Fig 1.
Kinship matrix dendrogram for the Arabidopsis mapping population.
Dendrogram of the EMMA kinship matrix for selected Arabidopsis thaliana accessions used for GWA mapping. Accessions were filtered for common flowering time (63.1 ± 0.95 (s.e.) days to flowering) to reduce effects from ontogeny. These accessions fall into approximately five major groups (I-V) as illustrated.
Table 1.
F-Tables of GLM for camalexin and lesion area.
F-tables from the whole experiment GLM for each phenotype using type II sums of squares. Significance was determined as follows: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ‘ 1. Both phenotypes show highly significant interaction between the host and pathogen genotype. All future results were split per isolate as a result.
Fig 2.
Proportion of variance (η2) for genotypic group vs accession genotype.
Bar graphs illustrating the proportion of variance (η2) explained by the five major groups (I-V) versus the individual accessions. Variance was determined using a standard guassian linear model where Phenotype = Experiment + Experiment(Plate) + Group + Group(Accession) for each Botrytis isolate.
Fig 3.
Common genes and co-expression networks found to associate with variation in camalexin production.
(A) Venn diagram showing the overlap of candidate genes identified among the four phenotypically diverse isolates for camalexin (ng/mm) accumulation. (B) ATTEDII Co-expression networks for genes Arabidopsis significantly associated with camalexin (ng/mm) accumulation across the Botrytis isolates. The suggested biological function of the five largest networks was determined via GO enrichment analysis. Putative biological function of the five largest networks are; I) Cell Cycle, Vesicle Trafficking, Protein Turn-over, Jasmonate Signaling, II) Defense Response and Salicylate Signaling, III) Reactive Oxygen Species (ROS) Tolerance, IV) DNA Methylation V) RNA Processing and Cell Wall Modification. Red nodes indicate a gene that was found in at least 3 isolates, dark green nodes indicate a gene was found for 2 isolates and light green indicates 1 isolate.
Fig 4.
Common genes and co-expression networks found to associate with lesion area.
(A) Venn diagram showing the overlap of candidate genes identified among the four phenotypically diverse isolates for lesion area (mm2). (B) ATTEDII Co-expression networks for genes Arabidopsis significantly associated with lesion size across the Botrytis isolates. The suggested biological function of the five largest networks was determined via GO enrichment analysis. Putative biological functions of the five largest networks are; I) Cell Cycle, Gravitropism, and Leaf Development, II) Disease Resistance, III) Amino Acid and Lipid Metabolism, IV) Catabolism and Metabolic Processes, and V) Trehalose and Polysaccharide Metabolism. Red nodes indicate a gene that was found in at least 3 isolates. Red nodes indicate a gene that was found in at least 3 isolates, dark green nodes indicate a gene was found for 2 isolates and light green indicates 1 isolate.
Fig 5.
Camalexin validation and network.
(A) Bargraphs showing the model corrected means for induced camalexin production of all four isolates on wildtype Col-0 versus pad4-1 and acd6-3 mutants. Significance of the difference in camalexin accumulation between Col-0 and the pad4-1 mutant with each isolate are shown as P< 0.001 ‘***’, 0.001 ‘**’ and 0.01 ‘*’. (B) Magnified images of the Cam.II co-expression network with visible gene names are shown with genes highlighted in the text circled. Single gene knockouts are circled in red while known major defense hormone receptor genes are circled in orange and major hubs are circled in blue.
Fig 6.
Bargraphs showing the model corrected means for the lesion area on wildtype Col-0 versus pad4-1, lhy-20, and at4g01880-2 mutants. Relevant co-expression networks for PAD4 and LHY1 are shown to right of the bargraph. Significance of the difference in camalexin accumulation between Col-0 and the mutant with each isolate are shown as P< 0.001 ‘***’, 0.001 ‘**’ and 0.01 ‘*’.
Table 2.
Significance of plant genotype terms for validated genetic lines.
Summary of p-values of an F-test from a GLM comparing each mutant separately to wildtype Col-0 using type II sums of squares. The GLM includes single terms for the experiment replicate, isolate genotype, and plant genotype as well as all two-way and three-way interaction terms. An expanded table can be found in Supporting Data.