Cross-phenotype association tests uncover genes mediating nutrient response in Drosophila

BMC Genomics

Table 1 Variants associated with metabolic traits

Screen^a	Phenotype(s)^b	Test^b	Chr^c	Position^c	Gene^c	% Var^d	p ^e	FDR^f
MAF ≥ 5 %	starvation resistance	genotype	2L	13967604	nimB3	18 %	3.70E-13	0 %
MAF ≥ 5 %	triglycerides	genotype	3R	14072066	14-3-3 ε	20 %	1.29E-14	10 %
MAF ≥ 5 %	starvation resistance and triglycerides on AL	SMAT	3L	11418293	CG7560	8 %	8.88E-16	0 %
MAF ≥ 5 %	starvation resistance and triglycerides on AL	SMAT	2R	16952034	Cht12	6 %	6.18E-11	10 %
MAF ≥ 5 %	starvation resistance and mass on AL	SMAT	3R	19635620	EIF4G2	8 %	1.71E-13	10 %
MAF ≥ 5 %	starvation resistance and mass on AL	SMAT	3R	24549344	htt	12 %	2.78E-12	10 %
MAF ≥ 5 %	starvation resistance and mass on DR	SMAT	X	6152605	schlank	3 %	4.44E-16	0 %
MAF ≥ 5 %	starvation resistance and mass on DR	SMAT	X	6152619	schlank	3 %	4.44E-16	0 %
MAF ≥ 5 %	starvation resistance and mass on DR	SMAT	X	6152558	schlank	2 %	6.66E-16	0 %
MAF ≥ 5 %	starvation resistance and mass on DR	SMAT	X	6152586	schlank	2 %	8.88E-16	0 %
MAF ≥ 25 %	body mass	genotype	X	12430723	CG43921	15 %	3.84E-13	0 %
MAF ≥ 25 %	glucose	interaction	3R	8877613	pic	4 %	5.94E-3	7 %
MAF ≥ 25 %	glucose	interaction	3R	8877592	pic	4 %	6.72E-3	7 %
MAF ≥ 25 %	glucose	interaction	3R	8877227	CG7966	5 %	6.75E-3	7 %
MAF ≥ 25 %	glucose	interaction	3R	8877378	CG7966	5 %	8.69E-3	8 %
MAF ≥ 25 %	starvation	genotype	2L	13967604	nimB3	18 %	3.70E-13	0 %
MAF ≥ 25 %	starvation resistance and mass on DR	SMAT	X	8903670	rdgA	15 %	1.27E-08	10 %
MAF ≥ 25 %	starvation resistance and triglycerides on DR	SMAT	3R	4279209	CG43462	8 %	1.29E-09	10 %

^aResults from association scans across markers meeting the indicated criterion. For results from the scaled multiple-phenotype association test (SMAT) applied to variants at frequency of ≥5 %, only human disease orthologs were tested
^bThe single phenotype whose measurements in animals reared on both diets were tested in a linear model with terms for diet, genotype, and the interaction between the two; or the pair of phenotypes whose measurements in animals reared on the indicated diet were tested via SMAT. DR, dietary restriction; AL, ad libitum
^cChromosome segment, position (in D. melanogaster genome version R5 coordinates), and gene in which the associating marker lay
^dPercent phenotypic variation explained by the indicated polymorphism. For pairs of phenotypes, the value reports results for the single phenotype with the highest % variance explained
^eNominal association p-value
^fFalse discovery rate at the association p-value according to permutation analysis

ISSN: 1471-2164