The Drosophila melanogaster Genetic Reference Panel

Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA.
Nature (Impact Factor: 41.46). 02/2012; 482(7384):173-8. DOI: 10.1038/nature10811
Source: PubMed

ABSTRACT A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the genotype-phenotype map were based on incomplete genotypic information. Here, we describe the Drosophila melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype-phenotype mapping using the power of Drosophila genetics.

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    • ". Correlation coefficients ( r ) of phenotypes measured in this study to those of Mackay et al . ( 2012 ) show several significant correlations ."
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    PLoS Genetics 03/2015; 11(3):e1005030. DOI:10.1371/journal.pgen.1005030 · 7.53 Impact Factor
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    • "A total of 1,294 candidate genes were detected with both SM and BSM, which represents ~14% of the total set of 1:1 orthologs between D. mojavensis and D. buzzatii. Positive selection seems pervasive in Drosophila (Sawyer et al. 2007; Singh et al. 2009; Sella et al. 2009; Mackay et al. 2012) and, using methods similar to ours, it has been estimated that 33% of single-copy orthologs in the melanogaster group have experienced positive selection (Drosophila 12 Genomes Consortium et al. 2007). The smaller fraction of genes putatively under positive selection in our analyses may be due to the fewer lineages considered in our study. "
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    ABSTRACT: Cactophilic Drosophila species provide a valuable model to study gene-environment interactions and ecological adaptation. D. buzzatii and D. mojavensis are two cactophilic species that belong to the repleta group, but have very different geographical distributions and primary host plants. To investigate the genomic basis of ecological adaptation, we sequenced the genome and developmental transcriptome of D. buzzatii and compared its gene content to that of D. mojavensis and two other non-cactophilic Drosophila species in the same subgenus. The newly sequenced D. buzzatii genome (161.5 Mb) comprises 826 scaffolds (> 3 kb) and contains 13,657 annotated protein-coding genes. Using RNA-Seq data of five life-stages we found expression of 15,026 genes, 80% protein-coding genes and 20% ncRNA genes. In total, we detected 1,294 genes putatively under positive selection. Interestingly, among genes under positive selection in the D. mojavensis lineage, there is an excess of genes involved in metabolism of heterocyclic compounds that are abundant in Stenocereus cacti and toxic to nonresident Drosophila species. We found 117 orphan genes in the shared D. buzzatii-D. mojavensis lineage. In addition, gene duplication analysis identified lineage-specific expanded families with functional annotations associated with proteolysis, zinc ion binding, chitin binding, sensory perception, ethanol tolerance, immunity, physiology and reproduction. In summary we identified genetic signatures of adaptation in the shared D. buzzatii-D. mojavensis lineage, and in the two separate D. buzzatii and D. mojavensis lineages. Many of the novel lineage-specific genomic features are promising candidates for explaining the adaptation of these species to their distinct ecological niches. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
    Genome Biology and Evolution 01/2015; 7(1). DOI:10.1093/gbe/evu291 · 4.23 Impact Factor
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    • "In this respect, one very significant difference between the sequencing projects compared here is the characteristics of the cohorts sequenced. The 39 fruit fly strains analyzed in [2] were taken from the DGRP, which consists of 192 inbred strains derived from a single outbred population (Raleigh, USA population [18]). In contrast, the human genomes originated from several geographically distant populations (Europe, East Asia, sub-Saharan Africa and the Americas [1]). "
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    Genomics Data 11/2014; 3. DOI:10.1016/j.gdata.2014.11.010
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