Combining powers of linkage and association mapping for precise dissection of QTL controlling resistance to gray leaf spot disease in maize (Zea mays L.)

Mammadov, Jafar; Sun, Xiaochun; Gao, Yanxin; Ochsenfeld, Cherie; Bakker, Erica; Ren, Ruihua; Flora, Jonathan; Wang, Xiujuan; Kumpatla, Siva; Meyer, David; Thompson, Steve

doi:10.1186/s12864-015-2171-3

Table 4 SNP markers associated with GLS resistance and days to silking (DTS) QTL identified by genome-wide association study

From: Combining powers of linkage and association mapping for precise dissection of QTL controlling resistance to gray leaf spot disease in maize (Zea mays L.)

Chr	GWAS QTL	Bi-parental counterpart	Bins	Marker associated with GLS resistance QTL	Source of variation^a	Minor allele frequency	Physical coordinate	SNP effects	Heritability of a SNP^b	Maximum heritability of a chromosome
1	DTS_1.1		1.01-1.02	GLS-SNP-5365	[T/G]	0.30	12,255,366	0.07989852	0.001049039	0.003070336
1	GLS1.1		1.02	GLS-SNP-1590	[T/C]	0.43	15,354,490	−0.01960145	0.003070336	0.003070336
1	DTS_1.2		1.02	GLS-SNP-0156	[T/C]	0.42	22,510,157	0.04407421	0.003070336	0.003070336
1	DTS_1.3		1.03	GLS-SNP-0538	[A/G]	0.23	35,460,539	0.04052954	0.003070336	0.003070336
1	DTS_1.4		1.03	PZE-101061225	[G/T]	0.12	45,115,245	−0.04252824	0.003070336	0.003070336
1	DTS_1.5		1.03	GLS-SNP-2651	[A/G]	0.32	48,092,652	0.41783421	0.003070336	0.003070336
1	DTS_1.6		1.05	GLS-SNP-2138	[T/C]	0.46	101,832,139	0.43211445	0.003070336	0.003070336
1	DTS_1.7		1.07	GLS-SNP-5094	[A/G]	0.49	203,245,095	−0.69856342	0.003070336	0.003070336
1	GLS 1.2	QTLGLSchr1	1.08	PZE-101188909	[A/G]	0.23	234,309,200	−0.01785890	0.001971469	0.003070336
6	GLS 6.1	QTLGLSchr6	6.04	PZE-106058730	[A/G]	0.34	107,475,955	−0.00632726	0.000293801	0.00093559
6	GLS 6.2		6.04	PZE-106066216	[T/C]	0.42	118,304,229	0.01101481	0.000935590	0.00093559
6	DTS_6.1		6.05	Mo17-10397	[T/C]	0.41	151,787,329	0.04365824	0.000243429	0.00093559
6	GLS 6.3		6.05	PZE-106100504	[T/C]	0.32	153,414,853	0.00639998	0.000282006	0.00093559
6	DTS_6.2		6.06	GLS-SNP-4138	[A/C]	0.45	155,634,139	0.06046048	0.000701479	0.00093559
6	GLS 6.4		6.06	MAGI_11553-2	[T/G]	0.37	156,981,627	0.00610662	0.000281211	0.00093559
7	DTS_7.1		7.00	PZE-107000932	[T/C]	0.50	1,121,016	−0.00193525	0.000617793	0.000660398
7	GLS 7.1		7.00	PZE-107004786	[T/C]	0.40	3,074,900	0.00916059	0.000660398	0.000660398
7	GLS 7.2	QTLGLSchr7	7.02	PZE-107020739	[G/A]	0.37	19,500,572	−0.00603602	0.000265353	0.000660398
7	DTS_7.2		7.02	PZE-107020739	[G/A]	0.37	19,500,572	0.00248297	0.000107170	0.000660398
7	DTS_7.3		7.02	PZE-107083430	[C/T]	0.23	125,687,825	0.00226143	0.000585325	0.000660398
7	DTS_7.4		7.03	PZE-107094672	[A/G]	0.4	144,404,803	−0.00229674	0.000599634	0.000660398
7	DTS_7.5		7.03	PZE-107099659	[T/C]	0.32	154,472,118	0.00345513	0.002230712	0.000660398
8	GLS 8.1		8.01	GLS-SNP-7688	[A/G]	0.26	6,253,558	−0.00608691	0.000242320	0.000585845
8	GLS 8.2	QTLGLSchr8a	8.02	PZE-108020413	[T/C]	0.48	19,550,800	0.00468907	0.000177343	0.000585845
8	GLS 8.2	QTLGLSchr8a	8.02	PZE-108022710	[T/G]	0.43	21,753,432	0.00584096	0.000269140	0.000585845
8	GLS 8.3	QTLGLSchr8b	8.03	PZE-108047250	[T/C]	0.46	79,142,282	−0.00521772	0.000218764	0.000585845
8	GLS 8.3	QTLGLSchr8b	8.03	PZE-108050268	[A/T]	0.10	87,682,262	0.00806870	0.000204892	0.000585845
8	GLS 8.4		8.05-8.06	GLS-SNP-1344	[A/G]	0.30	154,247,344	−0.00922446	0.000585845	0.000585845
8			8.05-8.06	PZE-108098666	[T/C]	0.23	155,016,277	−0.00709668	0.000296117	0.000585845
8			8.05-8.06	PZE-108098682	[A/G]	0.22	155,029,958	−0.00890310	0.000450864	0.000585845
8	GLS 8.5		8.05-8.06	PZE-108101351	[A/C]	0.13	157,169,975	−0.01000713	0.000374213	0.000585845
8	DTS_7.1		8.05-8.06	GLS-SNP-8600	[T/G]	0.25	145,906,568	−0.00301422	0.000131115	0.000585845
8	DTS_7.2		8.06	PZE-108109056	[A/C]	0.31	162,535,081	0.00382457	0.000270955	0.000585845
8	DTS_7.3		8.06	GLS-SNP-6472	[T/C]	0.38	162,586,473	0.00290281	0.000154292	0.000585845
8	DTS_7.4		8.06	GLS-SNP-8795	[T/G]	0.45	163,616,966	−0.00209331	0.000435068	0.000585845

^aUnderlined allele is associated with GLS resistance
^bIn this study the significance threshold was set to 0.3, indicating that only SNPs with at least 30 % of the maximum heritability of each chromosome would be picked as significant

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ISSN: 1471-2164

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