Genome-Wide Association Analysis of Oxidative Stress Resistance in Drosophila melanogaster

Background: Aerobic organisms are susceptible to damage by reactive oxygen species. Oxidative stress resistance is a quantitative trait with population variation attributable to the interplay between genetic and environmental factors. Drosophila melanogaster provides an ideal system to study the genetics of variation for resistance to oxidative stress. Methods and Findings: We used 167 wild-derived inbred lines of the Drosophila Genetic Reference Panel for a genomewide association study of acute oxidative stress resistance to two oxidizing agents, paraquat and menadione sodium bisulfite. We found significant genetic variation for both stressors. Single nucleotide polymorphisms (SNPs) associated with variation in oxidative stress resistance were often sex-specific and agent-dependent, with a small subset common for both sexes or treatments. Associated SNPs had moderately large effects, with an inverse relationship between effect size and allele frequency. Linear models with up to 12 SNPs explained 67–79 % and 56–66 % of the phenotypic variance for resistance to paraquat and menadione sodium bisulfite, respectively. Many genes implicated were novel with no known role in oxidative stress resistance. Bioinformatics analyses revealed a cellular network comprising DNA metabolism and neuronal development, consistent with targets of oxidative stress-inducing agents. We confirmed associations of seven candidate genes associated with natural variation in oxidative stress resistance through mutational analysis. Conclusions: We identified novel candidate genes associated with variation in resistance to oxidative stress that hav

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Quantitative genetic analysis of survival time on paraquat and MSB.

*<p>Phenotypic line-sex means adjusted for <i>Wolbachia</i> infection status.</p

Genome-wide association analyses for survival time on paraquat and MSB (sexes pooled).

<p>All SNPs from single marker analyses with a nominal <i>P</i><10⁻⁵ are shown. Associations based on females are depicted by red dots, males by blue dots, sexes pooled by black dots and SNP by sex interactions by green dots. The lower triangle depicts the degree of LD between SNPs as measured by <i>r²</i>, with the five major chromosome arms demarcated by the black lines. The heat map indicates the magnitude of LD with red corresponding to complete LD and blue to absence of LD. The upper panels show the significance threshold (−log₁₀<i>P</i>), the effect size in phenotypic standard deviation units (<i>a</i>/<i>σ_P</i>), and the minor allele frequency (MAF). (A) Survival time on paraquat. (B) Survival time on MSB.</p

Gene-centered predictive models of survival time on paraquat.

<p>Markers are listed in the order in which they entered the model. Estimates of effects are for (Minor allele – Major allele). In: intronic; cds: coding sequence;</p>#<p>: Missense; u3/5: 3′5′ UTR.</p

Analyses of variance of survival time on paraquat and MSB.

<p>df: degrees of freedom; MS: Type III Mean Squares; <i>σ²</i>: variance component.</p>*<p>Phenotypic line-sex means adjusted for <i>Wolbachia</i> infection status.</p

Genome-wide association analyses for females and males (treatments pooled).

<p>All SNPs from single marker analyses with a nominal <i>P</i><10⁻⁵ are shown. Associations based on survival on paraquat are depicted by red dots, survival on MSB by blue dots, treatments pooled by black dots and SNP by treatment interaction by green dots. The lower triangle depicts the degree of LD between SNPs as measured by <i>r²</i>, with the five major chromosome arms demarcated by the black lines. The heat map indicates the magnitude of LD with red corresponding to complete LD and blue to absence of LD. The upper panels show the significance threshold (−log₁₀<i>P</i>), the effect size in phenotypic standard deviation units (<i>a</i>/<i>σ_P</i>), and the minor allele frequency (MAF). (A) Females. (B) Males.</p

Validation of candidate oxidative stress susceptibility genes using mutants.

<p>Seven mutants <i>CG9650^BG01024</i>, <i>Eip75B^BG02737</i>, <i>ena^BG02189</i>, <i>fog^BG01196</i>, <i>hbn^MB04955</i>, <i>nAcRα-30D^MB06675</i>, and <i>rugose^MB01845</i> were tested for each sex and treatment along with their corresponding control. The averages are color coded: red, female mutant; pink female control; blue, male mutant; light blue, male control. All mutants were homozygous. (A) Survival time on paraquat. (B) Survival time on MSB. *: 0.01≤<i>P</i>≤0.05; **: 0.001≤<i>P</i>≤0.01; ***: <i>P</i><0.001; ns: <i>P</i>>0.05.</p

Variation in oxidative stress resistance among 167 DGRP lines.

<p>Line means for survival time on paraquat (A) and MSB (B) for females (red bars) and males (blue bars), and sexual dimorphism (female-male) (purple bars). (C) Genetic correlation of survival times on paraquat and MSB (<i>P</i><0.0001) for females and males separately. Mean phenotypic values for each line-sex are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034745#pone.0034745.s001" target="_blank">Table S1</a>.</p

Gene-centered predictive models of survival time on MSB.

<p>Markers are listed in the order in which they entered the model. Estimates of effects are for (Minor allele – Major allele). In: intronic; cds: coding sequence;</p>#<p>: Missense; u3/5: 3′5′ UTR.</p