SE148:/S1

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
Comment

doi: 10.1007/s11306-014-0702-6

Sample Information

ID	S1
Title	Soybean (Glycine max L.)
Organism - Scientific Name	Glycine max
Organism - ID	NCBI taxonomy: 3847
Compound - ID
Compound - Source
Preparation	BioSource Species Soybean Glycine max (9 varieties) Genotypes/Varieties Williams, A3127, A3469, A3555, A3733/CX329 (CX375), AG3701, AG3803, CX366, and AG3705 Organ specification Mature seeds Growth conditions Nine soybean varieties representing a genetic lineage from Williams (1972) to A3555 (2008) were grown at two sites in Illinois (Jerseyville [ILJA] and Jacksonville [ILJA]) during the 2011 season. Varieties included six conventional and three glyphosate-tolerant lines. Starting seeds were planted in a randomized complete block design with six replicates. Soybean plants were treated with maintenance pesticides as necessary throughout the growing season at both sites. The three Roundup Ready varieties were not treated with glyphosate. Experimental conditions Same as the growth conditions. Soybean seeds of 5-6 biological replications were harvested at maturity on 2011. Seeds for each replicate was homogenized by grinding with dry ice to a fine powder, lyophilized and stored frozen at approximately -20°C prior to analysis. We weighed 70 mg dry weight (DW) for CE-TOF-MS analysis, 5 mg DW for GC-TOF-MS analysis, 50 mg DW for LC-q-TOF-MS analysis to detect polar metabolites, and 15 mg DW for lipid profiling.
Sample Preparation Details ID
Comment

Table 1
Launch year and average yield of each variety

Variety	Launch year	Yield at ILJA	Yield at ILJE
Williams	1972	66.5	65.3
A3127	1979	68.2	61.0
CX366	1986	71.9	66.6
CX375(A3733/CX329)	1996	71.8	66.4
A3469	1997	80.3	73.5
AG3701	1999	72.8	71.1
AG3705	2006	80.6	77.2
A3555	2008	85.9	74.2
AG3803	2008	78.8	76.4

Bushels/acre. ILJA represents the Jacksonville, Illinois site and ILJE represents the Jerseyville, Illinois site