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

Stanford Kwenda,Paul R J Birch,Tshepiso V Motlolometsi,Lucy N Moleleki

doi:10.3389/fpls.2016.01905

Stanford Kwenda, Paul R J Birch + Show 2 more

Open Access

https://doi.org/10.3389/fpls.2016.01905

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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.

Highlights

Potato ranks fourth, after rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays), as the most important human food crop worldwide
We previously reported on a potato cultivar S. tuberosum cv BP1 that shows significant tolerance to P. c. brasilense strain 1692 (Pcb1692) compared to the more susceptible S. tuberosum cv Valor (Kubheka et al, 2013)
30 RNA samples from stem tissues of these two potato cultivars were obtained from the five time points and subjected to RNA-seq

Summary

Introduction

After rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays), as the most important human food crop worldwide (http://www.fao.org/faostat/en/# data/QC). Some of the most important bacterial pathogens of potatoes belong to the soft rot enterobacteriaceae (SRE) consisting of Dickeya and Pectobacterium spp. Brasiliense is growing with reports in countries such as Brazil, Canada, USA, New Zealand, China, and South Africa (Duarte et al, 2004; Glasner et al, 2008; van der Merwe et al, 2010; De Boer et al, 2012; Panda et al, 2012). Amongst the SRE are broad-host-range necrotrophic bacterial pathogens that employ plant cell wall degrading enzymes (PCWDEs) to macerate host tissues and obtain nutrients from dead cells (Davidsson et al, 2013). The use of resistant cultivars remains the most desirable option of combating SRE (Charkowski, 2015)

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