Anderson et al., 2017
Natural variation in stochastic photoreceptor specification and color preference in Drosophila
[10.7554/eLife.29593]

Description

The proportion of R7 photoreceptors expressing Spineless (SsON) was measured in F1 males from crosses of 203 DGRP lines to an ss deficiency, and green-versus-blue light preference in females of 54 lines. An insertion in ss (sin) lowered SsON and shifted the preference to blue.

Comments from curator

Phenotyping data comes from the two source data files of the paper (eLife, Figures and data; also on PMC):
- Figure 1—source data 1 (elife-29593-fig1-data1.xlsx, "DGRP % SsON phenotypes"): mean and standard deviation of the percentage of SsON R7 photoreceptors, for 203 DGRP lines.
- Figure 2—source data 1 (elife-29593-fig2-data1.xlsx, "DGRP behavior phenotypes"): mean, standard error and number of trials of the green-versus-blue light preference index, for 54 of these lines.
Only these per-line values were published (no per-retina or per-trial data), so the study has a summary dataset only. The lines are given as bare numbers (e.g. 730 = DGRP_730); all of them are DGRP lines of DGRPool.

The % SsON R7s are F1 phenotypes, not phenotypes of the inbred DGRP lines. Each DGRP line was crossed to Df(3R)Exel6269, a ~200 kb deficiency covering the spineless (ss) locus, and the F1 males (w¹¹¹⁸/Y; DGRP/+; DGRP/Df(3R)Exel6269) were scored. They are hemizygous for the ss locus of the DGRP line, heterozygous DGRP/lab stock for the rest of the autosomes, and carry the X chromosome of the lab stock. Adult retinas were stained for Rh4 (SsON, "yellow" R7s) and Rh3 (SsOFF, "pale" R7s), and the proportion of Rh4-expressing R7s was counted with semi-automated software (Fly Retina Analysis): 6 or more retinas per line, 100 or more R7s per retina (flies raised at 25 °C). Each value is assigned to the DGRP parent line, as in the authors' GWAS, and the cross is given in the phenotype names (_xExel6269). The lab stock had 62% SsON R7s in the same cross (not a DGRP line, not uploaded).

Color preference was measured on females of the DGRP lines themselves (no cross): for each trial, 100 females (raised at 25 °C on a 14:10 h light:dark cycle, starved for 8 h) were put in a T-maze under red light and given 20 s to choose between a green (525 nm, one layer of 3x neutral density filter) and a blue (450 nm, three layers) LED light. Preference index PI = (N_G − N_B)/(N_G + N_B), from −1 (all flies on the blue side) to +1 (all on the green side); 5 to 12 trials per line.

The summary dataset has:
- mn_SsON_xExel6269 and sd_SsON_xExel6269 (sex M, %): mean and standard deviation of the percentage of SsON (Rh4) R7s, the phenotype of the authors' GWAS. It ranges from 18.8% (DGRP_730) to 83.1% (DGRP_229), as in the paper ("19% to 83%").
- mn_GreenBluePI and se_GreenBluePI (sex F): mean and standard error of the preference index over trials.
- NTrials_GreenBluePI (obsolete, design information): the number of trials behind the mean.

The "Presence of sin" column of both files (the genotype of the line at the ss insertion, sin, found by the GWAS: 0 = no sin, 1 = line heterozygous, 2 = sin) is a DGRP genotype, not a phenotype, and was not uploaded. In these files, the 46 lines with sin have a lower mean % SsON than the 141 lines without (50.1% vs 64.7%), and the 23 lines with sin a lower mean PI than the 31 without (−0.077 vs 0.016), as in Figures 1H and 2C. The paper marks the PI difference as p < 0.05 without naming the test: a one-sided t-test on the published line means gives P = 0.034 (two-sided P = 0.068).

GWAS: the authors used plink (linear model, first 20 genomic principal components as covariates, max(T) permutations) with F1 genotypes simulated from the DGRP freeze 2 genotypes lifted to dm6 (homozygous alternative alleles coded heterozygous, or hemizygous inside the deficiency; heterozygous DGRP calls set to missing). Since each F1 carries one haplotype of its DGRP parent, this coding is proportional to the DGRP genotypes.

Not uploaded: the African lines, laboratory lines and CRISPR lines with and without sin, and the klumpfuss (klu) gain- and loss-of-function experiments (not DGRP lines, and only shown in figures); the SELEX-seq analysis of Klu binding (public data of Nitta et al. 2015) and the population genetics of sin.

203 DGRP lines 203 genotyped

DGRP_021 DGRP_026 DGRP_028 DGRP_031 DGRP_032 DGRP_038 DGRP_040 DGRP_041 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_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_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	5 phenotypes mn_GreenBluePI mn_SsON_xExel6269 sd_SsON_xExel6269 se_GreenBluePI	203 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_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_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