Comparison of defense responses of transgenic potato lines expressing three different Rpi genes to specific Phytophthora infestans races based on transcriptome profiling

Abstract

Potato late blight, one of the most devastating diseases in potato, is caused by the oomycete Phytophthora infestans. Over 20 resistance genes have been cloned including R1, R3a, and R3b. The distinctions between defense response mechanisms mediated by different resistance genes are still unclear. Here we performed transcriptome profiling in three transgenic lines, R1, R3a, and R3b, and wild-type Desiree under inoculation with two P. infestans isolates, 89148 (race 0) and CN152 (super race), using RNA-seq. Compared with wild type, specific differentially expressed genes (DEGs) were identified in the three transgenic lines. The highest number of DEGs occurred in transgenic R3b, with 779 DEGs in response to isolate 89148 and 864 DEGs in response to infection by CN152, followed by transgenic R1 lines with 408 DEGs for isolate 89148 and 267 DEGs for CN152. Based on gene ontology, the most common GO terms (15 for 89148 and 20 for CN152) were enriched in transgenic R3a and R3b lines. This indicates that the defense pathways mediated by R3a and R3b are more similar than those mediated by R1. Further separate GO analysis of up- or down-regulated DEGs showed that the down-regulated DEGs mainly functioned in mediating the resistance of potato to P. infestans 89148 by response to stress biological process and to CN152 by oxidation reduction biological process. KEGG pathways of DNA replication, plant-pathogen interaction and pentose and glucuronate interconversions are unique for transgenic R1, R3a, and R3b lines in incompatible interactions. Quantitative real-time PCR experimental validation confirmed the induced expression of DEGs in the late blight resistance signaling pathway. Our results will lay a solid foundation for further understanding the mechanisms of plant-pathogen interactions, and provide a theoretical reference for durable resistance in potato.

Comparative transcriptome analysis of R3a and Avr3a-mediated defense responses in transgenic tomato

“…Additionally, comparative analysis of defense responses of R1, R3a, and R3b transgenic potato lines with different Rpi genes to P. infestans race CN152 and 89148 indicated that defense pathways of the three R genes were similar. For example, plant-pathogen interaction, and pentose and glucuronate interconversions (ko00040), were specifically enriched but still had minor differences (Yang et al, 2020), and this finding was also proved in our research. Additionally, with the extension of the incompatible interaction time between R3a and Avr3a, the wilting degree of plant leaves intensified, and some down-regulated DEGs were enriched in carbon metabolism and photosynthesis process.…”

“…Additionally, the downstream genes of SA, NPR1 ( Solyc02g069310.3 , Solyc07g040690.3 , Solyc07g044980.3 , ko04075), and PR-1 ( Solyc01g106620.2 , ko04626), were significantly up-regulated at 2-h and returned to normal levels at 6-h; however, they were not differentially expressed in MM- Avr3a . The transcriptome analysis results of the incompatible interactions of three different Rpi genes with P. infestans were also enriched in these DEGs genes ( Yang et al., 2020 ). In addition, several DEGs involved in the ethylene signal transduction pathway were identified.…”

“…Total RNA from foliage samples of MM, MM- R3a-Avr3a , and MM- Avr3a plants after spraying DEX, with three bio-replicates, were extracted as described in the literature ( Yang et al., 2020 ). High integrity RNA was use to construct the sequencing library.…”

Transcriptome analysis reveals that exogenous ethylene activates immune and defense responses in a high late blight resistant potato genotype

“…Library construction and RNA sequencing. These methods were based on the published articles with some modifications 11,49 . Total RNA was extracted using the RNAprep Pure Plant Kit (Tiangen Biotech, Beijing, China) according to the protocol provided and treated with DNase I to generate 21 RNA libraries.…”