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).