Skip to main content

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 variationa Minor allele frequency Physical coordinate SNP effects Heritability of a SNPb 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 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 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
  1. aUnderlined allele is associated with GLS resistance
  2. 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