV) and CHKov1 (DMelSV) have been accounted for. The null distribution of expected P-values was obtained by permutation.

Figure 2. Manhattan plots of the P-values for the association between SNPs and virus resistance.

The horizontal lines are genome-wide significance thresholds of P = 0.05 (solid line) and P = 0.2 (dashed line) that were obtained by permutation. The five chromosome arms are different colours.

Figure 3. The effect of the three polymorphisms affecting susceptibility on four different viruses.

In Panel A, blue bars are the susceptible allele and red bars the resistant allele. The estimates and standard errors were obtained using a general linear mixed model with the mean survival or proportion infected in each vial as the response. Significant associations are controlled for when estimating the effects of other genes, and the estimates assume that the flies have the susceptible allele of other genes. Panel B, shows the survival curves of lines with the two alleles of pastrel (3L:7350895 Ala/Thr). The green lines show the combined survival of all the flies with each allele (combined across the different lines).

Figure 4. The effect of knocking down pastrel expression.

The effect of knocking down pastrel expression on (A) the survival of infected flies with a high or low dose of DCV (see methods) and (B) viral titres 14 days post infection with the low dose. Control 1 were flies in which a gene unrelated to viral infection was knocked down (CG10669), and Control 2 were flies with the same genetic background as the pastrel-RNAi flies. Error bars are standard errors. Observations on the high dose treatment stopped on day 9.