Table 3  Allele frequencies of significantly associated SNPs in the maize germplasm groups
Allele frequency(%)aNb
ChromosomeSNP physical position (bp)Allele increasing HRcSSNSSTSP-value*SSNSSTS
5183,737,260G83.341.593.80.000004184132
7148,173,418A0.014.629.00.03184131
9121,167,503G64.75.125.90.00001173927
1021,693,685G38.963.481.30.01184132
1021,722,883T33.371.886.70.0005183930
1021,823,409C33.353.876.70.01183930
  • SS, stiff stalk; NSS, non-stiff stalk; TS, tropical subtropical. * P-values after testing the null that the proportions (probabilities of success) in subpopulations are the same (prop.test in R software).

  • a Alleles are from homozygote genotypes.

  • b N, total number of lines included in analysis.

  • c Alleles that increase hypersensitive response in the LES (visual lesion score) and HTR (mutant:wild type ratio) traits.