COMPILE: a GWAS computational pipeline for gene discovery in complex genomes

BMC Plant Biology

Table 1 Genes associated with QTL for α/γ-tocopherol ratio in maize kernels by COMPILE^a

Chrom.	Marker	MLM	Distance	Maize Gene	Gene	BLAST	BLAST	BLAST	e-Value
Chrom.	Position	p-Value	to Gene	Number	Name	Match	Description	Score	e-Value
3	204,491,509	4.76E–06*	− 2050	Zm00001d043589	MADS36	Os01g0726400	MADS box floral identity	299	1.93E–103
3	204,491,509	4.76E–06*	− 2050	Zm00001d043589	MADS36	At5g60910	AGAMOUS-like 8	107	6.29E–28
5	205,827,506	2.28E–12***	−105	Zm00001d017746	VTE4	Os02g0701600	Tocopherol O-methyltransferase	543	0.0
5	205,827,506	2.28E–12***	−105	Zm00001d017746	VTE4	At1g64970	γ-tocopherol methyltransferase	420	2.31E–147
7	14,373,377	1.61E–06**	785	Zm00001d019057	Unknown	Os07g0189700	Similar to JHL07K02.7 protein	180	1.31E–56
7	14,373,377	1.61E–06**	785	Zm00001d019057	Unknown	At3g23760	Glycosyl group transferase	129	2.87E–37
8	132,442,986	1.54E–06**	− 3544	Zm00001d010894	None	Os01g0229300	(EMF1)-like protein	624	0.0
8	132,442,986	1.54E–06**	− 3544	Zm00001d010894	None	AT5G11530	Embryonic flower 1	43.1	0.013
8	132,442,986	1.54E–06*	−231	Zm00001d008091	None	[lncRNA]	[Long non-coding RNA]	–	–
8	132,442,986	1.54E–06**	867	Zm00001d010895	None	AT5G33406	hAT domain protein / transposase-like	115	6.17E–028
8	132,442,986	1.54E–06**	867	Zm00001d010895	None	Os09g0499600	DUF659 domain containing protein	114	3.32E–027

^aPhenotype data are from Lipka et al. [16]. All genes are identified by COMPILE as significant at a Benjamini-Hochberg FDR of 5%. Entries in bold indicate genes identified as significant by Lipka et al. [16] at a Benjamini-Hochberg FDR of 5% (***) or of 10% (**). Manual annotation of the long non-coding RNA is in brackets. *Not identified as significant in Lipka et al. [16]

ISSN: 1471-2229