Comparative transcriptome analysis of wheat isogenic lines provides insights into genes and pathways associated with stripe rust resistance

Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici (Pst) is one of the major biotic stress factors limiting wheat production worldwide. Despite the efficiency of fungicide treatments, genetic resistance is considered to be the most economical and environment-friendly way to control the disease. To study the early defense response induced by P. striiformis infection, RNA-seq was conducted between stripe rust-resistant and susceptible lines (FLW29, PBW343) under Pst-treated and control conditions. Seedlings of both genotypes were infected with pathotype 46S119, and leaf samples were collected at 12 hpi, 48 hpi, and 72 hpi. A total of 486 and 409 transcripts were differentially expressed respectively from both inoculated and mock inoculated samples. The identified DEGs comprised of defense-related genes such as WRKY, MYB, NAC transcriptional factors; PR proteins, MAPKs and serine/threonine-protein kinase signaling pathways. Further, the protein-protein Interaction (PPI) network was constructed and visualized, which will serve to identify regulatory relationships of the proteins encoded by the DEGs. The whole transcriptome sequencing study suggested key genes which can be further explored to understand the molecular mechanisms controlling stripe rust resistance in wheat.