EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments.

Environmental gene regulatory influence networks (EGRINs) coordinate the timing and rate of gene expression in response to environmental signals. EGRINs encompass many layers of regulation, which culminate in changes in accumulated transcript levels. Here, we inferred EGRINs for the response of five tropical Asian rice (Oryza sativa) cultivars to high temperatures, water deficit, and agricultural field conditions by systematically integrating time-series transcriptome data, patterns of nucleosome-free chromatin, and the occurrence of known cis-regulatory elements. First, we identified 5447 putative target genes for 445 transcription factors (TFs) by connecting TFs with genes harboring known cis-regulatory motifs in nucleosome-free regions proximal to their transcriptional start sites. We then used network component analysis to estimate the regulatory activity for each TF based on the expression of its putative target genes. Finally, we inferred an EGRIN using the estimated transcription factor activity (TFA) as the regulator. The EGRINs include regulatory interactions between 4052 target genes regulated by 113 TFs. We resolved distinct regulatory roles for members of the heat shock factor family, including a putative regulatory connection between abiotic stress and the circadian clock. TFA estimation using network component analysis is an effective way of incorporating multiple genome-scale measurements into network inference.

Using Carbon Stable Isotopes to Study C3 and C4 Photosynthesis: Models and Calculations.

Stable carbon isotopes are a powerful tool to study photosynthesis. Initial applications consisted of determining isotope ratios of plant biomass using mass spectrometry. Subsequently, theoretical models relating C isotope values to gas exchange characteristics were introduced and tested against instantaneous online measurements of 13C photosynthetic discrimination. Beginning in the twenty-first century, laser absorption spectroscopes with sufficient precision for determining isotope mixing ratios became commercially available. This has allowed collection of large data sets at lower cost and with unprecedented temporal resolution. More data and accompanying knowledge have permitted refinement of 13C discrimination model equations, but often at the expense of increased model complexity and difficult parametrization. This chapter describes instantaneous online measurements of 13C photosynthetic discrimination, provides recommendations for experimental setup, and presents a thorough compilation of equations available to researchers. We update our previous 2018 version of this chapter by including recently improved descriptions of (photo)respiratory processes and associated fractionations. We discuss the capabilities and limitations of the diverse 13C discrimination model equations and provide guidance for selecting the model complexity needed for different applications.

Minimum hydraulic safety leads to maximum water-use efficiency in a forage grass.

Understanding how water-use regulation relates to biomass accumulation is imperative for improving crop production in water-limited environments. Here, we examine how the vulnerability of xylem to water stress-induced cavitation and the coordination between water transport capacity and assimilation (A) influences diurnal water-use efficiency (WUE) and dry-matter production in Lolium perenne L. - a commercial forage grass. Plants were exposed to a range of water stresses, causing up to 90% leaf death, by withholding water and then rewatering to observe the recovery process. Leaf hydraulic conductance (K(leaf) ) declined to 50% of maximum at a leaf water potential (ψ(leaf) ) of -1 MPa, whereas complete stomatal closure occurred well after this point, at -2.35 MPa, providing no protection against hydraulic dysfunction. Instantaneous A remained maximal until >70% of hydraulic conductivity had been lost. Post-stress rewatering showed that 95% loss of K(leaf) could be incurred before the recovery of gas exchange exceeded 1 d, with a rapid transition to leaf death after this point. Plants exposed to sustained soil water deficits through restricted nightly watering regimes did not suffer cumulative losses in K(leaf) ; instead, ψ(leaf) and gas exchange recovered diurnally. The effect was improved WUE during the day and optimal ψ(leaf) during the night for the maintenance of growth.

Using Stable Carbon Isotopes to Study C3 and C4 Photosynthesis: Models and Calculations.

Stable carbon isotopes are a powerful tool to study photosynthesis. Initial applications consisted of determining isotope ratios of plant biomass using mass spectrometry. Subsequently, theoretical models relating C-isotope values to gas exchange characteristics were introduced and tested against instantaneous online measurements of 13C photosynthetic discrimination. Beginning in the twenty-first century, tunable diode laser spectroscopes with sufficient precision for determining isotope mixing ratios became commercially available. This has allowed collection of large data sets, at low cost and with unprecedented temporal resolution. With more data and accompanying knowledge, it has become apparent that there is a need for increased complexity in models and calculations. This chapter describes instantaneous online measurements of 13C photosynthetic discrimination, provides recommendations for experimental setup, and presents a thorough compilation of equations needed for different applications.

Estimation of Photorespiratory Fluxes by Gas Exchange.

Photorespiratory fluxes can be easily estimated by photosynthetic gas exchange using an infrared gas analyzer and applying the Farquhar, von Caemmerer, and Berry (Farquhar et al. Planta 149:78-90, 1980) photosynthesis model. For a more direct measurement of photorespiratory CO2 release from glycine decarboxylation, infrared gas analysis can be coupled to membrane-inlet mass spectrometry, capable of separating the total CO2 concentration into its 12CO2 and 13CO2 components in a continuous online fashion. This chapter discusses how to calculate rates of photorespiration from Rubisco kinetics and describes in detail a method for measuring the CO2 release from glycine decarboxylation using 13CO2.

Contrasting hydraulic regulation in closely related forage grasses: implications for plant water use.

Plant traits that improve crop water use efficiency are highly sought after but difficult to isolate. Here, we examine the integrated function of xylem and stomata in closely related forage grasses to determine whether quantitative differences in water transport properties could be used to predict plant performance under limited water conditions. Cultivars of two forage grass species with different drought tolerance ratings, Lolium multiflorum Lam. and Festuca arundinacea Schreb., were assessed for maximum hydraulic conductivity (Kmax), vulnerability of xylem to hydraulic dysfunction (P50) and stomatal sensitivity to leaf water potential. Species-specific differences were observed in several of these traits, and their effect on whole-plant performance was examined under well-watered and restricted watering conditions. It was shown that although P50 was comparable between species, for F. arundinacea cultivars, there was greater hydraulic risk associated with reduced stomatal sensitivity to leaf hydration. In contrast, L. multiflorum cultivars expressed a higher capacity for water transport, but more conservative stomatal regulation. Despite different susceptibilities to leaf damage observed during acute drought, under the sustained moderate drought treatment, the two strategies were balanced in terms of water conservation and hydraulic utilisation, resulting in similar dry matter production. Characterisation of water use patterns according to the key hydraulic parameters is discussed in terms of implications to yield across different environmental scenarios as well as the applicability of water transport related traits to breeding programs.