Quantifying Expression of WRKY33, PDF1.2, VQ16

Quantification of expression of WRKY33, PDF1.2 and VQ16 were conducted by Droplet Digital PCR (ddPCR) according to the methods described previously^{66 (link)}. RNA of Lm infected and mock inoculated Topas and Westar (from Group I), W-LepR1 (from Group II), T-LepR2 (from Group III) and T-LepR1 (from Group VI) at 3, 6, 9 dai were adjusted to 1 μg of RNA, and cDNA from three biological replicates was synthesized using an iScript™ Advanced cDNA Synthesis Kit according to the manufacturer’s protocol (Bio‐RAD). All primers and probes (Supp. Table 2) were designed using “Quest tool” complimented by IDT (https://www.idtdna.com/PrimerQuest/Home/Index) and “BnActin” was used as reference. ddPCR was performed using a QX100 Droplet Digital PCR (ddPCR™) System – Bio-Rad. The Bio-Rad QuantaSoft™ Analysis Pro (QuantaSoft AP) software was used to calculate the ratio signal of assay/Actin. In order to get RNAseq and ddPCR result comparable, heat map was generated based on: Log2 (Assay/Actin) (mean of replicates): inoculated with Lm/not inoculated control and Log2 RPKM (mean of replicates): inoculated with Lm/not inoculated control (Supp. Fig. 7).