Table 3 QTL significantly associated with reactions to Puccinia striiformis f. sp. tritici in at least three environments (genome-wide adjusted P < 0.1)
Stages of Growth
SeedlingFlowering to Grain Filling
SNP IWAaChrPosbAllelecITITSEVR2 (%)
MTVMTVPLMBLUEMTVPLMBLUEBLUE_ALL
20122012201420122013MTVPLMALL2012201420122013MTVPLMALLITSEV
55051A132.0A/G***********************************************4.894.04
32151A182.7A/Gnsns**********************************2.252.20
59631B46.0A/Cns********ns******************2.661.60
59151B97.1T/Cns************************************************2.251.86
621BNAA/G*****************************************4.843.12
25262A46.1T/Cns**********************************3.494.34
58242A72.3A/Gns***********************************************2.692.62
34013A131.4T/C****************************************************6.605.84
39814A85.2A/Gns**************nsns*ns*3.743.21
37744A131.7A/G*******************************************1.531.09
66974A184.2A/Gns*ns*****************************1.331.75
46514A193.2T/Cns****************************************1.021.53
34224A198.7T/Cns****ns***************ns*ns*****2.622.32
53814D22.4A/Gns**********************************6.125.00
50025A184.5A/G******************************************************2.752.94
51665B62.9T/Cns****************************************1.521.58
85956A204.5T/Cns**************************************0.861.08
72576B47.66T/Gns********************ns*nsnsnsnsns2.141.20
41696B62.22T/Gns***********************************1.401.14
3496B126.0T/Cns************************************************3.643.38
  • Marker-wise significance: * P < 0.05; ** P < 0.01; *** P < 0.001. Genome-wide significance: **** Benjamini-Hochberg FDR adjusted P < 0.10. SNP, single nucleotide polymorphisms; IWA, loci in linkage disequilibrium and with significant association with reaction to Pst; Chr, chromosome; Pos, position; IT, infection type; SEV, disease severity; MTV, Mount Vernon; PLM, Pullman; BLUE, best linear unbiased estimates; ALL, across environments; NA, not applicable; ns, not significant.

  • a SNP indexes from Illumina iSelect 9K wheat assay (Cavanagh et al. 2013). SNPs in bold were identified in the analyses using 1104 accessions with IT scores ≥ 3, and bold and underlined SNPs were detected in both the first and second approaches for GWAS. Loci in linkage disequilibrium 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, and 349/none.

  • b Scaled positions from the hexaploid wheat 9K SNP consensus map (Cavanagh et al. 2013).

  • c Resistance allele underscored.