"Supplementary Table S2: GO analysis. The analysis was performedusing Gowinda for (A) the complete set of significant SNPs, and (B-E) subsets of SNPs associated with Developmental Diet, Age-at-reproduction, Interaction and the LE populations, respectively, as determined by the clustering analyses. The 25 GO terms with the highest P-values are shown."									
									
A: GO term analysis of all significant SNPs combined using Gowinda									
GO term	P	FDR	Significant_genes	Total_genes	Description	Genes_in_term			
GO:0004190	0.00061	0.730775	4	16	aspartic-type endopeptidase activity	"fbgn0029093,fbgn0053128,fbgn0039381,fbgn0051926"			
GO:0070001	0.00061	0.730775	4	16	aspartic-type peptidase activity	"fbgn0029093,fbgn0053128,fbgn0039381,fbgn0051926"			
GO:0016070	0.00094	0.757112308	33	628	RNA metabolic process	"fbgn0034795,fbgn0031266,fbgn0011666,fbgn0003916,fbgn0033540,fbgn0024887,fbgn0033686,fbgn0031287,fbgn0031314,fbgn0086251,fbgn0031238,fbgn0010300,fbgn0000504,fbgn0030354,fbgn0031321,fbgn0034707,fbgn0028398,fbgn0030625,fbgn0039566,fbgn0027579,fbgn0005674,fbgn0053526,fbgn0038499,fbgn0027784,fbgn0003165,fbgn0259676,fbgn0027592,fbgn0003278,fbgn0051922,fbgn0026324,fbgn0030915,fbgn0003435,fbgn0261938"			
GO:0009409	0.00162	0.757112308	3	12	response to cold	"fbgn0034758,fbgn0036712,fbgn0040333"			
GO:0006556	0.00197	0.757112308	1	1	S-adenosylmethionine biosynthetic process	fbgn0005278			
GO:0004478	0.00197	0.757112308	1	1	methionine adenosyltransferase activity	fbgn0005278			
GO:0046500	0.00365	0.757112308	2	4	S-adenosylmethionine metabolic process	"fbgn0005278,fbgn0034276"			
GO:0004075	0.00399	0.757112308	2	3	biotin carboxylase activity	"fbgn0033246,fbgn0027580"			
GO:0034587	0.0044	0.757112308	2	7	piRNA metabolic process	"fbgn0086251,fbgn0027579"			
GO:0035303	0.00447	0.757112308	3	18	regulation of dephosphorylation	"fbgn0010316,fbgn0053526,fbgn0040967"			
GO:0035304	0.00447	0.757112308	3	18	regulation of protein dephosphorylation	"fbgn0010316,fbgn0053526,fbgn0040967"			
GO:0006352	0.00449	0.757112308	6	73	"DNA-templated transcription, initiation"	"fbgn0034795,fbgn0034707,fbgn0028398,fbgn0038499,fbgn0027592,fbgn0026324"			
GO:0016885	0.00526	0.757112308	2	4	"ligase activity, forming carbon-carbon bonds"	"fbgn0033246,fbgn0027580"			
GO:0001104	0.00563	0.757112308	6	38	RNA polymerase II transcription cofactor activity	"fbgn0034795,fbgn0052296,fbgn0034707,fbgn0027592,fbgn0003396,fbgn0001276"			
GO:0070461	0.00596	0.757112308	3	18	SAGA-type complex	"fbgn0031281,fbgn0053554,fbgn0026324"			
GO:0000124	0.00596	0.757112308	3	18	SAGA complex	"fbgn0031281,fbgn0053554,fbgn0026324"			
GO:0000398	0.00606	0.757112308	10	157	"mRNA splicing, via spliceosome"	"fbgn0031266,fbgn0003916,fbgn0024887,fbgn0031287,fbgn0000504,fbgn0030625,fbgn0039566,fbgn0027784,fbgn0051922,fbgn0030915"			
GO:0000377	0.00606	0.757112308	10	157	"RNA splicing, via transesterification reactions with bulged adenosine as nucleophile"	"fbgn0031266,fbgn0003916,fbgn0024887,fbgn0031287,fbgn0000504,fbgn0030625,fbgn0039566,fbgn0027784,fbgn0051922,fbgn0030915"			
GO:0044297	0.00622	0.757112308	12	72	cell body	"fbgn0262518,fbgn0041250,fbgn0016081,fbgn0010300,fbgn0262579,fbgn0283510,fbgn0260753,fbgn0027491,fbgn0003444,fbgn0033159,fbgn0015772,fbgn0000273"			
GO:0090304	0.00625	0.757112308	37	849	nucleic acid metabolic process	"fbgn0034795,fbgn0031266,fbgn0011666,fbgn0003916,fbgn0011766,fbgn0033540,fbgn0024887,fbgn0033686,fbgn0031287,fbgn0031314,fbgn0034726,fbgn0086251,fbgn0031238,fbgn0010300,fbgn0000504,fbgn0030354,fbgn0031321,fbgn0011606,fbgn0034707,fbgn0028398,fbgn0030625,fbgn0039566,fbgn0027579,fbgn0005674,fbgn0053526,fbgn0038499,fbgn0027784,fbgn0003165,fbgn0259676,fbgn0027592,fbgn0003278,fbgn0051922,fbgn0026324,fbgn0030915,fbgn0003435,fbgn0261938,fbgn0025680"			
GO:0006367	0.00637	0.757112308	5	63	transcription initiation from RNA polymerase II promoter	"fbgn0034795,fbgn0034707,fbgn0028398,fbgn0027592,fbgn0026324"			
GO:0019438	0.00637	0.757112308	24	374	aromatic compound biosynthetic process	"fbgn0034795,fbgn0000422,fbgn0261285,fbgn0000527,fbgn0011766,fbgn0033540,fbgn0005278,fbgn0051183,fbgn0010300,fbgn0000504,fbgn0031321,fbgn0034707,fbgn0028398,fbgn0053526,fbgn0038499,fbgn0024150,fbgn0086782,fbgn0259676,fbgn0030407,fbgn0027592,fbgn0003278,fbgn0026324,fbgn0003301,fbgn0261938"			
GO:0032774	0.00656	0.757112308	13	186	RNA biosynthetic process	"fbgn0034795,fbgn0033540,fbgn0010300,fbgn0000504,fbgn0034707,fbgn0028398,fbgn0053526,fbgn0038499,fbgn0259676,fbgn0027592,fbgn0003278,fbgn0026324,fbgn0261938"			
GO:0000375	0.00728	0.757112308	10	160	"RNA splicing, via transesterification reactions"	"fbgn0031266,fbgn0003916,fbgn0024887,fbgn0031287,fbgn0000504,fbgn0030625,fbgn0039566,fbgn0027784,fbgn0051922,fbgn0030915"			
GO:0009266	0.00763	0.757112308	13	125	response to temperature stimulus	"fbgn0000422,fbgn0031256,fbgn0034758,fbgn0265784,fbgn0036712,fbgn0002921,fbgn0265959,fbgn0031322,fbgn0040333,fbgn0086782,fbgn0262737,fbgn0003301,fbgn0000273"			
									
"B: GO term analysis of SNPs signficant for ""Developmental diet"" using Gowinda"									
GO term	P	FDR	Significant_genes	Total_genes	Description	Genes_in_term			
GO:0008202	0.00017	0.18509	5	43	steroid metabolic process	"fbgn0266435,fbgn0015582,fbgn0030598,fbgn0030593,fbgn0030592"			
GO:0042445	0.00027	0.18509	5	55	hormone metabolic process	"fbgn0266435,fbgn0015582,fbgn0030598,fbgn0030593,fbgn0030592"			
GO:0010817	0.00031	0.18509	5	56	regulation of hormone levels	"fbgn0266435,fbgn0015582,fbgn0030598,fbgn0030593,fbgn0030592"			
GO:0045455	0.00035	0.18509	4	33	ecdysteroid metabolic process	"fbgn0266435,fbgn0030598,fbgn0030593,fbgn0030592"			
GO:0034754	0.00053	0.223408	4	40	cellular hormone metabolic process	"fbgn0266435,fbgn0030598,fbgn0030593,fbgn0030592"			
GO:0042180	0.00086	0.280274444	4	48	cellular ketone metabolic process	"fbgn0266435,fbgn0030598,fbgn0030593,fbgn0030592"			
GO:0019101	0.00093	0.280274444	2	6	female somatic sex determination	"fbgn0000504,fbgn0001276"			
GO:0005351	0.00114	0.280274444	2	7	sugar:proton symporter activity	"fbgn0028560,fbgn0028563"			
GO:0005402	0.00114	0.280274444	2	7	cation:sugar symporter activity	"fbgn0028560,fbgn0028563"			
GO:0008812	0.0014	0.311873	2	7	choline dehydrogenase activity	"fbgn0030593,fbgn0030592"			
GO:0015295	0.00205	0.427593636	2	9	solute:proton symporter activity	"fbgn0028560,fbgn0028563"			
GO:0016534	0.00357	0.629816667	1	1	cyclin-dependent protein kinase 5 activator activity	fbgn0027491			
GO:0030237	0.00395	0.629816667	2	10	female sex determination	"fbgn0000504,fbgn0001276"			
GO:0018993	0.00424	0.629816667	2	8	somatic sex determination	"fbgn0000504,fbgn0001276"			
GO:0007619	0.00431	0.629816667	5	27	courtship behavior	"fbgn0000535,fbgn0015582,fbgn0283510,fbgn0000504,fbgn0003301"			
GO:0009361	0.0047	0.629816667	1	1	succinate-CoA ligase complex (ADP-forming)	fbgn0037643			
GO:0004775	0.0047	0.629816667	1	1	succinate-CoA ligase (ADP-forming) activity	fbgn0037643			
GO:0043539	0.0047	0.629816667	1	2	protein serine/threonine kinase activator activity	fbgn0027491			
GO:0050660	0.00543	0.629816667	4	61	flavin adenine dinucleotide binding	"fbgn0266435,fbgn0030598,fbgn0030593,fbgn0030592"			
GO:0050921	0.00599	0.629816667	3	8	positive regulation of chemotaxis	"fbgn0003090,fbgn0024836,fbgn0001085"			
GO:1902669	0.00599	0.629816667	3	8	positive regulation of axon guidance	"fbgn0003090,fbgn0024836,fbgn0001085"			
GO:0006707	0.00604	0.629816667	1	1	cholesterol catabolic process	fbgn0015582			
GO:0016127	0.00604	0.629816667	1	1	sterol catabolic process	fbgn0015582			
GO:0004324	0.00604	0.629816667	1	1	ferredoxin-NADP+ reductase activity	fbgn0015582			
GO:0015039	0.00604	0.629816667	1	1	NADPH-adrenodoxin reductase activity	fbgn0015582			
									
"C: GO term analysis of SNPs signficant for ""Age-at-reproduction"" using Gowinda"									
GO term	P	FDR	Significant_genes	Total_genes	Description	Genes_in_term			
GO:0044248	0.00139	0.823847907	9	358	cellular catabolic process	"fbgn0034276,fbgn0262517,fbgn0020257,fbgn0000024,fbgn0030320,fbgn0036490,fbgn0030914,fbgn0030354,fbgn0036324"			
GO:0015381	0.00146	0.823847907	2	8	high-affinity sulfate transmembrane transporter activity	"fbgn0034275,fbgn0036770"			
GO:0008271	0.00223	0.823847907	2	9	secondary active sulfate transmembrane transporter activity	"fbgn0034275,fbgn0036770"			
GO:0015116	0.00269	0.823847907	2	11	sulfate transmembrane transporter activity	"fbgn0034275,fbgn0036770"			
GO:0008272	0.00269	0.823847907	2	11	sulfate transport	"fbgn0034275,fbgn0036770"			
GO:0055072	0.00274	0.823847907	2	9	iron ion homeostasis	"fbgn0039561,fbgn0022355"			
GO:0019368	0.00358	0.823847907	1	1	"fatty acid elongation, unsaturated fatty acid"	fbgn0052072			
GO:0051354	0.00445	0.823847907	1	1	negative regulation of oxidoreductase activity	fbgn0030915			
GO:0050999	0.00445	0.823847907	1	1	regulation of nitric-oxide synthase activity	fbgn0030915			
GO:0051001	0.00445	0.823847907	1	1	negative regulation of nitric-oxide synthase activity	fbgn0030915			
GO:0032769	0.00445	0.823847907	1	1	negative regulation of monooxygenase activity	fbgn0030915			
GO:0031146	0.00494	0.823847907	3	44	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	"fbgn0020257,fbgn0030320,fbgn0036324"			
GO:2000624	0.00515	0.823847907	1	1	"positive regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay"	fbgn0030354			
GO:2000622	0.00515	0.823847907	1	1	"regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay"	fbgn0030354			
GO:0019005	0.00533	0.823847907	3	53	SCF ubiquitin ligase complex	"fbgn0020257,fbgn0030320,fbgn0036324"			
GO:1990116	0.00601	0.823847907	1	1	ribosome-associated ubiquitin-dependent protein catabolic process	fbgn0262517			
GO:0009922	0.00628	0.823847907	2	19	fatty acid elongase activity	"fbgn0036128,fbgn0052072"			
GO:0090053	0.00656	0.823847907	1	1	positive regulation of chromatin silencing at centromere	fbgn0003598			
GO:0030497	0.00702	0.823847907	2	22	fatty acid elongation	"fbgn0036128,fbgn0052072"			
GO:0035848	0.00706	0.823847907	1	1	oviduct morphogenesis	fbgn0000299			
GO:1901682	0.00828	0.823847907	2	18	sulfur compound transmembrane transporter activity	"fbgn0034275,fbgn0036770"			
GO:0004038	0.00846	0.823847907	1	1	allantoinase activity	fbgn0030914			
GO:0043605	0.00846	0.823847907	1	1	cellular amide catabolic process	fbgn0030914			
GO:0050897	0.00846	0.823847907	1	1	cobalt ion binding	fbgn0030914			
GO:0000256	0.00846	0.823847907	1	1	allantoin catabolic process	fbgn0030914			
									
"D: GO term analysis of SNPs signficant for ""Interaction"" using Gowinda"									
GO term	P	FDR	Significant_genes	Total_genes	Description	Genes_in_term			
GO:0044248	0.00136	0.827806222	9	358	cellular catabolic process	"fbgn0034276,fbgn0262517,fbgn0020257,fbgn0000024,fbgn0030320,fbgn0036490,fbgn0030914,fbgn0030354,fbgn0036324"			
GO:0015381	0.00145	0.827806222	2	8	high-affinity sulfate transmembrane transporter activity	"fbgn0034275,fbgn0036770"			
GO:0008271	0.00222	0.827806222	2	9	secondary active sulfate transmembrane transporter activity	"fbgn0034275,fbgn0036770"			
GO:0015116	0.00277	0.827806222	2	11	sulfate transmembrane transporter activity	"fbgn0034275,fbgn0036770"			
GO:0008272	0.00277	0.827806222	2	11	sulfate transport	"fbgn0034275,fbgn0036770"			
GO:0055072	0.00307	0.827806222	2	9	iron ion homeostasis	"fbgn0039561,fbgn0022355"			
GO:0019368	0.00345	0.827806222	1	1	"fatty acid elongation, unsaturated fatty acid"	fbgn0052072			
GO:0051354	0.00428	0.827806222	1	1	negative regulation of oxidoreductase activity	fbgn0030915			
GO:0050999	0.00428	0.827806222	1	1	regulation of nitric-oxide synthase activity	fbgn0030915			
GO:0051001	0.00428	0.827806222	1	1	negative regulation of nitric-oxide synthase activity	fbgn0030915			
GO:0032769	0.00428	0.827806222	1	1	negative regulation of monooxygenase activity	fbgn0030915			
GO:0031146	0.00484	0.827806222	3	44	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	"fbgn0020257,fbgn0030320,fbgn0036324"			
GO:2000624	0.00529	0.827806222	1	1	"positive regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay"	fbgn0030354			
GO:2000622	0.00529	0.827806222	1	1	"regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay"	fbgn0030354			
GO:0019005	0.00531	0.827806222	3	53	SCF ubiquitin ligase complex	"fbgn0020257,fbgn0030320,fbgn0036324"			
GO:1990116	0.00586	0.827806222	1	1	ribosome-associated ubiquitin-dependent protein catabolic process	fbgn0262517			
GO:0009922	0.00636	0.827806222	2	19	fatty acid elongase activity	"fbgn0036128,fbgn0052072"			
GO:0090053	0.00659	0.827806222	1	1	positive regulation of chromatin silencing at centromere	fbgn0003598			
GO:0030497	0.00708	0.827806222	2	22	fatty acid elongation	"fbgn0036128,fbgn0052072"			
GO:0035848	0.00711	0.827806222	1	1	oviduct morphogenesis	fbgn0000299			
GO:0007190	0.00795	0.827806222	1	2	activation of adenylate cyclase activity	fbgn0086782			
GO:1901682	0.00803	0.827806222	2	18	sulfur compound transmembrane transporter activity	"fbgn0034275,fbgn0036770"			
GO:0004038	0.00822	0.827806222	1	1	allantoinase activity	fbgn0030914			
GO:0043605	0.00822	0.827806222	1	1	cellular amide catabolic process	fbgn0030914			
GO:0050897	0.00822	0.827806222	1	1	cobalt ion binding	fbgn0030914			
									
"E: GO term analysis of SNPs signficant for ""LE"" using Gowinda"									
GO term	P	FDR	Significant_genes	Total_genes	Description	Genes_in_term			
GO:0006367	0.00047	0.32781	4	63	transcription initiation from RNA polymerase II promoter	"fbgn0026324,fbgn0027592,fbgn0034707,fbgn0028398"			
GO:0019438	0.00062	0.32781	13	374	aromatic compound biosynthetic process	"fbgn0005278,fbgn0053526,fbgn0051183,fbgn0261285,fbgn0000527,fbgn0011766,fbgn0026324,fbgn0030407,fbgn0027592,fbgn0261938,fbgn0034707,fbgn0003278,fbgn0028398"			
GO:0004478	0.00066	0.32781	1	1	methionine adenosyltransferase activity	fbgn0005278			
GO:0006556	0.00066	0.32781	1	1	S-adenosylmethionine biosynthetic process	fbgn0005278			
GO:0030532	0.00078	0.32781	4	85	small nuclear ribonucleoprotein complex	"fbgn0031266,fbgn0003916,fbgn0051922,fbgn0031287"			
GO:0006352	0.00138	0.446115714	4	73	"DNA-templated transcription, initiation"	"fbgn0026324,fbgn0027592,fbgn0034707,fbgn0028398"			
GO:1901362	0.00138	0.446115714	13	416	organic cyclic compound biosynthetic process	"fbgn0005278,fbgn0053526,fbgn0051183,fbgn0261285,fbgn0000527,fbgn0011766,fbgn0026324,fbgn0030407,fbgn0027592,fbgn0261938,fbgn0034707,fbgn0003278,fbgn0028398"			
GO:0018130	0.00216	0.4800525	12	389	heterocycle biosynthetic process	"fbgn0005278,fbgn0053526,fbgn0051183,fbgn0261285,fbgn0011766,fbgn0026324,fbgn0030407,fbgn0027592,fbgn0261938,fbgn0034707,fbgn0003278,fbgn0028398"			
GO:0034654	0.00225	0.4800525	11	320	nucleobase-containing compound biosynthetic process	"fbgn0005278,fbgn0053526,fbgn0051183,fbgn0261285,fbgn0011766,fbgn0026324,fbgn0027592,fbgn0261938,fbgn0034707,fbgn0003278,fbgn0028398"			
GO:0002274	0.00274	0.4800525	1	1	myeloid leukocyte activation	fbgn0015924			
GO:0045321	0.00274	0.4800525	1	1	leukocyte activation	fbgn0015924			
GO:0042116	0.00274	0.4800525	1	1	macrophage activation	fbgn0015924			
GO:0016070	0.00302	0.4800525	14	628	RNA metabolic process	"fbgn0031314,fbgn0031266,fbgn0053526,fbgn0003916,fbgn0027784,fbgn0051922,fbgn0031238,fbgn0026324,fbgn0027592,fbgn0261938,fbgn0031287,fbgn0034707,fbgn0003278,fbgn0028398"			
GO:0035014	0.00311	0.4800525	1	1	phosphatidylinositol 3-kinase regulator activity	fbgn0020622			
GO:0032774	0.00318	0.4800525	7	186	RNA biosynthetic process	"fbgn0053526,fbgn0026324,fbgn0027592,fbgn0261938,fbgn0034707,fbgn0003278,fbgn0028398"			
GO:0097525	0.00405	0.4800525	3	64	spliceosomal snRNP complex	"fbgn0031266,fbgn0003916,fbgn0031287"			
GO:0016005	0.00453	0.4800525	1	1	phospholipase A2 activator activity	fbgn0024314			
GO:0005686	0.00478	0.4800525	2	18	U2 snRNP	"fbgn0031266,fbgn0031287"			
GO:0008503	0.0052	0.4800525	1	1	benzodiazepine receptor activity	fbgn0031263			
GO:0090304	0.00543	0.4800525	16	849	nucleic acid metabolic process	"fbgn0031314,fbgn0031266,fbgn0053526,fbgn0003916,fbgn0011766,fbgn0027784,fbgn0051922,fbgn0031238,fbgn0026324,fbgn0027592,fbgn0261938,fbgn0031287,fbgn0034707,fbgn0003278,fbgn0025680,fbgn0028398"			
GO:0070461	0.00567	0.4800525	2	18	SAGA-type complex	"fbgn0026324,fbgn0031281"			
GO:0000124	0.00567	0.4800525	2	18	SAGA complex	"fbgn0026324,fbgn0031281"			
GO:0043196	0.00573	0.4800525	1	1	varicosity	fbgn0013323			
GO:0018445	0.00573	0.4800525	1	1	prothoracicotrophic hormone activity	fbgn0013323			
GO:0006954	0.00573	0.4800525	1	1	inflammatory response	fbgn0013323