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Table 2 SNPs significantly associated with resistance to stalk tunneling by MCB. The genotype of the parents, the number of RILs with favorable and unfavorable alleles, the additive value, the significance of the association, and the variance explained by each SNP are included in the table. Previous experiments with QTL detected in the same bin that the significant SNPs are shown in the last column of the table

From: Mapping of resistance to corn borers in a MAGIC population of maize

Significant SNPa bin A509 EP125 EP17 EP43 EP53 EP86 F473 PB130 Allelesb (No)c Additive effectd p-value e R2 f Previous experiments with co-localizing QTLg
S1_19252698 1.02 C T T C C C C T C/T 381/132 1.65 4.6E-05 0.03 MCB EP42xEP39 [17]; MCB EP125xPB130 [49]
S1_290934634 1.11 T T T C T N T N C/T 64/274 2.13 9.9E-05 0.05  
S2_14798875 2.02 T C N C C C N C T/C 212/242 1.48 9.76E-05 0.03  
S2_179803199 2.07 A G G G G N G A A/G 170/348 1.49 9.9E-05 0.03 ECB B73xB52 [50]; ECB B73xDe811 [51]; MCB EP125xPB130 [49]
S3_191332395 3.07 N G N N G C N G C/G 138/269 2.01 4.7E-06 0.05 ECB European Dent [30]
S3_212770896 3.08          G/C 60/451 2.16 7.16E-05 0.03  
S3_218807815 3.09 G G G G G G N T G/T 396/81 1.87 9.4E-05 0.03 ECB D06xD408 [52]
S3_218807820 3.09 G G G G G G N A G/A 397/80 1.92 6.5E-05 0.03  
S4_127856740 4.05 T N G G N G G G G/T 372/97 1.88 8.0E-05 0.03  
S4_127955231 4.05 A A G G N G G G G/A 399/128 1.77 3.6E-05 0.03  
S4_155128691 4.06 T T T N T N T T G/T 63/345 2.38 1.2E-05 0.05  
S4_155830369 4.06 C N C N C C N C T/C 43/361 2.55 3.2E-05 0.05  
S4_155830370 4.06 T N T N T T N T G/T 43/361 2.55 3.2E-05 0.05  
S4_155830400 4.06 G N G N G G N G T/G 43/361 2.55 3.2 E05 0.05  
S4_156193095 4.06 C C C N N C T C T/C 78/308 2.32 2.8E-06 0.06  
S4_181340312 4.09 C T N N C T N N T/C 207/144 1.69 9.3 E05 0.04  
S4_221752511 4.09 N N G G N G G G A/G 19/282 3.68 7.1 E05 0.05  
S5_24771445 5.03 A N G G G A G G G/A 345/117 1.82 2.4E-05 0.04 ECB D06xD408 [52]; MCB B73xCML103 [20]
S6_147725553 6.05 A A N A N N N N A/T 401/49 2.50 4.6E-05 0.04 ECB B73xDe811 [51]; MCB B73xCML103 [20]; MCB EP125xPB130 [49]
S6_150800759 6.05 A A N A G G G G A/G 247/264 1.42 7.0E-05 0.03  
S6_156035854 6.06 A N A A A N C C A/C 356/179 1.46 8.2E-05 0.03 ECB D06xD408 [52]; MCB EP125xPB130 [49]
S6_164776991 6.07 N A G A G G A G G/A 347/168 1.55 4.5E-05 0.03 ECB B73xMo47 [50]; MCB EP125xPB130 [49]
S7_109722251 7.02 G A A A N N G N G/A 244/246 1.42 9.9E-05 0.03 ECB B73xB52 [53]
S8_24527783 8.03 N G G G N N G G T/G 27/393 3.00 9.4E-05 0.04 ECB B73xMo47 [50]
S8_28525990 8.03 T G G G G G G G T/G 59/502 2.16 8.2 E05 0.03  
S8_28526020 8.03 A C C C C C C C A/C 59/503 2.16 8.1E-05 0.03  
S8_28526026 8.03 C A A A A A A A C/A 59/503 2.16 8.1 E05 0.03  
  1. aThe number before the underscore (_) indicates the chromosome number and the number after the underscore (_) indicates the physical position of the SNP in bp within the chromosome
  2. bThe allele before the slash (/) increases the trait and the allele after the slash decreases the trait
  3. cNo = number of homozygous lines for a given variant. The number before the slash refers to the allele that increases the trait and the number after the slash to the allele that decreases the trait
  4. dThe additive effect was calculated as half the difference between the mean of the homozygotes for the allele that increases the trait and the mean of the homozygote that decreases the trait
  5. eThe significance threshold based on the deviation of F observed from expected is p = 1 × 10−4
  6. fR2, proportion of the phenotypic variance explained by the SNP
  7. gIn the first place we show the corn borer species, in the second place the mapping population, and in the third place the reference. Different experiments are separated by semicolons