Transcriptomic responses of common wheat segregating for Wsm2 locus to wheat streak mosaic virus (WSMV) and mock infection

To understand transcriptomic responses of WSMV resistant (contains Wsm2 locus or Wsm2+) and susceptible wheat (absent Wsm2 locus or Wsm2-) to WSMV and mock treated conditions and identify possible causative genes underlying Wsm2 locus, we performed a RNA-seq study for differentially expressed genes (DEGs) and de novo transcriptome assembly analysis. Overall design: Illumina HiSeq 2000 were performed on RNA-seq libraries from four biological replicates of two genotypes (selected double haploids from Snowmass and Antero population contains or absent for Wsm2 locus, annotated as Wsm2+ and Wsm2-) under mock treated condition (Buffer) and WSMV treated (WSMV) condition. Raw reads were filtered to remove adaptor and low-quality reads, and then mapped to wheat reference genome IWGSC ReSeq v1.0. Expression was tabulated with Featurecounts and pairwise comparisons were performed on raw reads with DESeq2. De novo assembly of all cleaned reads were performed with Trinity software.