Redundancy Analysis (RDA)
To study the relative effect sizes and their statistical significance,
we carried out multivariate regression using Redundancy Analysis (RDA).
The analysis confirmed that the genotype and phenotype (resistant versus
susceptible) effects were highly statistically significant (P = 0.001
and P = 0.004), describing 35 % and 9 % of the overall variation
(Table 2). The effect of the inoculation treatment alone was not
significant (P = 0.238), but the combined effects of
genotype-by-experiment and phenotype-by-experiment were significant (P =
0.001 and P = 0.048, respectively), again suggesting genotype-specific
response profiles. Accordingly, the RDA plots displayed clear separation
when using genotype and phenotype as a covariate but not with
inoculation treatment (Figures 2a, b and c). Venn diagrams of the genes
contributing to the separation in the RDA analyses demonstrate that
while 87 genes contribute significantly to separation according to
genotype, only 7 genes contribute directly to the phenotypic variation
and 109 genes to the joint effect of phenotype-by-experiment (Figures 2
d and e).