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Table 3 SNPs significantly associated with kernel resistance to MCB attack. 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_11476253

1.01

N

N

N

G

A

G

A

A

A/G

282/88

0.22

9.3E-05

0.04

 

S1_29155773

1.02

C

C

N

N

N

C

T

C

C/T

323/37

0.32

4.9E-05

0.04

 

S1_37531738

1.03

C

C

C

G

N

N

N

C

C/G

367/23

0.39

5.7E-05

0.04

 

S1_295188904

1.12

G

G

G

G

G

N

N

N

G/A

322/32

0.35

3.4E-05

0.05

MCB EP42xEP39 [18]

S2_20109642

2.01

G

G

N

G

N

N

G

G

G/C

389/28

0.42

2.2E-06

0.05

 

S2_202280633

2.07

G

N

G

G

N

N

N

G

G/A

350/21

0.41

4.9E-05

0.05

 

S2_213160826

2.08

N

A

A

A

A

N

A

A

A/T

447/33

0.33

5.3E-05

0.03

 

S3_220658669

3.09

G

G

G

G

N

N

G

G

G/A

278/28

0.46

6.7E-07

0.09

MCB Association panel [34]

S3_220658703

3.09

A

A

A

A

N

A

A

A

A/G

326/20

0.47

7.2E-06

0.06

 

S4_236927609

4.09

T

T

N

T

N

N

A

T

T/A

173/136

0.21

3.9E-05

0.06

MCB Association panel [34]

S5_1442632

5.00

G

G

G

A

G

A

G

N

G/A

391/104

0.21

3.3E-05

0.04

 

S5_1848216

5.00

C

C

C

C

N

N

C

N

C/T

396/29

0.34

9.3E-05

0.04

 

S5_9090576

5.01

G

G

G

T

T

G

G

G

G/T

445/132

0.19

3.3E-05

0.03

MCB B73xCML103 [20]

S6_165637552

6.07

C

N

C

N

C

C

C

C

C/A

448/26

0.36

9.4E-05

0.03

 

S7_955804

7.00

C

C

C

C

C

C

C

N

C/A

428/34

0.32

3.7E-05

0.04

 

S7_958414

7.00

N

C

N

C

N

C

C

N

C/T

448/38

0.32

2.2E-05

0.04

 

S7_958454

7.00

N

C

N

C

C

C

C

N

C/T

488/45

0.27

8.8E-05

0.03

 

S7_1952227

7.00

T

T

N

T

N

T

N

C

T/C

312/113

0.22

9.5E-06

0.05

 

S7_1952249

7.00

G

G

N

G

N

G

N

A

G/A

312/113

0.22

9.5E-06

0.05

 

S9_37401486

9.01

G

N

N

N

G

G

N

G

G/T

325/58

0.26

4.7E-05

0.04

 

S9_37401504

9.01

C

N

N

N

C

C

N

C

C/G

325/58

0.26

4.7E-05

0.04

 

S9_147511039

9.06

G

N

N

G

G

N

G

N

G/A

353/24

0.41

1.5E-05

0.05

MCB A637xA509 [54]

S10_136106669

10.05

A

N

N

A

G

N

A

N

A/G

350/28

0.39

1.3E-05

0.06

 
  1. aThe number before the underscore (_) indicates the number of the chromosome 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 is for the allele that increases the trait and the number after the slash for 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
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BMC Plant Biology

ISSN: 1471-2229

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