Table 3 Loci significantly associated with IT or SEV in at least three environments (one at P < 0.01) and with experiment-wise Bonferroni P < 0.10
Marker IWA3892a980422424b52021034537569887257167
QTL nameQYr.ucw-1BQYr.ucw-1DQYr.ucw-2A.2QYr.ucw-2A.3QYr.ucw-3B.2QYr.ucw-4AQYr.ucw-4DQYr.ucw-5A.2QYr.ucw-6BQYr.ucw-6D
Chromosome1B1D2A2A3B4Ac4D5Ad6B6D
Positione123.449.39.978.33.9181.726.9189.2112.373.2
Alleles (R underscored)A/GA/CT/CT/CA/GT/CT/GT/CT/GA/C
GWAS for IT
 MTV_2012****fns***ns**************
 MTV_2013*****ns***ns****
 PLM_2011******ns********************
 PLM_2012ns******ns*****nsns******
 DVS_2011***nsns**************
 DVS_2012*ns***ns************
 BLUE_MTV***************ns******
 BLUE_PLM**ns****ns*****************
 BLUE_DVS*******nsns***************
 BLUE_ALL*****************************
GWAS for SEV
 MTV_2012***ns****ns****ns****
 MTV_2013******ns****ns****
 PLM_2011***ns***********ns***
 PLM_2012***************ns**********
 DVS_2011*nsnsnsns*************
 DVS_2012****nsns*************
 BLUE_MTV*******ns****ns****
 BLUE_PLM*******************
 BLUE_DVS********ns**************
 BLUE_ALL**********ns**************
GWAS seedling
 Significant racesPSTv40NonePstv14Pstv14 and 40NoneNonePstv4Pstv14NoneNone
Frequency R allele
 Overall0.700.440.310.700.370.170.100.160.230.10
 Subpop. 1A0.770.190.350.480.410.080.380.170.610.36
 Subpop. 1B0.870.170.100.830.520.040.120.100.320.10
 Subpop. 20.700.700.190.800.470.030.050.120.510.03
 Subpop.30.760.600.250.880.400.170.020.150.110.06
 Subpop. 4A0.530.340.560.260.090.390.100.380.060.05
 Subpop. 4B0.770.430.770.970.320.280.010.230.010.01
 Subpop. 4C0.700.200.930.350.120.000.880.880.000.95
% explained variation
 R2 IT BLUE-all0.7%1.2%0.4%1.0%2.2%0.9%0.9%1.6%1.8%0.7%
 R2 SEV-BLUE-all0.7%0.9%0.8%0.3%1.3%1.2%0.6%1.0%1.4%0.7%
  • IT, infection type; SEV, disease severity.

  • a SNP indexes from the Illumina iSelect 9K wheat assay (Cavanagh et al. 2013). Bold IWA names were identified in the GWAS including only the 593 accession with IT scores ≥ 3, and bold and underscored were significant in both analyses. SNP loci in LD and significantly associated to the Pst response (IWA): 3892/846, 980/642, 422/423/3468/3469, 424/none, 5202/4796, 1034/none, 5375/5766, 6988/none, 7257/none, 167/none.

  • b IWA424 was borderline significant in the Bonferroni test only for SEV and only in one location. Therefore, it should be considered with caution.

  • c IWA1034 is in the region of 4AL translocated from 7BS (homology 7AS/4AL/7DS) (Devos et al. 1995).

  • d IWA6988 is in the region of 5AL translocated from 4AL (homology 5AL/4BL/4DL) (Devos et al. 1995).

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

  • f Significance. Marker-wise: *P < 0.05, **P < 0.01, ***P < 0.001. Experiment-wise: ****Bonferroni P < 0.10.