RNA-seq profiling reveals defense responses in a tolerant potato cultivar to stem infection by Pectobacterium carotovorum ssp. Brasiliense

dc.contributor.authorKwenda, Stanford
dc.contributor.authorMotlolometsi, Tshepiso V.
dc.contributor.authorBirch, Paul R.J.
dc.contributor.authorMoleleki, Lucy N.
dc.contributor.emaillucy.moleleki@up.ac.zaen_ZA
dc.date.accessioned2017-01-30T04:34:23Z
dc.date.available2017-01-30T04:34:23Z
dc.date.issued2016-12-20
dc.descriptionFigure S1. RT-PCR validation of eight novel CDS candidates using agarose gel. Lane 1. 1 kb DNA ladder, Lane 2 and 3. Novel1253 in the tolerant and susceptible cultivars, respectively, Lane 4 and 5. Novel917 in the tolerant and susceptible cultivars, respectively, Lane 6, Novel806 in susceptible cultivar, Lane 7 and 9. Novel2142 in the susceptible cultivar, Lane 8. Novel1481 in the tolerant cultivar, Lane 10. Novel750 in the susceptible cultivar, Lane 11. Novel2049 in the susceptible cultivar, Lane 12. Novel2769 in the susceptible cultivar.en_ZA
dc.descriptionTable S1. Mapping statistics.en_ZA
dc.descriptionTable S2. List of identified novel CDS gene candidates.en_ZA
dc.descriptionTable S3. List of differentially expressed genes at each time-point between cultivars “Valor” and “BP1.”en_ZA
dc.descriptionTable S4. Common DE genes present in both “Valor” and “BP1” at each time-point compared to mock-inoculated samples.en_ZA
dc.descriptionTable S5. Cultivar-specific differentially expressed genes.en_ZA
dc.descriptionTable S6. Cultivar-specific DEGs overrepresented in various Gene Ontology biological processes.en_ZA
dc.descriptionTable S7. Differentially expressed candidate novel CDS transcripts in the time-course.en_ZA
dc.descriptionTable S8. Domains assigned to novel CDS candidates using InterProScan5 software tool.en_ZA
dc.descriptionTable S9. RT-qPCR primers used to validate RNA-seq data.en_ZA
dc.descriptionTable S10. RT-PCR primers used for novel CDS candidate transcripts validation.en_ZA
dc.description.abstractPectobacterium 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.en_ZA
dc.description.departmentAgricultural Economics, Extension and Rural Developmenten_ZA
dc.description.librarianam2017en_ZA
dc.description.sponsorshipThe National Research Foundation (NRF), South Africa through Thuthuka grant number 69362; Research Development Grant for Y-Rated Researchers 93357; Bioinformatics and Functional Genomics (BFG 93685). Additional support was from The Genomics Research Institute, University of Pretoria.en_ZA
dc.identifier.citationKwenda S, Motlolometsi TV, Birch PRJ and Moleleki LN (2016) RNA-seq Profiling Reveals Defense Responses in a Tolerant Potato Cultivar to Stem Infection by Pectobacterium carotovorum ssp. brasiliense. Frontiers in Plant Science. 7:1905. DOI: 10.3389/fpls.2016.01905.en_ZA
dc.identifier.issn1664-462X
dc.identifier.issn10.3389/fpls.2016.01905
dc.identifier.urihttp://hdl.handle.net/2263/58661
dc.language.isoenen_ZA
dc.publisherFrontiers Research Foundationen_ZA
dc.rights© 2016 Kwenda, Motlolometsi, Birch and Moleleki. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).en_ZA
dc.subjectPectobacteriumen_ZA
dc.subjectPotatoen_ZA
dc.subjectPlant defenseen_ZA
dc.subjectSoft rotentero bacteriaen_ZA
dc.subjectSolanum tuberosumen_ZA
dc.subjectRNA-seqen_ZA
dc.subjectPlant innate-immunityen_ZA
dc.subjectSoft rot Enterobacteriaceae (SRE)en_ZA
dc.titleRNA-seq profiling reveals defense responses in a tolerant potato cultivar to stem infection by Pectobacterium carotovorum ssp. Brasilienseen_ZA
dc.typeArticleen_ZA

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