Metabolomic profiles of Oryza sativa and influence of genetic diversity
| dc.contributor.author | Heuberger, Adam Lawrence, author | |
| dc.contributor.author | Brick, Mark, advisor | |
| dc.contributor.author | Leach, Jan, committee member | |
| dc.contributor.author | Ryan, Elizabeth, committee member | |
| dc.contributor.author | Byrne, Patrick, committee member | |
| dc.contributor.author | Thompson, Henry, committee member | |
| dc.date.accessioned | 2007-01-03T05:49:27Z | |
| dc.date.available | 2007-01-03T05:49:27Z | |
| dc.date.issued | 2011 | |
| dc.description.abstract | Food crops with enhanced health characteristics are being developed in many breeding programs. Rice (Oryza sativa L.) is an ideal candidate to study traits related to health due to its importance as both a global staple food and a model system for cereal crops. Evaluating metabolite profiles can be a high-throughput method to identify variation in health properties of dietary components. Metabolomics is a useful tool to assess the influence of genetics on total metabolite variation in the cooked grain. Cooked rice metabolite profiles for 10 diverse varieties were determined using ultra performance liquid chromatography coupled to mass spectrometry (UPLC-MS) on aqueous-methanol extracts. A total of 3,097 molecular features were detected, and 25% of the features varied among the 10 varieties (ANOVA, p < 0.001). Both z-score and partial least squares-discriminant analysis (PLS-DA) showed variation consistent with subspecies-based varietal groupings, and indicated genetic control over the metabolite profiles. Variation in total phenolics and vitamin E was also consistent with varietal groupings. Genes in biochemical pathways for health-related metabolites were interrogated for allelic variation by single nucleotide polymorphisms (SNPs). SNP variation may serve as an important mechanism by which genes influence metabolic variation. The influence of genetic diversity on the metabolite profile of the rice grain was also assessed for two interacting effects: genotype-environment interactions (GEI) and genotype-fermentation interactions (GFI). GEI was assessed by growing two diverse rice varieties in the field and the greenhouse. Gas-chromatography-MS (GC-MS) was used to detect primary metabolites from aqueous-methanol extracts of cooked rice. Genotype, environmental, and GEI effects were observed for many metabolites, including the amino acid phenylalanine, a precursor for many secondary metabolites related to human health. Genes associated with phenylalanine synthesis were screened in rice gene expression databases, and variation within and among the genes suggests they are a potential source of genetic variation for phenylalanine synthesis. Both the metabolite and gene expression patterns indicate a potential interaction between phenylalanine and serine synthesis. The GC-MS data implies the GEI effects on primary metabolism may correspond to variation in secondary metabolites that are predicted to affect human health. Additionally, human health attributes of the grain may be dependent on fermentation of rice metabolites by gut microorganisms. GFI effects were assessed by fermenting three highly similar rice varieties with Saccharomyces boulardii, a probiotic yeast. Metabolites were extracted and detected by GC-MS. A PLS-DA model showed evidence of fermentation (F) effects, but not GFI. However, when extracts were assessed for the ability to inhibit viability of lymphoma cells, both F and GFI effects were apparent. It is therefore likely that GFI effects may exist among diverse rice varieties, and that interactions affect the bioactivity of rice metabolites. In summary, total metabolite variation is largely influenced by the rice genotype, including interactions with environment and fermentation. These data describe both heritable and non-heritable sources of variation. Thus, although genetic variation in rice is sufficient to establish metabolite profiles specific to human health characteristics, the heritability of a secondary metabolite-associated health trait is likely influenced by both environment and fermentation effects. | |
| dc.format.medium | born digital | |
| dc.format.medium | doctoral dissertations | |
| dc.identifier | Heuberger_colostate_0053A_10683.pdf | |
| dc.identifier.uri | http://hdl.handle.net/10217/52063 | |
| dc.language | English | |
| dc.language.iso | eng | |
| dc.publisher | Colorado State University. Libraries | |
| dc.relation.ispartof | 2000-2019 | |
| dc.rights | Copyright and other restrictions may apply. User is responsible for compliance with all applicable laws. For information about copyright law, please see https://libguides.colostate.edu/copyright. | |
| dc.title | Metabolomic profiles of Oryza sativa and influence of genetic diversity | |
| dc.type | Text | |
| dcterms.rights.dpla | This Item is protected by copyright and/or related rights (https://rightsstatements.org/vocab/InC/1.0/). You are free to use this Item in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s). | |
| thesis.degree.discipline | Soil and Crop Sciences | |
| thesis.degree.grantor | Colorado State University | |
| thesis.degree.level | Doctoral | |
| thesis.degree.name | Doctor of Philosophy (Ph.D.) |
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