Resistant and susceptible cacao varieties exhibit defense gene polymorphism and different responses to Phytophthora megakarya inoculation

Four month old grafted cacao plants (scions SCA6 and NA32) were spray inoculated with Phytophthora megakarya zoospores or distilled water. Leaf tissue was collected along a time course to measure transcriptomic response. Biological replicates were two leaves, collected from different plants, pooled together for RNA extraction. Collection was performed at five time points (0, 6, 24, 48, 72 hai). Four biological replicates were collected per genotype and treatment at each time point, except for the 48 hour time point, in which only Phyopthora treated samples were collected. Leaves were placed in RNA later and shipped to Penn State for RNA extraction. RNA was extracted using Invitrogen plant RNA reagent. Sample quality was checked using a nanodrop and bioanalyzer. Samples were sequenced using an Illumina Hiseq 2500.