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Drosophila Genetic Reference Panel

Freeze Two

Freeze Two Release: February 2013

BAM files and other data

A cool DGRP paper

Epistasis dominates the genetic architecture of Drosophila quantitative traits

This paper compares the results of GWAS analysis using the DGRP, and extreme trait mapping using the flyland population—a population derived from 40 DGRP lines and bred to shuffle their alleles.

DGRP Graph
Measurements of Drosophila quantitative traits
 
 
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It finds that the overlap of putative quantitative trait alleles from the two methods is very small, but that we can detect extensive epistatic interaction between the alleles detected by both methods.

Networks of gene interactions can be detected which overlap with known gene networks and suggest new ones.

These networks probably represent the underlying genetic architecture of these traits better than a list of putative alleles.

Freeze One Publication

We are pleased to announce that freeze one of this great collaborative effort has been published in this paper:

The Drosophila melanogaster Genetic Reference Panel

Several companion papers also addressed this resource:

We would like to thank everyone involved in this collaborative effort.

Freeze One Release: August 2010

We announced the freeze one release of the Drosophila Genetic Reference Panel under the Fort Lauderdale pre-publication data sharing agreement. We provided the Illumina sequence of 162 inbred D. melanogaster lines generated from a natural population in Raleigh North Carolina by the laboratory of Trudy Mackay.

Fastq Files

Each of these inbred lines has a minimum of 8.5X, but an average of 15X aligned genome sequence coverage in BAM files. Fastq files are available in the NCBI short read archive here.

DGRP Lines

All of the DGRP lines are available from the Bloomington Stock Center here. In the future we will be adding additional lines, and sequences, to increase the power of this genome-wide association toolkit.

For each line we also have individual links to the NCBI SRA, in this table, as in some cases multiple sequencing experiments are linked to the same DGRP line.

BAM Files

BCM-HGSC: Freeze One read alignments, stored as BAM files and generated with BWA

SNPs

For the Illumina reads we also provide a list of single nucleotide polymorphisms (SNPs) here generated by Eric Stone using a new algorithm that takes account of expected allele frequencies from 20 generations of full-sib inbreeding, followed by maintenance by random mating within each line.

Microsatellite Variability

This is a table of microsatellite variability across the 162 inbred, developed by David Mittelman.

Population Statistics

Population statistics for this dataset have been generated by the group of Antonio Barbadilla, and can be visualized on popDrowser here.

About DGRP

An amazing phenotypic resource: Our collaborator Trudy Mackay has a large set of > 200 inbred D. melanogaster lines with significant amounts of quantitative phenotypic data. These will form the basis of a community wide Drosophila Genetic Reference Panel (DGRP) where members of the community can perform phenotypic assays on a presequenced set of Drosophila lines for performing association studies at high power. This approach amortizes the sequencing costs over the entire Drosophila community. The figure provides data on three phenotypes, male aggressiveness, ethanol sensitivity and lifespan.

The Mackay laboratory also has data on life span, alcohol sensitivity, male aggression, male copulation latency, locomotive behavior, starvation resistance, chill coma recovery, abdominal bristle number, sternal pleural bristle number, adult mRNA transcription levels and olfactory behavior.

Additionally many other laboratories have promised to assay hundreds of additional phenotypes once sequence is available.

Community Involvement

Join our DGRP mailing list

Anyone can sign up for the public mailing list for DGRP-related discussion.

Data Release

As a service to the community we are releasing all sequence data for this project pre-publication and as soon as possible here—often pre-analysis on this ftp site. The data is released here under the standard genome sequence release agreements.

Users are free to use the data in scientific papers analyzing particular genes and regions if the providers of this data are properly acknowledged. Please cite the BCM-HGSC web site or publications from BCM-HGSC referring to the genome sequence. BCM-HGSC plans to publish the assembly and genomic annotation of the dataset, including genome wide molecular population genetic analyses, large-scale identification of regions of evolutionary conservation and quantitative trait association studies. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement.

Data will also be deposited into the trace archive and other appropriate depositories once all QC/QA tests are passed.

DGRP line numbers correspond to Bloomington Drosophila Stock Center designations for these lines: e.g., DGRP_360 is the same as RAL-360.

Berkeley Drosophila Reference Sequencing Strain ((y[1]; cn[1] bw[1] sp[1]) b) Adams, M. D. et al. The genome sequence of Drosophila melanogaster. Science 287, 2185-95 (2000). This strain was kindly provided by Dr, Susan Celiniker at the BDGP. It is also available at the Bloomington Drosophila Stock Center.

DGRP line 375: 12X 454-long read (500bp) data, aligned sequence in fastm format. (The long read data was generated in house by 454 in Dec 2007 and Jan 2008 prior to the release of their next generation long read platform. We thank 454 Inc. for allowing us to release this data to the public, pre-publication.)



Related Publications

Comparative validation of the D. melanogaster modENCODE transcriptome annotation., Chen, Zhen-Xia, Sturgill David, Qu Jiaxin, Jiang Huaiyang, Park Soo, Boley Nathan, Suzuki Ana Maria, Fletcher Anthony R., Plachetzki David C., FitzGerald Peter C., et al. , Genome research, 2014 Jul, Volume 24, Issue 7, p.1209-23, (2014) Abstract
Evidence for Stabilizing Selection on Codon Usage in Chromosomal Rearrangements of Drosophila pseudoobscura., Fuller, Zachary L., Haynes Gwilym D., Zhu Dianhui, Batterton Matthew, Chao Hsu, Dugan Shannon, Javaid Mehwish, Jayaseelan Joy C., Lee Sandra, Li Mingmei, et al. , G3 (Bethesda, Md.), 2014 Oct 17, (2014) Abstract
Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology., English, Adam C., Richards Stephen, Han Yi, Wang Min, Vee Vanesa, Qu Jiaxin, Qin Xiang, Muzny Donna M., Reid Jeffrey G., Worley Kim C., et al. , PloS one, 2012, Volume 7, Issue 11, p.e47768, (2012) Abstract
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution., Richards, Stephen, Liu Yue, Bettencourt Brian R., Hradecky Pavel, Letovsky Stan, Nielsen Rasmus, Thornton Kevin, Hubisz Melissa J., Chen Rui, Meisel Richard P., et al. , Genome research, 2005 Jan, Volume 15, Issue 1, p.1-18, (2005) Abstract
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