Data from: Large-scale proteomics of the cassava storage root and identification of a target gene to reduce post-harvest deterioration

Cassava (Manihot esculenta) is the most important root crop in the tropics, but rapid postharvest physiological deterioration (PPD) of the root is a major constraint to commercial cassava production. We established a reliable method for image-based PPD symptom quantification and used label-free quantitative proteomics to generate an extensive cassava root and PPD proteome. Over 2600 unique proteins were identified in the cassava root, and nearly 300 proteins showed significant abundance regulation during PPD. We identified protein abundance modulation in pathways associated with oxidative stress, phenylpropanoid biosynthesis (including scopoletin), the glutathione cycle, fatty acid α-oxidation, folate transformation, and the sulfate reduction II pathway. Increasing protein abundances and enzymatic activities of glutathione-associated enzymes, including glutathione reductases, glutaredoxins, and glutathione S-transferases, indicated a key role for ascorbate/glutathione cycles. Based on combined proteomics data, enzymatic activities, and lipid peroxidation assays, we identified glutathione peroxidase as a candidate for reducing PPD. Transgenic cassava overexpressing a cytosolic glutathione peroxidase in storage roots showed delayed PPD and reduced lipid peroxidation as well as decreased H2O2 accumulation. Quantitative proteomics data from ethene and phenylpropanoid pathways indicate additional gene candidates to further delay PPD. Cassava root proteomics data are available at www.pep2pro.ethz.ch for easy access and comparison with other proteomics data.Supplemental Data Set 1Proteins identified in cassava samples from 4 PPD time pointsSupplemental Data Set 2Supplemental Data Set 3T3PQ-based protein abundances of identified proteins in cassava roots at time 0 hSupplemental Data Set 4Label-free MS1-based quantitative data and statistical analysis of cassava proteins detected in cassava samples from 4 PPD time pointsSupplemental Data Set 5List of proteins identified with single PSM and their corresponding spectrum.Supplemental File 1Please note: The package must be installed with admin rights on a win machine. The MATLAB Compiler Runtime (MCR, MathWorks, http://www.mathworks.ch/products/compiler/mcr/) should be installed prior to the installation of the PPD Symptom Score Software. The clk_root_sec_hist.exe is extracted in the same folder and can be executed as follows: i) a figure file is chosen; ii) the root section is marked with a polygon and finished by a double click or return (points can be deleted with backspace) iii) Histogram data and distribution parameter including the PPD score are written in a csv file in the subfolder Regionhist. Disclaimer: The program is provided without any guarantees or warranty. Although the author has attempted to find and correct any bugs in the free software programs, the author is not responsible for any damage or losses of any kind caused by the use or misuse of the programs. The author is under no obligation to provide support, service, corrections, or upgrades to the free software programs.clk_root_sec_hist.zi