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

Hill, Matthew J.; Penning, Bryan W.; McCann, Maureen C.; Carpita, Nicholas C.

doi:10.1186/s12870-022-03668-9

BMC Plant Biology

Table 2 Genes associated with QTL for growing-degree-day-adjusted days to flowering identified by COMPILE^a

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

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
1	94,342,987	5.19E–08	− 3107	Zm00001d029918	None	Os10g0324600	Zinc finger, C2H2 domain	48.9	4.31E–06
1	94,342,987	5.19E–08	− 3107	Zm00001d029918	None	At5g61190	C2H2-type zinc finger domain	41.6	2.00E–03
1	[270554226]	–	–	Zm00001d033673	TB1	Os03g0706500	TCP Negative reg. lat. branch.	327	4.11E–110
1	[270554226]	–	–	Zm00001d033673	TB1	At1g67260	TCP family transcription factor	102	4.11E–110
1	[270919031]	–	–	Zm00001d033680	DWARF8	Os03g0707600	DELLA Gibberellin repressor	966	0.0
1	[270919031]	–	–	Zm00001d033680	DWARF8	At2g01570	GRAS transcription factor	648	0.0
1	[272191275]	–	–	Zm00001d033719	COL2	Os03g0711100	CONSTANS-like (COL)	454	5.95E–158
1	[272191275]	–	–	Zm00001d033719	COL2	At1g25440	B-box type Zn-finger/CCT domain	233	7.05E–72
1	[274082082]	–	–	Zm00001d033799	PHYA1	Os03g0719800	Phytochrome A, Photoreceptor	2064	0.0
1	[274082082]	–	–	Zm00001d033799	PHYA1	AT1G09570	Phytochrome A	1518	0.0
2	208,886,674	1.41E–06	2175	Zm00001d006461	None	Os07g0508300	SH3 domain-containing protein like	642	0.0
2	208,886,674	1.41E–06	2175	Zm00001d006461	None	AT4G18060	SH3 domain-containing protein	462	3.30E–164
3	162,993,079	1.85E–06	− 1834	Zm00001d042355	None	Os04g0290800	Predicted protein	813	0.0
3	162,993,079	1.85E–06	− 1834	Zm00001d042355	None	At3g45890	RUS1 UVB sensitive-like (DUF647)	596	0.0
7*	[181090142]	–	–	Zm00001d022613	DLF1	Os09g0540800	Leucine zipper (β-ZIP)	125	2.73E–36
7*	[181090142]	–	–	Zm00001d022613	DLF1	At2g17770	Leucine zipper motif 27	79.7	1.90E–18
8	116,806,871	7.35E–10	1222	Zm00001d010470	UbiE3	AT5G13530	E3 Ubiquitin-protein ligase	2198	0.0
8	116,806,871	7.35E–10	1222	Zm00001d010470	UbiE3	Os05g0392050	UbiE3 Ubiquitin-ligase	349	4.91E–108
8	126,885,610	2.34E–08	− 4150	Zm00001d010752	PEBP8	Os05g0518000	Hd3a, Promotor flowering	279	2.17E–97
8	126,885,610	2.34E–08	− 4150	Zm00001d010752	PEBP8	At1g65480	PEBP family protein	219	5.26E–73
8	136,010,257	1.79E–07	393	Zm00001d010987	RAP2.7	Os05g0121600	AP2/EREBP	396	2.34E–135
8	136,010,257	1.79E–07	393	Zm00001d010987	RAP2.7	At4g36920	Integrase-type DNA-binding	283	3.55E–92
9	135,980,380	5.87E–07	−242	Zm00001d047573	F-box	Os03g0321300	Cyclin-like F-box domain protein	533	0.0
9	135,980,380	5.87E–07	−242	Zm00001d047573	F-box	AT5G46170	F-box family protein	308	1.47E–101
10	10,315,088	7.02E–08	− 914	Zm00001d023565	TCP	AT1G58100	TCP family transcription factor	204	9.25E–62
10	10,315,088	7.02E–08	− 914	Zm00001d023565	TCP	Os12g0173300	Transcription factor, TCP protein	366	2.12E–124
10	92,331,033	1.41E–08	361	Zm00001d024885	WD40-like	Os03g0403400	TolB-like domain β-propeller	1065	0.0
10	92,331,033	1.41E–08	361	Zm00001d024885	WD40-like	At1g21680	DPP6 N-terminal domain-like	351	1.23E–110
10	94,277,277	2.04E–08	154,896	Zm00001d024909	CCT1	Os07g0261200	CCT (CONSTANS)	138	4.40E–40
10	94,277,277	2.04E–08	154,896	Zm00001d024909	CCT1	At5g24930	Zn-finger CONSTANS-like	78.2	1.54E–16
10	133,736,251	2.03E–07	244	Zm00001d025915	Syntaxin81	At1g51740	Syntaxin81	185	6.42E–59
10	133,736,251	2.03E–07	244	Zm00001d025915	Syntaxin81	Os04g0530400	t-Snare domain containing protein	255	1.34E–86

^aPhenotype data are from Romay et al. [8]. All genes are identified as significant by COMPILE at a Benjamini-Hochberg FDR of 5%. Entries in bold are those identified as significant by Romay et al. [8]. Genes without p-value or gene distance annotations represent genes not identified by COMPILE. For these genes, “Marker Position” annotations in brackets represent gene midpoint coordinates. Entries in normal text were identified as significant by COMPILE but not by Romay et al. [8]

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ISSN: 1471-2229

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