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Table 3 SNP identification (SNP ID), additive effect and allelic variants for the SNP, proportion of total variance explained by the SNPs significantly associated with resistance traits (TL, SD, and KR), and significance values for the association between the SNP and the phenotype ( P -value and RMIP)

From: Genome-wide association study reveals a set of genes associated with resistance to the Mediterranean corn borer (Sesamia nonagrioides L.) in a maize diversity panel

Trait a SNP ID b Alleles c (N o ) d Additive effect e P -value ( R 2 ) f RMIP g
TL S2_168004182 G/T 225/36 3.09 9.51 × 10−6 0.08 0.51
TL S3_7081859 T/A 207/55 2.52 1.38 × 10−5 0.07 0.50
TL S4_190444179 G/A 218/38 3.18 3.26 × 10−6 0.09 0.37
TL ss4_190679094h G/A 226/41 3.09 3.37 × 10−6 0.08 0.45
TL S7_154739818 G/C 248/14 4.25 5.28 × 10−5 0.07 0.37
TL S7_154741622 C/T 217/47 2.84 9.84 × 10−6 0.08 0.56
TL S7_155702328 T/A 171/67 2.43 1.55 × 10−5 0.08 0.38
TL S10_133337924 G/T 133/99 −1.30 7.40 × 10−5 0.07 0.30
TL S10_133337925 G/C 133/99 −1.30 7.40 × 10−5 0.07 0.30
TL S10_133337950 T/C 133/99 −1.30 7.40 × 10−5 0.07 0.30
SD S1_208315891 C/A 126/106 1.09 7.86 × 10−6 0.09 0.63
SD S1_293163491 T/A 207/37 1.37 2.39 × 10−5 0.08 0.38
SD S2_59729532 A/T 235/17 1.90 2.93 × 10−5 0.07 0.32
SD ss5_176870721h G/A 228/38 1.37 1.12 × 10−5 0.08 0.41
KR S3_187742562 C/A 244/12 −0.38 1.30 × 10−5 0.08 0.48
KR S3_204458505 T/A 186/65 −0.19 4.14 × 10−5 0.07 0.40
KR S3_204586960 C/G 251/13 −0.37 1.25 × 10−5 0.08 0.44
KR S3_222733400 C/T 142/110 −0.15 4.90 × 10−5 0.07 0.34
KR S4_227101950 C/T 242/17 −0.30 1.26 × 10−5 0.08 0.43
KR S4_227101985 A/T 242/17 −0.30 1.26 × 10−5 0.08 0.43
KR S5_93580059 C/T 230/28 −0.24 2.27 × 10−5 0.07 0.31
KR S6_88149024 A/G 187/55 −0.17 6.83 × 10−5 0.07 0.48
KR S6_88149036 G/C 187/55 −0.17 6.83 × 10−5 0.07 0.48
KR S7_15072370 G/A 230/24 −0.26 3.65 × 10−5 0.07 0.46
KR S7_19347596 A/G 250/11 −0.40 7.47 × 10−5 0.06 0.36
  1. a TL, tunnel length in cm; SD, stem damage in percentage; and KR, kernel resistance on a subjective visual scale of 1 to 9 in which 1 indicates completely damaged and 9 indicates no damage.
  2. b The number before the underscore (_) indicates the chromosome number and the number after the underscore (_) indicates the physical position in bp within the chromosome.
  3. c The letter before the diagonal (/) is the nucleotide more frequent ; and the letter after the diagonal the nucleotide less frequent.
  4. d N° = number of inbred lines homozygous for a determined allelic variant. The number before the diagonal (/) represents the number of individuals with the mayor allele; and the number after the diagonal represents the number of individuals with the minor allele.
  5. e The additive effect was calculated as half the difference between the mean of the homozygous for the minor and the mean of the homozygous for the major allele.
  6. f R 2, proportion of the phenotypic variance explained by the SNP.
  7. g RMIP, resample model inclusion probability.
  8. h Based on SNPs from Illumina chip, the remaining locations without a superscript are based on SNPs obtained by GBS.