Campbell et al., 2019
Genome-Wide Association Analysis of Anoxia Tolerance in Drosophila melanogaster
[10.1534/g3.119.400421][FBrf0243370]

Description

Anoxia tolerance (proportion alive 24 h later) was measured in replicate vials of adult females and males of 171 DGRP lines after 6 h of anoxia and of third-instar larvae of 169 lines after 1 h. Tolerance was strongly correlated between sexes but only weakly between larvae and adults.

Comments from curator

Phenotyping data comes from File S1 (File S1-phenotype means.xlsx) of the Supplemental Material on GSA figshare. For 195 DGRP lines, it gives the number of replicate vials (N), and the mean, standard error and variance of the proportion of flies surviving anoxia, for adult females, adult males and larvae. The values per vial were not published, so only this summary dataset is available.

Adults (sex F and M): 3-4 day-old flies, separated by sex under CO₂ at least one day before, were exposed in groups of 10-20 flies per food vial to 6 h of anoxia (humidified nitrogen), and the flies able to move were counted after 24 h of recovery. The proportion surviving per vial was averaged over the replicate vials of the line and sex (3 to 6 vials, mostly 4): mn_AnoxiaSurv_Adult, with its standard error (se_AnoxiaSurv_Adult) and the variance among vials (var_AnoxiaSurv_Adult). Both sexes were measured for 171 lines.

Larvae (sex NA, not sexed): late third-instar larvae, in groups of 10-20 per vial, were exposed to 1 h of anoxia, and the pupae present 24 h later were counted as survivors: mn_AnoxiaSurv_Larva, se_AnoxiaSurv_Larva and var_AnoxiaSurv_Larva, for 169 lines (2 to 4 vials). 147 lines have both adult and larval data. Of note, 21 lines have only 2 larval replicate vials in File S1, although the methods state a minimum of three replicates per line.

The number of replicate vials of each line and sex (or stage) was kept as the obsolete phenotypes NVials_Adult and NVials_Larva. The variance is the sample variance among vials (variance = SE² × N for all lines). Lines 161 and 387 are listed in File S1 without any value; they are kept in the dataset with NA values and disabled.

Corrections to File S1: six male SE cells are written as text "0/.xxx" (lines 301, 304, 306, 307, 555 and 559); they were read as 0.xxx, which agrees with the variance and N of these lines. For line 373, six cells hold two values separated by a line break (N and variance of females, of males and of larvae); the first value was kept, as it agrees with the mean and SE of the line and with the degrees of freedom of the ANOVA, and the second one (female N 3 and variance 0.052, larval N 3 and variance 0.07) was dropped. With these readings, File S1 reproduces the ANOVA of Table 1 of the paper (females: 170 and 479 degrees of freedom, line and error mean squares 0.2979 and 0.0488 vs 0.2980 and 0.0488; males: 170 and 474, 0.2042 and 0.0430 vs 0.2041 and 0.0429; larvae: 168 and 344, 0.0676 and 0.0205 vs 0.0677 and 0.0204) and the correlation between female and male survival (r = 0.840, paper: r = 0.839). The correlation between larval survival and the average of female and male survival is r = 0.20 (P = 0.015, 147 lines) with these line means, vs r = 0.18 (P = 0.02) in the paper.

The GWAS was run on the DGRP2 web pipeline with the line means of females, males, their average and their difference, and of larvae. The average and the difference between sexes can be derived from mn_AnoxiaSurv_Adult (F and M). The larval escape behaviour (proportion of larvae climbing out of the food during anoxia, 13.3-88.3%) was measured but not published per line (only its correlation with larval survival, in Figure S1). The RNAi knockdowns of candidate genes (TRiP lines) and the tests of SNP alleles on F1 crosses between DGRP lines are not phenotypes of DGRP lines and were not uploaded.

195 DGRP lines 194 genotyped 1 not_genotyped

DGRP_021 DGRP_026 DGRP_028 DGRP_031 DGRP_032 DGRP_038 DGRP_040 DGRP_042 DGRP_045 DGRP_048 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_227 DGRP_228 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_332 DGRP_335 DGRP_336 DGRP_338 DGRP_340 DGRP_348 DGRP_350 DGRP_352 DGRP_354 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_375 DGRP_377 DGRP_379 DGRP_380 DGRP_381 DGRP_382 DGRP_383 DGRP_385 DGRP_386 DGRP_387 DGRP_390 DGRP_391 DGRP_392 DGRP_395 DGRP_397 DGRP_399 DGRP_405 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_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_843 DGRP_849 DGRP_850 DGRP_852 DGRP_853 DGRP_855 DGRP_857 DGRP_859 DGRP_861 DGRP_879 DGRP_882 DGRP_884 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	8 phenotypes mn_AnoxiaSurv_Adult mn_AnoxiaSurv_Larva se_AnoxiaSurv_Adult se_AnoxiaSurv_Larva var_AnoxiaSurv_Adult var_AnoxiaSurv_Larva	195 DGRP lines DGRP_021 DGRP_026 DGRP_028 DGRP_031 DGRP_032 DGRP_038 DGRP_040 DGRP_042 DGRP_045 DGRP_048 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_227 DGRP_228 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_332 DGRP_335 DGRP_336 DGRP_338 DGRP_340 DGRP_348 DGRP_350 DGRP_352 DGRP_354 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_375 DGRP_377 DGRP_379 DGRP_380 DGRP_381 DGRP_382 DGRP_383 DGRP_385 DGRP_386 DGRP_387 DGRP_390 DGRP_391 DGRP_392 DGRP_395 DGRP_397 DGRP_399 DGRP_405 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_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_843 DGRP_849 DGRP_850 DGRP_852 DGRP_853 DGRP_855 DGRP_857 DGRP_859 DGRP_861 DGRP_879 DGRP_882 DGRP_884 DGRP_890 DGRP_892 DGRP_894 DGRP_897 DGRP_900 DGRP_907 DGRP_908 DGRP_911 DGRP_913	Download