Summary of Study ST000561
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000412. The data can be accessed directly via it's Project DOI: 10.21228/M8SS33 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000561 |
| Study Title | Exploring the link between genotype, phenotype and metabolome for tomato seed quality attributes |
| Study Type | Tomato Seed Metabolites Profiling (dry seed and 6 hour imbibed seeds comparision) |
| Study Summary | In this study the F8 population of 100 Recombinant Inbred Lines (RILs) obtained from a cross between Solanum lycopersicum X Solanum pimpinellifolium were intelligently allocated to two sub-populations optimized for the distribution of parental alleles using the R-procedure DesignGG (Li et al., 2009; Joosen et al., 2013); hence 50 RIL lines were used for dry seeds and 50 lines for 6h imbibed seeds |
| Institute | Wageningen University & Research |
| Department | Plant Physiology |
| Laboratory | Wageningen Seed Lab, Lab |
| Last Name | Ligterink |
| First Name | Wilco |
| Address | Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands |
| wilco.ligterink@wur.nl | |
| Phone | 31 317 48 28 09 |
| Submit Date | 2017-02-07 |
| Num Groups | 1 |
| Total Subjects | 100 |
| Publications | Metabolomic analysis of tomato seed germination, Metabolomics DOI: 10.1007/s11306-017-1284-x |
| Analysis Type Detail | GC-MS |
| Release Date | 2017-10-25 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000412 |
| Project DOI: | doi: 10.21228/M8SS33 |
| Project Title: | Metabolomic analysis of tomato seed germination |
| Project Summary: | Genomic approaches have accelerated the study of the quantitative genetics that underlie phenotypic variation. We have utilized gas chromatography-time-of-flight/mass spectrometry (GC-TOF-MS) metabolite profiling to characterize tomato seeds during dry and imbibed stages using a recombinant inbred line (RIL) population of Solanum lycopersicum x Solanum pimpinellifolium. In this article we describe, for the first time in tomato, the use of a generalized genetical genomics (GGG) model to study metabolite changes in tomato seeds incorporating genetics as well as environmental effects in a single QTL analysis. The GGG design was used to map genetic quantitative trait loci (G QTLs) and environmental changes by genetic-by-environment interactions (G x E QTLs). A significant canonical correlation was found between metabolites and seed quality traits, revealing a close link between seed quality phenotypes and a specific combination of metabolites. Densely connected metabolites were extracted using graph clustering from correlation networks, and the clusters were evaluated by biochemical-pathway enrichment analysis. The evidence from this study suggests that the number of significant correlations varied among individual metabolites and that the obtained clusters were significantly enriched for metabolites involved in specific biochemical pathways. Thus, the methods described here have the potential to reveal regulatory networks that contribute to our understanding of the complex nature of seed quality. |
| Institute: | Wageningen University & Research |
| Laboratory: | Lab. Of Plant Physiology |
| Last Name: | Henk W.M. Hilhorst |
| First Name: | Henk |
| Address: | Wageningen, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands |
| Email: | henk.hilhorst@wur.nl |
| Phone: | 31 317 48 28 09 |
| Funding Source: | Technology Foundation (STW) and Higher Education Commission, Pakistan |
