Strand-specific, mRNA multiplexed libraries and RNA-Seq reads were processed as described above. EdgeR was used to determine normalized expression values as FPKM (Trapnell et al. 2010) and to determine DE transcripts between the resistant and susceptible samples (12 samples each) with a false-discovery rate (FDR) significance threshold of FDR ≤ 0.05, after Benjamini–Hochberg multiple comparison corrections. This experiment is referred to as the eQTL study in the following sections.