RNA-seq Profiling Reveals Defense Responses in a Tolerant Potato Cultivar to Stem Infection by Pectobacterium carotovorum ssp. brasiliense

Abstract

Pectobacterium carotovorum subsp. brasiliense is a member of the soft rot Enterobacteriaceae (SRE) family that causes tuber soft rot and blackleg diseases of stems in potato plants. Currently, there are no effective chemical strategies for the control of members of the SRE. Thus, an understanding of the inducible defense responses in stems of potato plants is important, particularly during colonization of the vascular system. Here, time-course RNA-sequencing analysis was used to compare expressed genes between a susceptible potato cultivar (Solanum tuberosum cv Valor) and a tolerant cultivar (S. tuberosum cv BP1) at 0, 6, 12, 24, and 72 h post-inoculation with P. c. brasiliense. In total, we identified 6139 and 8214 differentially expressed genes (DEGs) in the tolerant and susceptible cultivars, compared to mock-inoculated controls, respectively. Key DEGs distinguishing between tolerance and susceptibility were associated with negative regulation of cell death and plant-type cell wall organization/biogenesis biological processes in the tolerant and susceptible cultivars, respectively. Among these were DEGs involved in signaling (mainly MAPK cascade and ethylene pathway), defense-related transcription regulation including WRKY transcription factors, and downstream secondary cell biosynthesis. Together, our results suggest that S. tuberosum cv BP1 likely employs quantitative defense response against P. c. brasiliense. Overall, our study provides the first transcriptome-wide insight into the molecular basis of tolerance and/or resistance of potato stems to SRE infection.

Tolerance of olive (Olea europaea) cv Frantoio to Verticillium dahliae relies on both basal and pathogen‐induced differential transcriptomic responses

“…Global gene expression profiling studies in which differential responses between susceptible and tolerant cultivars were compared upon phytopathogen infection are available for a number of pathosystems (i.e. Goyer et al ., ; Kwenda et al ., ; Matić et al ., ), including olive (Giampetruzzi et al ., ). However, comparative analysis of basal gene expression level between host cultivars displaying different disease susceptibility prior to the challenge with the pathogen is frequently overlooked.…”

Identification of differentially expressed genes in tolerant and susceptible potato cultivars in response to Spongospora subterranea f. sp. subterranea tuber infection

“…Similarly, AtWRKY33 was highly up‐regulated in the tolerant cultivar compared to susceptible cultivar in response to P. carotovorum subsp. brasiliense potato stem infection (Kwenda et al ., ).…”

“…Transcriptome comparisons between resistant and susceptible varieties have been used to elucidate gene expression profiling of potato in response to infection by Phytophthora infestans (Gao et al ., ), Streptomyces turgidiscabies (Dees et al ., ), potato virus Y (Goyer et al ., ) and Pectobacterium carotovorum subsp . brasiliense (Kwenda et al ., ). Many genes were found associated with resistance signal transduction and defence mechanisms in potatoes.…”

Cytosolic glyceraldehyde‐3‐phosphate dehydrogenases play crucial roles in controlling cold‐induced sweetening and apical dominance of potato (Solanum tuberosum L.) tubers

“…Finally, the mRNA‐Seq libraries were sequenced with an Illumina HiSeq 2000 sequencer generating 90 bp paired‐end reads. Gene expression analysis was performed as described by Kwenda, Motlolometsi, Birch, and Moleleki ().…”