Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

Abstract

The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to identify 4,853,802 single nucleotide polymorphisms (SNPs) and 1,296,080 non-SNP variants. Our molecular population genomic analyses show higher deletion than insertion mutation rates and stronger purifying selection on deletions. Weaker selection on insertions than deletions is consistent with our observed distribution of genome size determined by flow cytometry, which is skewed toward larger genomes. Insertion/ deletion and single nucleotide polymorphisms are positively correlated with each other and with local recombination, suggesting that their nonrandom distributions are due to hitchhiking and background selection. Our cytogenetic analysis identified 16 polymorphic inversions in the DGRP. Common inverted and standard karyotypes are genetically divergent and account for most of the variation in relatedness among the DGRP lines. Intriguingly, variation in genome size and many quantitative traits are significantly associated with inversions. Approximately 50% of the DGRP lines are infected with Wolbachia, and four lines have germline insertions of Wolbachia sequences, but effects of Wolbachia infection on quantitative traits are rarely significant. The DGRP complements ongoing efforts to functionally annotate the Drosophila genome. Indeed, 15% of all D. melanogaster genes segregate for potentially damaged proteins in the DGRP, and genome-wide analyses of quantitative traits identify novel candidate genes. The DGRP lines, sequence data, genotypes, quality scores, phenotypes, and analysis and visualization tools are publicly available.[Supplemental material is available for this article.]Studies in Drosophila melanogaster have revealed basic principles and mechanisms underlying fundamental genetic concepts of linkage and recombination and were instrumental in identifying canonical and evolutionarily conserved cell signaling pathways.Most D. melanogaster genes are evolutionarily conserved, leading to fly models for understanding common human diseases and behavioral disorders, dipteran disease vectors, and insects impacting agriculture, medicine, and forensics. Despite nearly a century of research on D. melanogaster, however, a large fraction of its coding and noncoding sequence has no known function (McQuilton et al. 2012). Recent efforts to induce mutations in every protein coding gene utilize transposable elements (Bellen et al. 2004(Bellen et al. , 2011, which have a different spectrum of allelic effects than SNPs and small insertions and deletions (indels). Comprehensive efforts to identify regulatory DNA elements in Drosophila (The Ó 2014 Huang et al.

Genetic basis of natural variation in body pigmentation inDrosophila melanogaster

“…xQTL mapping in an AIP can be done with very large numbers of individuals, such that top variants can achieve significance following a strict Bonferroni correction for multiple tests; but unless many generations of recombination are allowed, local LD is much higher than in the DGRP, decreasing the mapping precision. In addition, association mapping in the DGRP can only be performed using common variants (minor allele frequencies > 0.05), 40 whereas the effects of private variants in any of the 6 parental lines used to construct the AIP can be assessed. However, this replication approach will only work if gene action of the causal variants is additive; in the presence of epistatic gene action, differences in allele frequency between the DGRP and the AIP will lead to failure of replication.…”

Behavioral individuality reveals genetic control of phenotypic variability

“…It consists of a collection of isofemale lines derived from a single field collection from the Raleigh NC farmers market, followed by 20 generations of fullsib mating that rendered most loci homozygous within lines (expected F= 0.986 22 ). As a result, the genetic variation that was present between individual flies in the natural population is now captured between lines in the panel.…”

“…GWAS was performed using the code and approach decribed in 22 (dgrp2.gnets.ncsu.edu). In a first step phenotypic stores were adjusted for the potential effect of Wolbachia and known large inversions segregating in this panel (namely: In(2L)t, In(2R)NS, In(3R)P, In(3R)K, and In(3R)Mo) none of them were associated with variability turning bias.…”

“…To test this possibility, we scored additional phenotypes from our Y-maze data, namely, the total number of turns (a measure of overall activity); the mutual leftright information between successive turns; and the regularity of turn timing. We also analyzed other phenotypes previously measured on the DGRP (starvation resistance 22 , chill coma recovery 22 , startle response 22 , and night sleep 23 ). We found significant genetic variation for variability in all these phenotypes, confirming that genetic control of variability is ubiquitous across phenotypes.…”

“…The DGRP lines have been fully sequenced 22 , allowing for whole-genome association mapping using the variability (i.e. MAD) of turning bias as a trait.…”