Fig 1.
Seedling disease levels and field disease (coefficient of infection, COI) correlations.
(a) Left (black and white) panel showing seedling disease distributions; X-axis represents linearized 0–9 scales; (b) Right (orange and blue) panel showing field disease correlations. Diagonals are histogram for each environment (Crookston CRK12,Saint Paul StP12-15).
Table 1.
Phenotype correlations among field and seedling traits (Race.1, Race.CA1.2, Race.Mix, Field.COI, FIELD.SEV, FIELD.IT).
Fig 2.
Linkage disequilibrium based on 18924 SNP markers.
For color fitted LD decay lines: red represents A genome; green represents B genome; blue represents D genome. Orange bar indicates LD decay level (R2 = 0.2).
Fig 3.
Population structure: model based approach and PCA approach.
(a) model based approach for population structure analysis. (b) PCA approach for population structure analysis. Orange: sub-population 1; Red: sub-population 2; Blue: sub-population 3. Asterisks (*) on PCA plot indicate accessions that are typical of each sub-population. Sub-population 3 also has lines from North America. Both sub-pop2 and sub-pop 3 might include lines from Asia, Europe etc.
Fig 4.
Different sub populations of this AM panel are associated with different levels of leaf rust disease severity (measured using coefficient of infection Field.COI).
Table 2.
A total of 46 QTLs were identified that were significantly associated with field or seedling leaf rust disease resistant (p.MLM < 0.001).
Fig 5.
Manhattan plots for field (a) and seedling (b) traits. Red line indicates SimpleM bonferroni corrected p-value threshold for significance (7.7x10-5); Green line indicates p-value of 1x10-3.
Fig 6.
Venn diagrams (a) Overlap between QTLs under different field environments. (b) Overlap between field and seedling QTLs.
Table 3.
Most significant (top 10) QTLs and representative SNPs for field and seedling traits.
Fig 7.
Scatterplot of phenotypic values versus genotypic fitted values using markers representing top ten QTLs for field resistance.