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 3 Genes associated with QTL for European corn borer stem penetration

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	211,798,518	3.67E-05	1079	Zm00001d032079	RboS-L	Os09g0438000	Riboflavin synthase-like	1418	0.0
1	211,798,518	3.67E-05	1079	Zm00001d032079	RboS-L	At1g19230	Riboflavin synthase-like	1093	0.0
1	283,651,183	4.84E-05	− 1304	Zm00001d034084	WRKY31^a	At3g01080	WRKY DNA-binding (WRKY58)	218	1.52E-66
1	283,651,183	4.84E-05	− 1304	Zm00001d034084	WRKY31^a	Os12g0507300	WRKY DNA binding (WRKY96)	231	4.72E-72
1	283,651,183	4.84E-05	1803	Zm00001d034085	DUF1336^a	At3g29180	DUF1336	427	4.06E-147
1	283,651,183	4.84E-05	1803	Zm00001d034085	DUF1336^a	Os03g55180	DUF1336	577	0.0
2	1,413,891	6.11E-06	852	Zm00001d001813	RLK-L^a	Os04g42620	Ser/Thr RLK-like	634	0.0
2	1,413,891	6.11E-06	852	Zm00001d001813	RLK-L^a	Os03g0759000	LysM RLK-like	407	3.26E-141
2	28,958,597	4.46E-05	− 2883	Zm00001d002991	MYB-L^a	Os06g0190900	MYB-SANT-like protein	164	1.65E-502
2	28,958,597	4.46E-05	− 2883	Zm00001d002991	MYB-L^a	[At3g11290]	Unknown	38	0.007
2	84,078,171	7.44E-05	− 4593	Zm00001d004120	P4H	At2g43080	P4H isoform 1	313	6.39E-109
2	84,078,171	7.44E-05	− 4593	Zm00001d004120	P4H	Os04g0346000	P4H1	118	1.18E-34
2	239,762,997	5.45E-06	− 644	Zm00001d007788	CHUP1	Os07g0188266	FKBP-type peptidyl-prolyl isomerase	285	6.45E-93
2	239,762,997	5.45E-06	− 644	Zm00001d007788	CHUP1	At3g25690	CHUP1	42	6e-04
3	207,872,378	4.36E-05	2565	Zm00001d043701	IAH	Os01g0706900	Similar to Auxin amidohydrolase.	639	0.0
3	207,872,378	4.36E-05	2565	Zm00001d043701	IAH	At1g51760	IAA-Ala peptidase	488	1.71E-171
5	981,132	2.63E-05	418	Zm00001d012838	GDA1-L	Os05g0498700	GDA1-like	461	6.23E-164
5	981,132	2.63E-05	418	Zm00001d012838	GDA1-L	At3g27090	DCD domain protein	328	1.25E-111
7	91,467,624	4.37E-05	− 5168	Zm00001d020093	UGE5	At4g10960	UDP-D-Glc epimerase5 (UGE5)	228	5.79E-75
7	91,467,624	4.37E-05	− 5168	Zm00001d020093	UGE5	Os09g0323000	UDP-D-Glc/UDP-D-Gal 4-epimerase	261	3.36E-88
8	144,702,617	9.44E-06	− 4196	Zm00001d011256	OHP3	At1g34000	One-helix LHC protein2 (OHP2)	160	3.13E-50
8	144,702,617	9.44E-06	− 4196	Zm00001d011256	OHP3	Os01g0589800	High-light inducible protein	145	5.29E-46
8	144,702,617	9.44E-06	16,216	Zm00001d011257	AGP22-L^a	At5g53250	Arabinogalactan protein22	45.1	4.50E-8
8	144,702,617	9.44E-06	16,216	Zm00001d011257	AGP22-L^a	Os01g0592500	DUF1070 family protein	39.3	6.46E-6
9	19,551,832	2.67E-06	109	Zm00001d045360	None	Os06g0147300	Unknown	107	3.55E-31
9	19,551,832	2.67E-06	109	Zm00001d045360	None	At5g13000	Unknown	27	5.5
10	3,599,714	6.09E-05	881	Zm00001d023332	WRKY63^a	Os09t0334500	WRKY74	86	1E-17
10	3,599,714	6.09E-05	881	Zm00001d023332	WRKY63^a	At2g40750	WRKY54	76	3E-15

^aGene identity defined manually by alignment with rice and Arabidopsis homologs closest in sequence

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