Fig 1.
Photographs showing common scab phenotypic reactions.
A, the scab-resistant cultivar Hindenburg (HB); and B, the scab susceptible cultivar Green Mountain (GM). More scab lesions can be seen in the forms of pitted-lesions or necrosis on the skin of GM.
Fig 2.
Experimental layout for scab infection trial under controlled environment.
Planting conditions and treatments are indicated by number 1–4. Treatment 1: naClean, non-autoclaved soil planted with certified clean seed; Treatment 2: naScab, non-autoclaved soil planted with scab-infected seed from the 2018 infected field. Treatment 3: acClean, autoclaved soil planted with certified clean seed; Treatment 4: acInoScab, autoclaved soil inoculated with scab inoculum and planted with scab-infected seed from the 2018 infected field. Each cultivar (GM and HB) was grown in three replicates in each treatment.
Table 1.
List of primers used for RNAseq data validation using qPCR.
Table 2.
Common scab symptoms observed in Hindenburg and Green Mountain grown in heavily infested field plots at AAFC Harrington farm in 2016.
The disease symptoms were rated and expressed as % incidence, % of tuber surface area covered and severity rating on a scale of 1 to 3.
Fig 3.
Scab symptoms (dark dots) as observed in Green Mountain (GM) and Hindenburg (HB) grown in a greenhouse experiment under four treatments consisting of a combination of three soil and two seed types.
A) Scab symptoms on tubers collected from GM and HB at time point 1; B) Scab symptoms on tubers collected from GM and HB at time point 2.
Table 3.
Scab rating from four treatments, two time points and two potato cultivars GM (susceptible) and HB (resistant) in a greenhouse experiment.
ANOVA test levels are shown. Rating parameters were variates and treatment, cultivar and time point were taken as fixed effects.
Table 4.
Summary statistics of the RNAseq transcriptome sequencing reads and mapping to the reference genome.
Fig 4.
Hierarchical clustering heat map showing differentially expressed genes in triplicated samples of the scab susceptible cultivar Green Mountain and the resistant cultivar Hindenburg.
Complete linkage and Euclidian distance were used as a measure of similarity to display expression patterns of DEGs with absolute fold change ≥2. Each row corresponds to a gene and each column corresponds to an individual replicate for each cultivar. The cultivar GM and HB are color-coded in purple and magenta, respectively. The normalized expression z-score scale is indicated by the color key in the top left corner. Blue, down-regulated genes; Yellow, up-regulated genes.
Fig 5.
Scatter plot of gene expression levels in the scab susceptible cultivar Green Mountain and resistant cultivar Hindenburg.
Genes with absolute fold change ≥2 and P<0.05 are indicated by red dots. Genes with absolute fold change ≥2 but not significant at P<0.05 level are indicated by yellow dots, and genes with unchanged gene expression in the two cultivars are indicated by grey dots.
Fig 6.
Volcano plot of gene expression levels in the scab susceptible cultivar Green Mountain and resistant cultivar Hindenburg.
Log2 change and P-value obtained from the comparison of the average for each group were plotted as volcano plot. Significant genes which absolute fold change ≥2 and P<0.05 are indicated by blue and yellow dots.
Fig 7.
KEGG pathways assignment to DEGs in the scab susceptible cultivar Green Mountain and resistant cultivar Hindenburg.
A total of 273 enriched DEGs were assigned to 34 KEGG pathways with high confidence. Levels of significance are indicated by red asterisks with *, **, and *** for P<0.05, P<0.01, and P<0.001, respectively.
Fig 8.
Bar plot representation of the GO term gene enrichment of DEGs between the scab susceptible cultivar Green Mountain and resistant cultivar Hindenburg using David tool.
A, biological process; B, Cellular component; C, Molecular function. Levels of significance are indicated by red asterisks with *, **, and *** for P<0.05, P<0.01, and P<0.001, respectively.
Table 5.
Summary table of genes in key pathways found to be altered in GM compared with HB.
Fig 9.
qPCR expression profiles for thirteen selected genes from the RNAseq dataset for validation.
The expression data are expressed as normalized fold change to the 18S RNA expression and shown as the mean of three independent replicates. Vertical bars represent the standard deviation of the means.
Table 6.
RNAseq gene expression validation using by qPCR.
Fold change expression observed by qPCR is shown along with the observed expression in RNAseq profiling.
Fig 10.
Principal component analysis (PCA) plot showing association between time-course of signaling and priming-associated genes gene expressions at time point 1 and 2 with scab disease symptom rating.
Only variations explained by PCA score 1 and 2 are shown.