Redundancy analysis of the count
data
We used vegan package (Oksanen et al., 2018) for redundancy analysis
(RDA) of the count data to identify genetic variation significantly
associated with the key conditions in our experiment: Inoculation,
Genotype, and Phenotype as well as the interactions of
Genotype-by-Inoculation and Phenotype-by-Inoculation. The statistical
significance of each of the conditions was tested with a permutation
test (permtest) with 10000 permutations. The genes contributing to
significant differences along the RDA axes were identified using cut off
of three standard deviations (corresponding to two-tailed p-value =
0.0027 in Z test). The overlap among gene sets was analyzed using Venn
diagrams in R using venn package (Dusa, 2018).