Huang et al., 2014
Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
[10.1101/gr.171546.113][FBrf0225536]

Description

This study produced the genotyping data for the main 205 genotyped DGRP lines. Afterward, the authors mainly focused on genome architecture and population genetics traits such as inversion landscape, or relatedness of the DGRP lines (which mainly comes from the inversions), or variations in genome sizes. The authors also measured Wolbachia pipientis infection status, which extends the measurements done in the DGRP original study. It's worth noting that many of these phenotypes were recognized as covariates and thus are now standardly used as such for all GWAS analyses of the DGRP lines.

Comments from curator

This paper is one of the founding papers for the DGRP lines, along with the main study: (MacKay et al, 2012).

Many of the phenotypes described there are used as covariates for GWAS analyses (Wolbachia status, Large Chromosomal inversion). This is the case on this website or for e.g. in the DGRP2 website. The following covariates are the ones used as covariates for any GWAS analysis:

• Wolbachia Status
• Inversion (2L)t
• Inversion (2R)NS
• Inversion (3R)P
• Inversion (3R)K
• Inversion (3R)Mo

Phenotypes were extracted from the Supplemental_Data_Files.xlsx file in the Supplemental Material section. In particular:

• Number and % segregating variants in each DGRP line, by chromosome arm, was found in Supp. data file S5
• Cytological analysis of polymorphic inversions was found in Supp. data file S6 (ST = homozygous for the standard arrangement, INV/ST = heterozygous, INV = homozygous for the inversion)
• Wolbachia infection status was found in Supp. data file S7 (y = infected, n = not infected). It extends the original Wolbachia status that was carried out in the original DGRP study.
• Genome size estimates from flow cytometry (done in females only) were found in Supp. data file S8

The Wolbachia infection status is a binary value, compatible with PLINK, i.e. values can be 1 (not infected) or 2 (infected). Similarly, inversion phenotypes were recoded as 0 (ST/ST), 1 (INV/ST) and 2 (INV/INV).

205 DGRP lines 193 available 12 genotyped

DGRP_021 DGRP_026 DGRP_028 DGRP_031 DGRP_032 DGRP_038 DGRP_040 DGRP_041 DGRP_042 DGRP_045 DGRP_048 DGRP_049 DGRP_057 DGRP_059 DGRP_069 DGRP_073 DGRP_075 DGRP_083 DGRP_085 DGRP_088 DGRP_091 DGRP_093 DGRP_100 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_189 DGRP_195 DGRP_208 DGRP_217 DGRP_223 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_319 DGRP_320 DGRP_321 DGRP_324 DGRP_325 DGRP_332 DGRP_335 DGRP_336 DGRP_338 DGRP_340 DGRP_348 DGRP_350 DGRP_352 DGRP_354 DGRP_355 DGRP_356 DGRP_357 DGRP_358 DGRP_359 DGRP_360 DGRP_361 DGRP_362 DGRP_365 DGRP_367 DGRP_370 DGRP_371 DGRP_373 DGRP_374 DGRP_375 DGRP_377 DGRP_379 DGRP_380 DGRP_381 DGRP_382 DGRP_383 DGRP_385 DGRP_386 DGRP_390 DGRP_391 DGRP_392 DGRP_395 DGRP_397 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_505 DGRP_508 DGRP_509 DGRP_513 DGRP_517 DGRP_528 DGRP_530 DGRP_531 DGRP_535 DGRP_551 DGRP_555 DGRP_559 DGRP_563 DGRP_566 DGRP_584 DGRP_589 DGRP_595 DGRP_596 DGRP_627 DGRP_630 DGRP_634 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_748 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_819 DGRP_820 DGRP_821 DGRP_822 DGRP_832 DGRP_837 DGRP_843 DGRP_849 DGRP_850 DGRP_852 DGRP_853 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_900 DGRP_907 DGRP_908 DGRP_911 DGRP_913

Datasets

Dataset	Phenotypes	DGRP lines
Summary dataset	35 phenotypes Inversion_2L_t Inversion_2R_NS Inversion_2R_Y1 Inversion_2R_Y2 Inversion_2R_Y3 Inversion_2R_Y4 Inversion_2R_Y5 Inversion_2R_Y6 Inversion_2R_Y7 Inversion_3L_M Inversion_3L_P Inversion_3L_Y Inversion_3R_C Inversion_3R_K Inversion_3R_Mo Inversion_3R_P SegregVariants_2L SegregVariants_2R SegregVariants_3L SegregVariants_3R SegregVariants_X TotalVariants_2L TotalVariants_2R TotalVariants_3L TotalVariants_3R TotalVariants_X WolbachiaStatus mn_GenomeSize pc_SegregVariants_2L pc_SegregVariants_2R pc_SegregVariants_3L pc_SegregVariants_3R pc_SegregVariants_X se_GenomeSize	205 DGRP lines DGRP_021 DGRP_026 DGRP_028 DGRP_031 DGRP_032 DGRP_038 DGRP_040 DGRP_041 DGRP_042 DGRP_045 DGRP_048 DGRP_049 DGRP_057 DGRP_059 DGRP_069 DGRP_073 DGRP_075 DGRP_083 DGRP_085 DGRP_088 DGRP_091 DGRP_093 DGRP_100 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_189 DGRP_195 DGRP_208 DGRP_217 DGRP_223 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_319 DGRP_320 DGRP_321 DGRP_324 DGRP_325 DGRP_332 DGRP_335 DGRP_336 DGRP_338 DGRP_340 DGRP_348 DGRP_350 DGRP_352 DGRP_354 DGRP_355 DGRP_356 DGRP_357 DGRP_358 DGRP_359 DGRP_360 DGRP_361 DGRP_362 DGRP_365 DGRP_367 DGRP_370 DGRP_371 DGRP_373 DGRP_374 DGRP_375 DGRP_377 DGRP_379 DGRP_380 DGRP_381 DGRP_382 DGRP_383 DGRP_385 DGRP_386 DGRP_390 DGRP_391 DGRP_392 DGRP_395 DGRP_397 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_505 DGRP_508 DGRP_509 DGRP_513 DGRP_517 DGRP_528 DGRP_530 DGRP_531 DGRP_535 DGRP_551 DGRP_555 DGRP_559 DGRP_563 DGRP_566 DGRP_584 DGRP_589 DGRP_595 DGRP_596 DGRP_627 DGRP_630 DGRP_634 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_748 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_819 DGRP_820 DGRP_821 DGRP_822 DGRP_832 DGRP_837 DGRP_843 DGRP_849 DGRP_850 DGRP_852 DGRP_853 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_900 DGRP_907 DGRP_908 DGRP_911 DGRP_913	Download