MacKay et al., 2012
The Drosophila melanogaster Genetic Reference Panel
[10.1038/nature10811][FBrf0217434]

Description

This is the founding paper of the Drosophila melanogaster Genetic Reference Panel (DGRP) lines. It contains the original 192 inbred DGRP lines derived from a single outbred population, that were later extended. It also contains the original genotyping that was performed on 168 lines, and later extended to 205 lines (Huang et al, 2014). They also measured the presence of transposable elements (TEs) in each genome, the presence of Wolbachia pipientis in the lines, as well as other phenotypes such as starvation stress resistance (SR), chill coma recovery time (CC), and startle response (ST).

Comments from curator

This paper is the founding paper for the DGRP lines, along with the extended genotyping study: (Huang et al, 2014).

Phenotyping data were extracted from the Supplementary Tables pdf file, found in the Supplementary information section. It contained the following phenotypes:

• Supplementary table 4: Number and ratio of segregating sites, by chromosome arm.
• Supplementary table 6: Numbers of transposable elements (TEs) in the DGRP lines. Of note: Unique TEs are a subset of Novel TEs which exist in only one line.
• Supplementary table 9: Wolbachia infection status (Yes or No), transformed into 1:No and 2:Yes to match PLINK's format
• Supplementary table 20: Mean phenotypic values for starvation stress resistance (SRR), chill coma recovery (CC) and startle response (ST)
• Supplementary table 28: Eco R1-RFLP genotypes were NOT included here, because this table is not cited in the main text

Note: Most of the overlapping phenotypes between this study and (Huang et al, 2014) show a good correlation. Except for the Number of segregating variants on chromosome X which does not correlate at all between the two studies.

Other external data available

SRP000694 Whole Genome Sequencing (WGS) of 192 DGRP lines

169 DGRP lines 157 available 2 unavailable 10 genotyped

DGRP_021 DGRP_026 DGRP_028 DGRP_038 DGRP_040 DGRP_041 DGRP_042 DGRP_045 DGRP_049 DGRP_057 DGRP_059 DGRP_069 DGRP_073 DGRP_075 DGRP_083 DGRP_085 DGRP_088 DGRP_091 DGRP_093 DGRP_101 DGRP_105 DGRP_109 DGRP_129 DGRP_136 DGRP_138 DGRP_142 DGRP_149 DGRP_153 DGRP_158 DGRP_161 DGRP_176 DGRP_177 DGRP_181 DGRP_195 DGRP_208 DGRP_217 DGRP_227 DGRP_228 DGRP_229 DGRP_233 DGRP_235 DGRP_237 DGRP_239 DGRP_256 DGRP_280 DGRP_287 DGRP_301 DGRP_303 DGRP_304 DGRP_306 DGRP_307 DGRP_309 DGRP_310 DGRP_313 DGRP_315 DGRP_317 DGRP_318 DGRP_320 DGRP_321 DGRP_324 DGRP_325 DGRP_332 DGRP_335 DGRP_338 DGRP_350 DGRP_352 DGRP_356 DGRP_357 DGRP_358 DGRP_359 DGRP_360 DGRP_362 DGRP_365 DGRP_367 DGRP_370 DGRP_371 DGRP_373 DGRP_374 DGRP_375 DGRP_377 DGRP_378 DGRP_379 DGRP_380 DGRP_381 DGRP_383 DGRP_386 DGRP_391 DGRP_392 DGRP_399 DGRP_405 DGRP_406 DGRP_409 DGRP_426 DGRP_427 DGRP_437 DGRP_439 DGRP_440 DGRP_441 DGRP_443 DGRP_461 DGRP_486 DGRP_491 DGRP_492 DGRP_502 DGRP_508 DGRP_509 DGRP_513 DGRP_517 DGRP_531 DGRP_535 DGRP_555 DGRP_563 DGRP_589 DGRP_591 DGRP_595 DGRP_639 DGRP_642 DGRP_646 DGRP_703 DGRP_705 DGRP_707 DGRP_712 DGRP_714 DGRP_716 DGRP_721 DGRP_727 DGRP_730 DGRP_732 DGRP_737 DGRP_738 DGRP_757 DGRP_761 DGRP_765 DGRP_774 DGRP_776 DGRP_783 DGRP_786 DGRP_787 DGRP_790 DGRP_796 DGRP_799 DGRP_801 DGRP_802 DGRP_804 DGRP_805 DGRP_808 DGRP_810 DGRP_812 DGRP_818 DGRP_820 DGRP_822 DGRP_832 DGRP_837 DGRP_852 DGRP_855 DGRP_857 DGRP_859 DGRP_861 DGRP_879 DGRP_882 DGRP_884 DGRP_887 DGRP_890 DGRP_892 DGRP_894 DGRP_897 DGRP_907 DGRP_908 DGRP_911

Datasets

Dataset	Phenotypes	DGRP lines
Summary dataset	19 phenotypes Novel_TEs SegregVariants_2L SegregVariants_2R SegregVariants_3L SegregVariants_3R SegregVariants_X Shared_TEs Total_TEs Unique_TEs WolbachiaStatus mn_ChillComaRec mn_StartleRes mn_StarvationRes mn_StarvationRes_ADJ pc_SegregVariants_2L pc_SegregVariants_2R pc_SegregVariants_3L pc_SegregVariants_3R pc_SegregVariants_X	169 DGRP lines DGRP_021 DGRP_026 DGRP_028 DGRP_038 DGRP_040 DGRP_041 DGRP_042 DGRP_045 DGRP_049 DGRP_057 DGRP_059 DGRP_069 DGRP_073 DGRP_075 DGRP_083 DGRP_085 DGRP_088 DGRP_091 DGRP_093 DGRP_101 DGRP_105 DGRP_109 DGRP_129 DGRP_136 DGRP_138 DGRP_142 DGRP_149 DGRP_153 DGRP_158 DGRP_161 DGRP_176 DGRP_177 DGRP_181 DGRP_195 DGRP_208 DGRP_217 DGRP_227 DGRP_228 DGRP_229 DGRP_233 DGRP_235 DGRP_237 DGRP_239 DGRP_256 DGRP_280 DGRP_287 DGRP_301 DGRP_303 DGRP_304 DGRP_306 DGRP_307 DGRP_309 DGRP_310 DGRP_313 DGRP_315 DGRP_317 DGRP_318 DGRP_320 DGRP_321 DGRP_324 DGRP_325 DGRP_332 DGRP_335 DGRP_338 DGRP_350 DGRP_352 DGRP_356 DGRP_357 DGRP_358 DGRP_359 DGRP_360 DGRP_362 DGRP_365 DGRP_367 DGRP_370 DGRP_371 DGRP_373 DGRP_374 DGRP_375 DGRP_377 DGRP_378 DGRP_379 DGRP_380 DGRP_381 DGRP_383 DGRP_386 DGRP_391 DGRP_392 DGRP_399 DGRP_405 DGRP_406 DGRP_409 DGRP_426 DGRP_427 DGRP_437 DGRP_439 DGRP_440 DGRP_441 DGRP_443 DGRP_461 DGRP_486 DGRP_491 DGRP_492 DGRP_502 DGRP_508 DGRP_509 DGRP_513 DGRP_517 DGRP_531 DGRP_535 DGRP_555 DGRP_563 DGRP_589 DGRP_591 DGRP_595 DGRP_639 DGRP_642 DGRP_646 DGRP_703 DGRP_705 DGRP_707 DGRP_712 DGRP_714 DGRP_716 DGRP_721 DGRP_727 DGRP_730 DGRP_732 DGRP_737 DGRP_738 DGRP_757 DGRP_761 DGRP_765 DGRP_774 DGRP_776 DGRP_783 DGRP_786 DGRP_787 DGRP_790 DGRP_796 DGRP_799 DGRP_801 DGRP_802 DGRP_804 DGRP_805 DGRP_808 DGRP_810 DGRP_812 DGRP_818 DGRP_820 DGRP_822 DGRP_832 DGRP_837 DGRP_852 DGRP_855 DGRP_857 DGRP_859 DGRP_861 DGRP_879 DGRP_882 DGRP_884 DGRP_887 DGRP_890 DGRP_892 DGRP_894 DGRP_897 DGRP_907 DGRP_908 DGRP_911	Download