Suppression subtractive hybridization and microarray analysis reveal differentially expressed genes in the Lr39/41-mediated wheat resistance to Puccinia triticina

Wheat leaf rust caused by Puccinia triticina (Pt) is one of the most severe fungal diseases threatening the global wheat production. The use of leaf rust resistance (Lr) genes in wheat breeding programs is the major solution to solve this issue. Wheat isogenic line carrying the Lr39/41 gene has shown a moderate to high resistance to most of the Pt pathotypes detected in China. In the present study, a typical hypersensitive response (HR) was observed using microscopy in leaves of the Lr39/41 isogenic line inoculated with the avirulent Pt pathotype THTT from 48 h-post inoculation. Two Lr39/41 resistance-associated suppression subtractive hybridization (SSH) libraries with a total of 6000 clones were established. Microarray hybridizations were performed on all obtained SSH clones using RNAs extracted from leaves of the Pt-inoculated and non-inoculated Lr39/41 isogenic lines, and leaves of the Pt-inoculated and non-inoculated Thatcher susceptible lines. Differentially expressed clones were analyzed by significance analysis of microarrays (SAM), followed by further sequencing. A total of 36 Lr39/41-resistance-related differentially expressed genes (DEGs) were identified, many of which had been previously reported to be involved in the plant defense response. The expression levels of eight selected DEGs during different stages of the Lr39/41-mediated resistance were further quantified by a qRT-PCR assay. Several pathogenesis-related (PR) and HR-related genes seem to be crucial for the Lr39/41-mediated resistance. In general, a brief profile of DEGs associated with the Lr39/41-mediated wheat resistance to Pt was drafted.