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Sample Set Information

ID TSE1321
Title Assessing metabolomic and chemical diversity of a soybean lineage representing 35 years of breeding
Description Information on crop genotype- and phenotype-metabolite associations can be of value to trait development as well as to food security and safety. The unique study presented here assessed seed metabolomic and ionomic diversity in a soybean lineage representing ~35 years of breeding (launch years 1972–2008) and increasing yield potential. Selected varieties included six conventional and three genetically modified (GM) glyphosate-tolerant lines. A metabolomics approach utilizing capillary electrophoresis (CE)-time-of-flight-mass spectrometry (TOF-MS), gas chromatography (GC)-TOF-MS and liquid chromatography (LC)-quadrupole (q)-TOFMS resulted in measurement of a total of 732 annotated peaks. Ionomics through inductively-coupled plasma (ICP)-MS profiled twenty mineral elements. Orthogonal partial least squares-discriminant analysis (OPLS-DA) of the seed data successfully differentiated newer higher-yielding soybean from earlier lower-yielding accessions at both field sites. This result reflected genetic fingerprinting data that demonstrated a similar distinction between the newer and older soybean. Correlation analysis also revealed associations between yield data and specific metabolites. There were no clear metabolic differences between the conventional and GM lines. Overall, observations of metabolic and genetic differences between older and newer soybean varieties provided novel and significant information on the impact of varietal development on biochemical variability. Proposed applications of omics in food and feed safety assessments will need to consider that GM is not a major source of metabolite variability and that trait development in crops will, of necessity, be associated with biochemical variation.
Authors Miyako Kusano, Ivan Baxter, Atsushi Fukushima, Akira Oikawa, Yozo Okazaki, Ryo Nakabayashi, Denise J. Bouvrette, Frederic Achard, Andrew R. Jakubowski, Joan M. Ballam, Jonathan R. Phillips, Angela H. Culler, Kazuki Saito, George G. Harrigan
Reference Metabolomics April 2015, Volume 11, Issue 2, pp 261–270

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Data Analysis Details Information

Title Data processing (GC-MS)
Description Data processing for GC-TOF-MS data

Nonprocessed MS data from GC-TOF-MS analysis were exported in NetCDF format generated by chromatography processing- and mass spectral deconvolution software (Leco ChromaTOF version 3.22; LECO, St. Joseph, MI, USA) to MATLAB 6.5 or MATLAB2011b (Mathworks, Natick, MA, USA) for the performance of all data-pretreatment procedures, e.g. smoothing, alignment, time-window setting H-MCR, and RDA (Jonsson P, et al. (2006) Predictive metabolite profiling applying hierarchical multivariate curve resolution to GC-MS data--a potential tool for multi-parametric diagnosis. J Proteome Res 5(6):1407-1414.). The resolved MS spectra were matched against reference mass spectra using the NIST mass spectral search program for the NIST/EPA/NIH mass spectral library (version 2.0) and our custom software for peak-annotation written in JAVA. Peaks were identified or annotated based on their RIs, a comparison of the reference mass-spectra with the Golm Metabolome Database (GMD) released from CSB.DB (Kopka J, et al. (2005) GMD@CSB.DB: the Golm Metabolome Database. Bioinformatics 21(8):1635-1638), and our in-house spectral library. The metabolites were identified by comparison with RIs from the library databases (GMD and our own library) and the RIs of authentic standards. The metabolites were defined as annotated metabolites after comparison with the mass spectra and the RIs from these two libraries. The data matrix was normalized using the CCMN algorithm for further analysis (Redestig H, et al. (2009) Compensation for systematic cross-contribution improves normalization of mass spectrometry based metabolomics data. Anal Chem 81(19):7974-7980).


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