Quantitative proteomics and transcriptomics of potato in response to Phytophthora infestans in compatible and incompatible interactions

Abstract

BackgroundIn order to get global molecular understanding of one of the most important crop diseases worldwide, we investigated compatible and incompatible interactions between Phytophthora infestans and potato (Solanum tuberosum). We used the two most field-resistant potato clones under Swedish growing conditions, which have the greatest known local diversity of P. infestans populations, and a reference compatible cultivar.ResultsQuantitative label-free proteomics of 51 apoplastic secretome samples (PXD000435) in combination with genome-wide transcript analysis by 42 microarrays (E-MTAB-1515) were used to capture changes in protein abundance and gene expression at 6, 24 and 72 hours after inoculation with P. infestans. To aid mass spectrometry analysis we generated cultivar-specific RNA-seq data (E-MTAB-1712), which increased peptide identifications by 17%. Components induced only during incompatible interactions, which are candidates for hypersensitive response initiation, include a Kunitz-like protease inhibitor, transcription factors and an RCR3-like protein. More secreted proteins had lower abundance in the compatible interaction compared to the incompatible interactions. Based on this observation and because the well-characterized effector-target C14 protease follows this pattern, we suggest 40 putative effector targets.ConclusionsIn summary, over 17000 transcripts and 1000 secreted proteins changed in abundance in at least one time point, illustrating the dynamics of plant responses to a hemibiotroph. Half of the differentially abundant proteins showed a corresponding change at the transcript level. Many putative hypersensitive and effector-target proteins were single representatives of large gene families.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-497) contains supplementary material, which is available to authorized users.

Targeted Proteomics Approach for Precision Plant Breeding

“…Thus, 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 development of a bi-parental crossing population and a machine learning classifier model for phenotypic prediction based on the generated SRM data (Figure 1). Steps a-c were performed previously, 20 wherein secretome proteome analyses were performed at four different time-points (before infection, and 6, 24 and 72 hours post-infection) from P. infestans infected leaves of Desirée (sensitive to late blight) and SW93-1015 (resistant to late blight). 19,20 In this work, the shotgun proteomics raw data were re-analyzed to identify potential peptide markers which showed differential expression under the studied conditions.…”

Overview and Breeding Strategies of Table Potato Production in Sweden and the Fennoscandian Region

“…Certain novel techniques, e.g. genomic selection and site directed mutagenesis, hold a great promise to enhance the efficiency of potato breeding (Nicolia et al 2015) as well as analyses with RNAseq, proteomics, and effector screening (Ali et al 2014;Chawade et al 2016;Lenman et al 2016). Diploid and F 1 hybrid breeding in potato (for example www.solynta.com) also shows great potential to overcome some of the limitations of traditional crossing with tetraploid material and speed up the development of new hybrid cultivars, thus further increasing the potential economic output.…”

What the transcriptome does not tell — proteomics and metabolomics are closer to the plants’ patho-phenotype

“…For example, in response to Phytophthora infestans only about half of differentially affected potato proteins showed corresponding changes in the transcriptome [24 ]. Global analysis of transcript and peptide intensities indicated a rapid decline of proteins while the transcriptome increased [24 ]. In specific cases, matches between increased transcript levels and increased abundance of apoplastic proteins were reported, but the magnitude of the transcript changes was generally larger than that of the protein levels [19,25].…”

“…For example, in response to Phytophthora infestans only about half of differentially affected potato proteins showed corresponding changes in the transcriptome [24 ]. Global analysis of transcript and peptide intensities indicated a rapid decline of proteins while the transcriptome increased [24 ].…”