Table 3.
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 |
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
bThe allele before the slash (/) increases the trait and the allele after the slash decreases the trait
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
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
eThe significance threshold based on the deviation of F observed from expected is p = 1 × 10− 4
fR2, proportion of the phenotypic variance explained by the SNP
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