Comments from curator
No phenotype data: this study was rejected because no new phenotype was measured on DGRP lines.The DGRP analyses of this paper use the starvation resistance, startle response and chill coma recovery data of the 168 Freeze 1.0 DGRP lines published by
Mackay et al., 2012. These data are in
DGRPool study 21 (mn_StarvationRes, mn_StartleRes and mn_ChillComaRec). The authors reused the single-SNP GWAS results of that paper and ran new genome-wide scans for pairwise epistasis (FastEpistasis) between the trait-associated SNPs and all other DGRP SNPs.
The new phenotyping was done on
Flyland, an outbred advanced intercross population derived from 40 DGRP lines, crossed in a round-robin design and then randomly mated for 70 generations (800 flies per generation). From generation 70, 2,000 females were phenotyped for each trait as in Mackay et al., 2012. Pools of 300 extreme females were then sequenced to map trait-associated SNPs by extreme QTL mapping: the top and bottom 15% for startle response and chill coma recovery, and the 300 longest-surviving starved females against 300 unstarved females for starvation resistance. Flyland flies are outbred individuals that do not belong to any DGRP line, so their phenotypes cannot be stored per DGRP line. They are only shown as distributions in Fig. 1 of the
paper (
PMC version).
The supplementary
Dataset S1 holds only SNP- and gene-level results: sequencing of the pools (Table S1), significant Flyland SNPs (Tables S2-S4), GO enrichments (Tables S5 and S9) and significant epistatic SNP pairs in the DGRP (Tables S6-S8). The SI Appendix is cited for supplementary figures only. There is therefore nothing to upload to DGRPool.
The 40 Flyland founder lines are DGRP_208, 301, 303, 304, 306, 307, 313, 315, 324, 335, 357, 358, 360, 362, 365, 375, 379, 380, 391, 399, 427, 437, 486, 514, 517, 555, 639, 705, 707, 712, 714, 730, 732, 765, 774, 786, 799, 820, 852 and 859. The pool sequencing data are in NCBI BioProject
PRJNA167659 (SRA studies SRP013733-SRP013735).
