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ARS Home » Midwest Area » Columbia, Missouri » Plant Genetics Research » Research » Publications at this Location » Publication #302758
Title: Assessing metabolomic and chemical diversity of a soybean lineage representing 35 years of breeding

Author
item KUSANOA, MIYAKO - Riken Institute
item Baxter, Ivan
item FUKUSHIMA, ATSUSHI - Riken Institute
item OIKAWA, AKIRA - Riken Institute
item OKAZAKI, YOZO - Riken Institute
item NAKABAYASHI, RYO - Riken Institute
item BOUVRETTE, DENISE - Monsanto Corporation
item ACHARD, FREDERIC - Monsanto Corporation
item JAKUBOWSKI, ANDREW - Monsanto Corporation
item BALLAM, JOAN - Monsanto Corporation
item PHILLIPS, JONATHAN - Monsanto Corporation
item CULLER, ANGELA - Monsanto Corporation
item SAITO, KAZUKI - Riken Institute
item HARRIGAN, GEORGE - Monsanto Corporation

Submitted to: Metabolomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/5/2014
Publication Date: 4/1/2015
Publication URL: http://handle.nal.usda.gov/10113/61190
Citation: Kusanoa, M., Baxter, I.R., Fukushima, A., Oikawa, A., Okazaki, Y., Nakabayashi, R., Bouvrette, D.J., Achard, F., Jakubowski, A.R., Ballam, J.M., Phillips, J.R., Culler, A.H., Saito, K., Harrigan, G.G. 2015. Assessing metabolomic and chemical diversity of a soybean lineage representing 35 years of breeding. Metabolomics. 11(2):261-270.

Interpretive Summary: The last 40 years have seen major advances in the yields of soybeans grown in the United States through both conventional breeding as well as through genetic modification (GM) technologies. While GM lines have been compared to their non-GM siblings and found to have few unintended differences, the effects of the overall effect of the breeding processon the diverse chemical components in the seed has not been studied. In this study, 9 elite Monsanto lines from a 35 year span of breeding (launch years 1972-2008), including 3 GM varieties, were grown at two Illinois locations in 2011. We used genetic fingerprinting to characterize the lines and applied 5 different profiling techniques to analyze the chemical diversity of the seeds. Using these techniques, we were able to quantify 732 different chemical compounds and 20 mineral elements. We observed large differences between the lines and between the two environments. The biggest difference in the lines appeared to be driven by the release date, with the older and newer lines separating into different groups. The GM lines were not distinguishable from the non-GM lines in the statistical analysis. The large variability between lines due to breeding history and environment suggests that line to line comparisons needs to be considered if profiling techniques are going to be used to assess food and feed safety but also suggests no scientific rationale for prioritizing GM as a source of unintended effects.

Technical Abstract: 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 glyphosate-tolerant lines grown concurrently at two replicated field sites in the U.S. during 2011. 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 glyphosate-tolerant lines as established by several statistical approaches including variance component analysis and equivalence testing. 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 genetic modification (GM) is not a major source of metabolite variability and that trait development in crops will, of necessity, be associated with biochemical variation.