Genome-scale metabolic models promise important insights into cell function. However, the definition of pathways and functional network modules within these models, and in the biochemical literature in general, is often based on intuitive reasoning. Although mathematical methods have been proposed to identify modules, which are defined as groups of reactions with correlated fluxes, there is a need for experimental verification. We show here that multivariate statistical analysis of the NMR-derived intra-and extracellular metabolite profiles of single-gene deletion mutants in specific metabolic pathways in the yeast Saccharomyces cerevisiae identified outliers whose profiles were markedly different from those of the other mutants in their respective pathways. Application of flux coupling analysis to a metabolic model of this yeast showed that the deleted gene in an outlying mutant encoded an enzyme that was not part of the same functional network module as the other enzymes in the pathway. We suggest that metabolomic methods such as this, which do not require any knowledge of how a gene deletion might perturb the metabolic network, provide an empirical method for validating and ultimately refining the predicted network structure.
SU MMARYOutcomes of developmental yield formation processes in oats, namely number of panicles/m 2 , number of grains/panicle, mean grain weight and incidences of aborted and tertiary grains, were measured in a series of experiments in Northern Ireland and the Republic of Ireland in 1997/98 and 1998/99. Seed rate (200 and 300 seeds/m 2 ), nitrogen (0-200 kg/ha) and plant growth regulator (chlormequat chloride) treatments were applied to the spring oat varieties Aberglen and Barra in one spring-and two autumn-sown experiments, and to the winter varieties Gerald and Image in one autumn-sown experiment. Large variation in number of panicles/m 2 and grains/panicle was observed between the experiments and varieties and in response to seed rate, with number of grains/panicle generally being inversely related to number of panicles/m 2 . At the higher rates of nitrogen rate both number of panicles/m 2 and grains per panicle increased. Mean grain weights were relatively constant and were largely determined by variety. Chlormequat chloride had relatively little effect on the yield components, the most consistent being small reductions in mean grain weight.Tertiary grains occurred rarely in the varieties and agronomic treatments used in the programme but were more frequent at higher rates of nitrogen in most of the experiments. Numbers of aborted grains were usually higher where grain numbers were higher although the effects of variety, seed rate and nitrogen on aborted grains were not consistent. Structure of the grain population, i.e. the relative proportions of primary and secondary grain, was stable despite the large differences in number of panicles/m 2 , spikelet numbers and mean grain weight.The greater yield and growth enhancing effects of nitrogen compared with seed rate and plant growth regulator were apparent in responses by developmental processes active later in the life cycle, namely production of tertiary grains and grain filling.Wide variation in number of panicles/m 2 (c. 200-450) and number of grains/panicle (c. 55-145) produced in the crops grown under a very full expression of agro-ecological conditions in this programme was accompanied by small variation in mean grain weight (c. 38-47 mg/primary grain and c. 22-29 mg/secondary grain) and in numbers of tertiary (<2/panicle) and aborted grains (<10/ panicle). Plasticity of development throughout the life cycle, manifested both as the established yield components and in numbers of tertiary and aborted grains, was largely effective in ensuring stability of mean grain weight and quality in oats.
(1)H NMR measurements on protein-free extracts from wheat leaf and stem tissue were used to investigate the biochemical correlates of partial resistance to fungal species implicated in the Fusarium head blight (FHB) disease complex. The wheat genotypes included five commercial wheat cultivars and 116 wheat genotypes, from the CIMMYT international FHB breeding programme in Mexico, that had been bred for FHB disease resistance, utilizing exotic, typically Chinese, resistance sources. Principal component analysis of the nuclear magnetic resonance (NMR)-derived metabolite profiles revealed distinct separation of the commercial wheat cultivars from the majority of the CIMMYT wheat genotypes with the commercial cultivars exhibiting markedly higher carbohydrate concentrations. A cross-validated partial least squares (PLS) regression model of the metabolite profile against the partial disease resistance component latent period (delay in sporulation of the fungus on the plant tissue) predicted latent periods that were significantly correlated with the experimentally determined values (R(2) = 0.34, P < 0.001). Identified metabolites that were found in plants with shorter latent periods (higher disease susceptibility) included choline, the single most influential metabolite in the PLS model, betaine, the amino acids glutamine, glutamate and alanine, trans-aconitate and sucrose. Metabolites related to increased disease resistance included glucose and unassigned resonances in the carbohydrate and aromatic regions of the NMR spectra. The current study has demonstrated the potential of metabolite profiling as a tool for marker-assisted selection in commercial breeding for resistance to FHB in wheat.
A large environmental influence on phenotypic estimates of disease resistance and the complex polygenic nature of Fusarium head blight (FHB) resistance in wheat (Triticum aestivum) are impediments to developing resistant cultivars. The objective of this research was to investigate the utility of a detached leaf assay, inoculated using inoculum from isolates of Microdochium nivale var. majus, to identify components of FHB resistance among 30 entries of U.S. soft red winter wheat in the 2002 Uniform Southern FHB Nursery (USFHBN). Whole plant FHB resistance of the USFHBN entries was evaluated in replicated, mist-irrigated field trials at 10 locations in eight states during the 2001-2002 season. Incubation period (days from inoculation to the first appearance of a dull gray-green water-soaked lesion) was the only detached leaf variable significantly correlated across all FHB resistance parameters accounting for 45% of the variation in FHB incidence, 27% of FHB severity, 30% of Fusarium damaged kernels, and 26% of the variation in grain deoxynivalenol (DON) concentration. The results for incubation period contrasted with previous studies of moderately resistant European cultivars, in that longer incubation period was correlated with greater FHB susceptibility, but agreed with previous findings for the Chinese cultivar Sumai 3 and CIMMYT germ plasm containing diverse sources of FHB resistance. The results support the view that the detached leaf assay method has potential for use to distinguish between specific sources of FHB resistance when combined with data on FHB reaction and pedigree information. For example, entry 28, a di-haploid line from the cross between the moderately resistant U.S. cultivar Roane and the resistant Chinese line W14, exhibited detached leaf parameters that suggested a combination of both sources of FHB resistance. The USFHBN represents the combination of adapted and exotic germ plasm, but four moderately resistant U.S. commercial cultivars (Roane, McCormick, NC-Neuse, and Pat) had long incubation and latent periods and short lesion lengths in the detached leaf assay as observed in moderately FHB resistant European cultivars. The dichotomy in the relationship between incubation period and FHB resistance indicates that this may need to be considered to effectively combine exotic and existing/adapted sources of FHB resistance.
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