RNAseq of TxD hybrid poplar infected with Sphaerulina musiva isolate WV-4 : Genotype383 48 Hours Post-inoculation , Replicate Rep3
Four genotypes were selected for the RNAseq study, based upon their disease phenotype scores. Two genotypes were resistant (383, 424) and two were susceptible (526, 852). The resistant genotypes were selected based upon having the lowest possible canker count and disease severity across all replicates. Similarly, the susceptible genotypes were selected based upon consistently displaying high canker count and disease severity. Tree cambium tissue was taken from two different internodal regions at inoculation sites on 30-cm tall individuals, and combined into a single sample. Samples were homogenized with a bead-based homogenizer and RNA was extracted with the Dynabeads mRNA DIRECT Kit according to the manufacturers protocol, with a slight modification: Ambion Plant Isolation Aid was added to the lysis buffer prior to use, and a 24:1 Chloroform:Isoamyl alcohol cleanup step was performed after lysate was centrifuged. The mRNA samples were submitted to BGI Genomics, and resulting clean read data was evaluated with FastQC to ensure quality was sufficient before subsequent downstream analyses.