Regulatory feedback response mechanisms to phosphate starvation in rice

Phosphorus is a growth-limiting nutrient for plants. The growing scarcity of phosphate stocks threatens global food security. Phosphate-uptake regulation is so complex and incompletely known that attempts to improve phosphorus use efficiency have had extremely limited success. This study improves our understanding of the molecular mechanisms underlying phosphate uptake by investigating the transcriptional dynamics of two regulators: the Ubiquitin ligase PHO2 and the long non-coding RNA IPS1. Temporal measurements of RNA levels have been integrated into mechanistic mathematical models using advanced statistical techniques. Models based solely on current knowledge could not adequately explain the temporal expression profiles. Further modeling and bioinformatics analysis have led to the prediction of three regulatory features: the PHO2 protein mediates the degradation of its own transcriptional activator to maintain constant PHO2 mRNA levels; the binding affinity of the transcriptional activator of PHO2 is impaired by a phosphate-sensitive transcriptional repressor/inhibitor; and the extremely high levels of IPS1 and its rapid disappearance upon Pi re-supply are best explained by Pi-sensitive RNA protection. This work offers both new opportunities for plant phosphate research that will be essential for informing the development of phosphate efficient crop varieties, and a foundation for the development of models integrating phosphate with other stress responses

Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)

<p>Abstract</p> <p>Background</p> <p>Global transcriptional analysis of loblolly pine (<it>Pinus taeda </it>L.) is challenging due to limited molecular tools. PtGen2, a 26,496 feature cDNA microarray, was fabricated and used to assess drought-induced gene expression in loblolly pine propagule roots. Statistical analysis of differential expression and weighted gene correlation network analysis were used to identify drought-responsive genes and further characterize the molecular basis of drought tolerance in loblolly pine.</p> <p>Results</p> <p>Microarrays were used to interrogate root cDNA populations obtained from 12 genotype × treatment combinations (four genotypes, three watering regimes). Comparison of drought-stressed roots with roots from the control treatment identified 2445 genes displaying at least a 1.5-fold expression difference (false discovery rate = 0.01). Genes commonly associated with drought response in pine and other plant species, as well as a number of abiotic and biotic stress-related genes, were up-regulated in drought-stressed roots. Only 76 genes were identified as differentially expressed in drought-recovered roots, indicating that the transcript population can return to the pre-drought state within 48 hours. Gene correlation analysis predicts a scale-free network topology and identifies eleven co-expression modules that ranged in size from 34 to 938 members. Network topological parameters identified a number of central nodes (hubs) including those with significant homology (E-values ≤ 2 × 10^-30) to 9-cis-epoxycarotenoid dioxygenase, zeatin O-glucosyltransferase, and ABA-responsive protein. Identified hubs also include genes that have been associated previously with osmotic stress, phytohormones, enzymes that detoxify reactive oxygen species, and several genes of unknown function.</p> <p>Conclusion</p> <p>PtGen2 was used to evaluate transcriptome responses in loblolly pine and was leveraged to identify 2445 differentially expressed genes responding to severe drought stress in roots. Many of the genes identified are known to be up-regulated in response to osmotic stress in pine and other plant species and encode proteins involved in both signal transduction and stress tolerance. Gene expression levels returned to control values within a 48-hour recovery period in all but 76 transcripts. Correlation network analysis indicates a scale-free network topology for the pine root transcriptome and identifies central nodes that may serve as drivers of drought-responsive transcriptome dynamics in the roots of loblolly pine.</p

Variation in phosphorus efficiency among 73 bread and durum wheat genotypes grown in a phosphorus-deficient calcareous soil

A greenhouse experiment was carried out to study the severity of phosphorus (P) deficiency symptoms on leaves, shoot dry matter production, and shoot concentration and content (the total amount per shoot) of P in 39 bread wheat (Triticum aestivum L.) and 34 durum wheat (Triticum durum L.) genotypes grown in a severely P-deficient calcareous soil with low (20mgPkg−1 soil) and adequate (80mgPkg−1 soil) P supply for 39 days. As the seed P concentration or content can affect plant performance under P-deficient conditions, the seeds of the genotypes used in the present study were also analyzed for P concentration. Phosphorus efficiency (relative shoot growth) of genotypes, calculated by the ratio of shoot dry matter production under low P to that under adequate P supply, significantly differed among the genotypes, and varied between 46.7% and 78.6%. Phosphorus efficiency ranged from 51% to 71% with an average of 61% for bread and from 47% to 79% with an average of 66% for durum wheat genotypes. There was no correlation between P efficiency ratio and P concentration of plants (R 2=0.0001), but P efficiency of all bread and durum wheat genotypes showed a very significant correlation with the P content (the total amount of P per shoot) (R 2=0.333***). The relationship between the P efficiency and total amount of P per shoot was much more significant in bread (R 2=0.341***) than in durum wheat (R 2=0.135*). Like shoot P concentrations, also severity of visible leaf symptoms of P deficiency on older leaves, including leaf chlorosis and necrosis, did not correlate with P efficiency. In most cases, genotypes showing higher P efficiency had higher absolute shoot dry weight under P deficient conditions. Under P deficient conditions, the absolute shoot dry weight very significantly correlated with shoot P content (R 2=0.665***), but the correlation between the absolute shoot dry weight and shoot P concentration tended to be negative. There was also variation in native seed P reserve of the genotypes, but this variation had no influence on the P efficiency. The results indicate that the total amount of P per shoot and shoot dry matter production at low P supply are most reliable parameters in ranking genotypes for P efficiency at early growth stage. In wheat germplasm tested in the present study, several wheat genotypes are available showing both very high P efficiency and very high shoot content and concentration of P suggesting that P acquisition ability should be most important mechanism for high P efficiency in such genotypes. On the other hand, there are also genotypes in the germplasm having more or less same P concentration or P content in shoot but differing substantially in P efficiency, indicating importance of P utilization at cellular level in P efficiency. All these results suggest that P efficiency mechanisms can be different from one genotype to other within a given plant species