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Table 2 Summary of Genome-wide association study (GWAS) for kernel resistance to fumonisin contamination using a maize inbred panel evaluated under inoculation with Fusarium verticillioides in two years

From: Genome-wide association analysis for fumonisin content in maize kernels

QTL Bin1 Allele+ R2 QTL SI SNP position2 p-value RMIP containing-SNP gene_v23 containing-SNP gene_v4
1 1.07 0.95 0.11 220,709,603–222,205,493 220,941,497 9.04*10−9 0.80 GRMZM2G078401 Zm00001d032372
2 1.09 0.93 0.08 256,662,974–256,798,243 256,669,820 7.85*10−7 0.56 GRMZM2G149028 Zm00001d033386
      256,692,784 2.56*10−7 0.63 GRMZM2G100448 Zm00001d033388
      256,692,818 2.54*10−7 0.63   
      256,693,243 2.56*10−7 0.63   
3 2.08 0.93 0.07 213,583,622–213,815,822 213,588,927 3.84*10−7 0.51 GRMZM2G422576 Zm00001d007029
      213,588,940 3.72*10−7 0.51   
4 3.02 0.94 0.09 6,970,377–7,206,031 7,119,636 1.25*10− 8 0.58 GRMZM2G104176 Zm00001d039513
5 3.04 0.91 0.10 15,040,634–15,127,310 15,056,252 1.85*10−7 0.70 GRMZM2G165044 Zm00001d039769
      15,057,326 5.40*10−9 0.74   
      15,057,331 2.59*10−8 0.64   
      15,057,578 2.25*10−8 0.73   
6 3.05 0.93 0.09 147,969,891–148,289,200 147,971,443 4.11*10−9 0.69 GRMZM2G701801 Zm00001d042061
7 3.06 0.94 0.11 169,052,376–169,117,125 169,073,710 1.04*10−10 0.60 GRMZM2G026855 Zm00001d042555
      169,073,715 1.04*10−10 0.60   
      169,073,720 1.05*10−10 0.60   
      169,078,446 4.77*10−9 0.56   
8 3.06 0.93 0.08 173,006,714–173,381,106 173,283,279 5.89*10−7 0.53 GRMZM2G060255 Zm00001d042658
9 3.08 0.91 0.10 206,261,823–207,246,656 206,605,245 1.22*10−6 0.56 GRMZM2G169654 Zm00001d043782
       4.68*10−8 0.62 GRMZM2G028467 Zm00001d043801
10 3.09 0.89 0.09 217,324,678–217,572,395 217,558,124 2.46*10−8 0.53 GRMZM2G042421 Zm00001d044173
11 4.02 0.93 0.08 5,405,928–5,466,378 5,406,694 2.03*10−7 0.57 GRMZM2G154414 Zm00001d048837
      5,410,388 2.09*10−7 0.55   
12 4.05 0.87 0.12 centromere 82,892,426 3.60*10−8 0.58   
      82,892,436 3.60*10−8 0.58   
      82,892,557 3.60*10−8 0.58 GRMZM2G111117 Zm00001d050400
      83,027,805 3.60*10−8 0.58 GRMZM2G178169 Zm00001d050401
      83,033,318 3.60*10−8 0.58   
      83,572,578 2.10*10−8 0.74 AC198937.4_FG005 Zm00001d050410
      83,738,156 2.11*10−8 0.77   
      84,453,345 3.44*10−8 0.73 GRMZM2G123362 Zm00001d050434
      88,069,675 2.54*10−8 0.56   
      88,098,841 2.50*10−8 0.52   
      96,545,683 1.17*10−7 0.54 GRMZM2G140095 Zm00001d050575
13 5.02 0.95 0.08 14,815,481–14,839,860 14,839,828 6.99*10−9 0.58 GRMZM2G066449 Zm00001d013611
14 6.07 0.90 0.10 164,365,931–164,378,580 164,369,763 3.76*10−9 0.61 GRMZM2G038183 Zm00001d038998
15 7.05 0.93 0.10 171,058,866–171,182,450 171,182,417 2.89*10−9 0.64 GRMZM2G009021 Zm00001d022400
16 8.07 0.85 0.10 167,189,708–167,286,546 167,284,361 3.19*10−9 0.54 GRMZM2G177324 Zm00001d012329
17 9.03 0.91 0.09 centromere 87,360,835 1.88*10−8 0.50 GRMZM2G159641 Zm00001d046455
  1. 1Bin in which QTLs are located; Allele+ stands up for the frequency of favorable allele; R2 for the proportion of the phenotypic variance explained by the QTL; QTL SI for the supporting interval of the QTL on the RefGenB73_v2, region in which appreciable linkage disequilibrium is observed between SNPs (r2 > 0.4), SI could not be visualized using LD plots from TASSEL when SNP were localized in centromeric regions where LD is extremely high
  2. 2SNP position for the position in bp of the significant SNP on the RefGenB73_v2; p-value for the association between polymorphic variation at the SNP and phenotypic variation for fumonisin content; RMIP for resample model inclusion probability
  3. 3Filtered genes in the RefGenB73_v2 and RefGenB73_v4 versions of the B73 sequence that contain the significant SNP (or the closest filtered gene in bold)