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. Overall design: 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.

本数据集以4月龄嫁接可可植株为实验材料，其接穗品种为SCA6与NA32，分别采用可可疫霉（Phytophthora megakarya）游动孢子（zoospores）或蒸馏水进行喷雾接种。沿时间梯度采集叶片组织，以检测植株的转录组响应。
总体实验设计如下：生物学重复为取自不同植株的两片叶片，混合后用于RNA提取。实验共设置5个采样时间点（0、6、24、48、72小时接种后（hours after inoculation, hai））。每个基因型与处理组在各时间点均设置4个生物学重复，仅48小时时间点除外，该时间点仅采集可可疫霉处理的样本。将采集的叶片置于RNA later（RNA稳定剂）中，运送至宾夕法尼亚州立大学（Penn State）进行RNA提取；采用Invitrogen植物RNA提取试剂完成总RNA提取。使用超微量紫外分光光度计（nanodrop）与生物分析仪（bioanalyzer）检测样本质量，随后采用Illumina Hiseq 2500测序平台完成样本测序。