Transcriptome analysis reveals key defense related differentially expressed genes in response to stripe rust on wheat

A near isogenic line FLW29 containing yellow rust resistance gene Yr17 introgressed from wild wheat species (Triticum ventricosa) in wheat cv. PBW343 background and the recipient parent FLW29 were used for studying the differential gene expression with Puccini striiformis pathotype 46S119. The pathotype was used to inoculate wheat cultivars PBW343 (susceptible) and FLW29 (resistant), such that for each cv., a total of 5 pots (5 mock-inoculated and 5 inoculated) with three biological replicates were used for the experiments. Fresh uredinospore were harvested from infected wheat plant and resuspended in sterile distilled water evenly mixed with soltrol (20mg/100ml) was used to inoculate seedlings grown. Seedlings at two-leaf stage/flag leaves (approx 20 days after sowing), were inoculated with the spore suspension using a automizer and then kept in dark at 10 degree C for 16-h light/8-hdark to maintain the relative high humidity. Leaf samples were collected at 3 different time periods i,e. for 12, 48 and 72 hr post-inoculation (HPI). The collected samples were immediately placed in RNA later and stored at -20 degree C until use. The RNA from leaf samples were extracted using Qiagen RNeasy Mini kit (Qiagen Inc, USA). Samples were IIumina sequenced on a single HiSeq 4000 machines yielding at least 895M 150bp paired-end reads per sample. Each sample represents one experimental condition (pathogen/mock; time points; genotype).