The Drosophila melanogaster Genetic Reference Panel

By T. Mackay, S. Richards, Eric A. Stone, A. Barbadilla, Julien F. Ayroles, Dianhui Zhu, Sònia Casillas, Yi Han, M. Magwire, J. Cridland and 42 more. Nature, 2012

1,640 citations recorded by the source corpus.

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.

Subfields: Genetics, Insect Science, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d643d78e46c40c7b965dc777e02284f41e5da52b

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Citations in the corpus

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines (2014, methodology): “Non-random distribution of SNPs and indels Previously, we found that SNP nucleotide polymorphism (π) in the DGRP was reduced near centromeres and telomeres, and was positively associated with local recombination rate (for recombination rates 2 cM/Mb) (Mackay et al., 2012).”
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions (2013, background): “To evaluate the power of this approach as a function of the contiguity of this initial assembly, we sought to reassemble simulated contigs of varying size derived from the human reference genome.”
FlyBase: a guided tour of highlighted features (2022, background): “…et al. 2007; Leader et al. 2018) and a developmental proteome (Casas-Vila et al. 2017), and variation data from the DGRP reference strains panel (Mackay et al. 2012), protein–protein interactomes (Guruharsha et al. 2011; Rhee et al. 2014; Shokri et al. 2019), and DNA-binding site data from…”
Inaugural Article: Epistasis dominates the genetic architecture of Drosophila quantitative traits (2012, positive): “and starvation resistance exactly as described previously (16).”
Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species (2012, neutral): “…cost and skyrocketing throughput of DNA sequencing has begun to enable sequencing of entire genomes of study populations of some focal species [1,2]; however, even in traditional model species (e.g., humans, laboratory mice, and Drosophila ) resources for complete genome resequencing of large…”
Pitfalls of predicting complex traits from SNPs (2013, methodology): “We downloaded genotype data of the Drosophila Genetics Reference Panel and simulated phenotypes under the null hypothesis, i.e., random association between each of the > 1 million SNPs and phenotype.”