Blocking and re-arrangement of pots in greenhouse experiments: which approach is more effective?

Exploring associations between metabolites and gene transcripts of common bean (Phaseolus vulgaris L.) in response to rust (Uromyces appendiculatus) infection

Common bean (Phaseolus vulgaris L.) faces escalating challenges resulting from the increasing prevalence of fungal pathogens such as rust caused by Uromyces appendiculatus, threatening yields and quality of the crop. Understanding P. vulgaris' disease response mechanisms is pivotal for the crop's resilience and food security. Current scientific understanding of underlying molecular mechanisms of P. vulgaris to U. appendiculatus is limited, particularly with respect to specialised molecular data, including metabolite profiles and gene expression. There is a significant knowledge gap in explicating precise metabolomic and transcriptional changes that occur in P. vulgaris upon interaction with U. appendiculatus, which limits strategies aimed at enhancing pathogen resistance. In this study, biological stress response strategies of common bean to the rust pathogen were elucidated through a combined metabolomic and transcriptomic profiling approach. Our findings revealed that U. appendiculatus triggered diverse levels of 30 known metabolites, primarily flavonoids, lipids, nucleosides, and phenylpropanoids among others. Transcriptome sequencing detected over 3000 differentially expressed genes, including multiple transcription factor families such as heat shock proteins (HSPs), cytochrome P450 monooxygenases (CYP), terpene synthases and WRKY transcription factors (TFs) among others. Integrative metabolome and transcriptome analysis showed that rust infection enriched metabolomic pathways, biosynthesis of secondary metabolites, protein processing in the endoplasmic reticulum, and purine metabolism among others. The metabolome and transcriptome integration approach employed in this study provides insights on molecular mechanisms underlying U. appendiculatus response in P. vulgaris' key developmental stages.

Controlled temperature contrasts of three native and one highly invasive annual plant species in California

Plant responses to changes in temperature can be a key factor in predicting the presence and managing invasive plant species while conserving resident native plant species in dryland ecosystems. Climate can influence germination, establishment, and seedling biomass of both native and invasive plant species. We tested the hypothesis that common and widely distributed native and an invasive plant species in dryland ecosystems in California respond differently to increasing temperatures. To test this, we examined the effects of temperature variation on germination, establishment, and per capita seedling biomass of three native and one invasive plant species (Bromus rubens) in independent 6 week growth trial experiments in a controlled greenhouse. Higher relative temperatures reduced the germination and establishment of the tested invasive species and two tested native species, however, per capita biomass was not significantly affected. Specifically, germination and establishment of the invasive species B. rubens and the native species Phacelia tanacetifolia was significantly reduced. This invasive species can often outcompete natives, but increasing temperature could potentially shift the balance between the germination and establishment of natives. A warming climate will likely have negative impacts on native annual plant species in California tested here because increasing temperatures can co-occur with drought. This study shows that our tested native annual plant species tested here have some resilience to relatively significant increases in temperature, and this can favor at least one native species relative to at least one highly noxious invasive plant species.

Changes in Growth and Metabolic Profile of Scutellaria baicalensis Georgi in Response to Sodium Chloride

Scutellaria baicalensis Georgi is a valuable medicinal plant of the Lamiaceae family. Its roots have been used in Traditional Chinese Medicine (under the name Huang-qin) since antiquity and are nowadays included in Chinese and European Pharmacopoeias. It is abundant in bioactive compounds which constitute up to 20% of dried root mass. These substances are lipophilic flavones with unsubstituted B-ring, baicalein, and wogonin and their respective glucuronides-baicalin and wogonoside being the most abundant. The content of these compounds is variable and the environmental factors causing this remain partially unknown. The role of these compounds in stress response is still being investigated and in our efforts to measure the effect of NaCl treatment on S. baicalensis growth and metabolic profile, we hope to contribute to this research. Short-term exposure to salt stress (50, 100, and 150 mM NaCl) resulted in a marked increase of baicalein from 1.55 mg to 2.55 mg/g DM (1.6-fold), baicalin from 8.2 mg to 14.7 mg (1.8-fold), wogonin from 4.9 to 6.8 (1.4-fold), and wogonoside from 3.3 to 6.8 mg/g DM (2-fold) in the roots. Conversely, in the aerial parts, the content of individual major flavonoids: carthamidine-7-O-glucuronide and scutellarein-7-O-glucuronide decreased the most by 10-50% from 18.6 mg to 11.3 mg/g (1.6-fold less) and from 6.5 mg to 3.4 mg/g DM (0.52-fold less), respectively. The amino acid profile was also altered with an increase in root concentrations of the following amino acids: arginine from 0.19 to 0.33 mg/g (1.7-fold), glutamate from 0.09 to 0.16 mg/g DM (1.6-fold), alanine from 0.009 to 0.06 mg/g (6.8-fold), proline from 0.011 to 0.029 (2.4-fold) and lysine from 0.016 to 0.063 mg/g (3.9-fold). Aspartate concentration decreased from 0.01 to 0.002 mg/g (4.8-fold less) at 150 mM NaCl. In the aerial parts, the concentration and variation in levels of specific amino acids differed among groups. For instance, the glutamate content exhibited a significant increase exclusively in the treatment group, rising from 0.031 to 0.034 mg/g, representing a 1.2-fold increase. Proline concentration showed a marked increase across all treated groups with the highest from 0.011 to 0.11 mg/g (10-fold). In conclusion, moderate salt stress was shown to increase S. baicalensis root biomass and flavonoid content which is rarely observed in a glycophyte species and provides a foundation for further studies on the mechanisms of osmotic stress adaptation on the specialized metabolism level.

iPOTs: Internet of Things-based pot system controlling optional treatment of soil water condition for plant phenotyping under drought stress

A cultivation facility that can assist users in controlling the soil water condition is needed for accurately phenotyping plants under drought stress in an artificial environment. Here we report the Internet of Things-based pot system controlling optional treatment of soil water condition (iPOTs), an automatic irrigation system that mimics the drought condition in a growth chamber. The Wi-Fi-enabled iPOTs system allows water supply from the bottom of the pot, based on the soil water level set by the user, and automatically controls the soil water level at a desired depth. The iPOTs also allows users to monitor environmental parameters, such as soil temperature, air temperature, humidity, and light intensity, in each pot. To verify whether the iPOTs mimics the drought condition, we conducted a drought stress test on rice (Oryza sativa L.) varieties and near-isogenic lines, with diverse root system architecture, using the iPOTs system installed in a growth chamber. Similar to the results of a previous drought stress field trial, the growth of shallow-rooted rice accessions was severely affected by drought stress compared with that of deep-rooted accessions. The microclimate data obtained using the iPOTs system increased the accuracy of plant growth evaluation. Transcriptome analysis revealed that pot positions in the growth chamber had little impact on plant growth. Together, these results suggest that the iPOTs system is a reliable platform for phenotyping plants under drought stress.

Linear Variance, P-splines and Neighbour Differences for Spatial Adjustment in Field Trials: How are they Related?

Nearest-neighbour methods based on first differences are an approach to spatial analysis of field trials with a long history, going back to the early work by Papadakis first published in 1937. These methods are closely related to a geostatistical model that assumes spatial covariance to be a linear function of distance. Recently, P-splines have been proposed as a flexible alternative to spatial analysis of field trials. On the surface, P-splines may appear like a completely new type of method, but closer scrutiny reveals intimate ties with earlier proposals based on first differences and the linear variance model. This paper studies these relations in detail, first focussing on one-dimensional spatial models and then extending to the two-dimensional case. Two yield trial datasets serve to illustrate the methods and their equivalence relations. Parsimonious linear variance and random walk models are suggested as a good point of departure for exploring possible improvements of model fit via the flexible P-spline framework.