Table 4 Frequencies of stripe rust resistance alleles
ChrPosaSNP IWAbAllelescPanelSubpopulationACIMPTOrigin
EuropeAmericas
1A1B2BreedingGeneticCultivarCultivatedLandraceAsiaEastWestSouthNorthNorthSouth
1A132.05505A/G0.500.420.140.940.220.000.230.450.810.860.320.230.550.290.090.08
1A182.73215A/G0.670.670.850.510.660.570.760.710.610.530.670.870.810.810.620.72
1B46.05963A/C0.940.970.990.860.941.000.980.950.920.870.971.000.991.000.960.97
1B97.15915T/C0.660.780.900.250.780.860.830.730.470.350.740.960.770.850.800.92
1BNA62A/G0.070.060.010.130.000.140.020.040.120.140.040.020.040.010.010.03
2A46.12526T/C0.310.390.440.090.260.290.440.470.210.130.460.480.280.630.160.47
2A72.35824A/G0.600.730.780.240.660.710.730.710.450.310.670.820.780.810.720.75
3A131.43401T/C0.090.070.000.210.030.000.040.100.150.190.080.030.040.000.040.03
4A85.23981A/G0.900.780.981.000.781.000.890.870.950.950.730.990.930.990.800.97
4A131.73774A/G0.200.070.050.530.070.000.090.080.360.470.050.060.040.090.080.14
4A184.26697A/G0.910.910.880.940.930.860.880.870.930.940.910.870.870.910.880.97
4A193.24651T/C0.230.090.690.020.420.140.410.190.040.030.180.600.110.610.280.81
4A198.73422T/C0.730.680.650.880.560.710.670.700.850.840.610.700.780.740.620.50
4D22.45381A/G0.920.960.930.840.891.000.930.950.910.840.951.000.931.000.930.94
5A184.55002A/G0.170.190.070.200.140.000.130.220.190.190.150.110.230.130.170.06
5B62.95166T/C0.170.050.580.000.300.140.330.140.030.030.090.560.070.510.140.69
6A204.58595T/C0.350.420.330.270.310.140.390.470.310.260.430.370.460.300.410.14
6B47.77257T/G0.240.480.110.000.270.140.320.340.160.050.560.200.360.140.230.17
6B62.24169T/G0.490.690.200.400.480.710.420.640.470.450.700.300.420.250.520.36
6B126.0349T/C0.450.200.390.890.240.140.350.280.650.770.200.430.280.350.220.36
Mean reaction to stripe rust
Infection type (0–9 scale)5546554556535364
Disease severity (0–100%)52533267525641505967502849276030
  • Chr, chromosome; Pos, position; SNP, single nucleotide polymorphisms; IWA, loci in linkage disequilibrium and with significant association with reaction to Pst; ACIMPT, population structure subgroups in improvement status of accessions.

  • a Scaled position from hexaploid wheat consensus map (Cavanagh et al. 2013).

  • b SNP indexes from Illumina iSelect 9K wheat assay (Cavanagh et al. 2013). SNPs in bold were identified in the analyses using the 1104 accessions with IT scores ≥ 3, and bold and underlined SNPs were detected in both the first and second approaches for GWAS. Loci in LD and with significant association with reaction to Pst (IWA): 5505/475/4934, 3215/none, 5963/none, 5915/5749, 62/none, 2526/none, 5824/5495, 3401/2263/2264/2265/2266, 3981/none, 3774/none, 6697/none, 4651/none, 3422/none, 5381/none, 5002/none, 5166/none, 8595/none, 4169/none, 7257/none, 349/none.

  • c Resistance allele underscored.