Melanie J. Correll

Phytochromes A and B Mediate Red-Light-Induced Positive Phototropism in Roots

The interaction of tropisms is important in determining the final growth form of the plant body. In roots, gravitropism is the predominant tropistic response, but phototropism also plays a role in the oriented growth of roots in flowering plants. In blue or white light, roots exhibit negative phototropism that is mediated by the phototropin family of photoreceptors. In contrast, red light induces a positive phototropism in Arabidopsis roots. Because this red-light-induced response is weak relative to both gravitropism and negative phototropism, we used a novel device to study phototropism without the complications of a counteracting gravitational stimulus. This device is based on a computer-controlled system using real-time image analysis of root growth and a feedback-regulated rotatable stage. Our data show that this system is useful to study root phototropism in response to red light, because in wild-type roots, the maximal curvature detected with this apparatus is 30° to 40°, compared with 5° to 10° without the feedback system. In positive root phototropism, sensing of red light occurs in the root itself and is not dependent on shoot-derived signals resulting from light perception.Phytochrome (Phy)A andphyB were severely impaired in red-light-induced phototropism, whereas the phyD and phyEmutants were normal in this response. Thus, PHYA and PHYB play a key role in mediating red-light-dependent positive phototropism in roots. Although phytochrome has been shown to mediate phototropism in some lower plant groups, this is one of the few reports indicating a phytochrome-dependent phototropism in flowering plants.

A novel phototropic response to red light is revealed in microgravity

The aim of this study was to investigate phototropism in plants grown in microgravity conditions without the complications of a 1-g environment. Experiments performed on the International Space Station (ISS) were used to explore the mechanisms of both blue-light- and red-light-induced phototropism in plants. This project utilized the European Modular Cultivation System (EMCS), which has environmental controls for plant growth as well as centrifuges for gravity treatments used as a 1-g control. Images captured from video tapes were used to analyze the growth, development, and curvature of Arabidopsis thaliana plants that developed from seed in space. A novel positive phototropic response to red light was observed in hypocotyls of seedlings that developed in microgravity. This response was not apparent in seedlings grown on Earth or in the 1-g control during the space flight. In addition, blue-light-based phototropism had a greater response in microgravity compared with the 1-g control. Although flowering plants are generally thought to lack red light phototropism, our data suggest that at least some flowering plants may have retained a red light sensory system for phototropism. Thus, this discovery may have important implications for understanding the evolution of light sensory systems in plants.

In Vitro Gastric and Intestinal Digestions of Pulsed Light-Treated Shrimp Extracts

Pulsed ultraviolet light (PUV), a novel technology most commonly used for microbial inactivation, has recently been employed to effectively mitigate food allergens in peanuts, soybean, shrimp, and almond. Putative mechanisms for the efficacy of PUV in reducing allergen reactivity include photothermal, photochemical, and photophysical effects. To date, there are no published data highlighting the effects of in vitro simulated gastric and intestinal digestion on the stability of PUV reduced allergen reactivity of food. In this study, PUV-treated shrimp extracts were subjected to simulated gastric fluid containing pepsin and simulated intestinal fluid containing trypsin and chymotrypsin, and then tested for changes in allergen potency. SDS-PAGE showed no major band deviation between undigested and digested PUV-treated shrimp extracts. IgE binding to tropomyosin remained markedly decreased as seen in Western blot analysis. Total shrimp allergen reactivity remained unchanged following in vitro peptic digestion and was markedly reduced following in vitro intestinal digestion as illustrated in indirect ELISA. The PUV reduced shrimp allergens remained at a low level under the in vitro simulated digestive conditions. The results inferred that PUV could be a potential method to create less allergenic shrimp products that would remain at a low allergen level under human gastric and intestinal digestive conditions.

Extraction and labeling methods for microarrays using small amounts of plant tissue.

Procedures were developed to maximize the yield of high-quality RNA from small amounts of plant biomass for microarrays. Two disruption techniques (bead milling and pestle and mortar) were compared for the yield and the quality of RNA extracted from 1-week-old Arabidopsis thaliana seedlings (approximately 0.5-30 mg total biomass). The pestle and mortar method of extraction showed enhanced RNA quality at the smaller biomass samples compared with the bead milling technique, although the quality in the bead milling could be improved with additional cooling steps. The RNA extracted from the pestle and mortar technique was further tested to determine if the small quantity of RNA (500 ng-7 microg) was appropriate for microarray analyses. A new method of low-quantity RNA labeling for microarrays (NuGEN Technologies, Inc.) was used on five 7-day-old seedlings (approximately 2.5 mg fresh weight total) of Arabidopsis that were grown in the dark and exposed to 1 h of red light or continued dark. Microarray analyses were performed on a small plant sample (five seedlings; approximately 2.5 mg) using these methods and compared with extractions performed with larger biomass samples (approximately 500 roots). Many well-known light-regulated genes between the small plant samples and the larger biomass samples overlapped in expression changes, and the relative expression levels of selected genes were confirmed with quantitative real-time polymerase chain reaction, suggesting that these methods can be used for plant experiments where the biomass is extremely limited (i.e. spaceflight studies).

Next generation crop models: A modular approach to model early vegetative and reproductive development of the common bean (Phaseolus vulgaris L)

The next generation of gene-based crop models offers the potential of predicting crop vegetative and reproductive development based on genotype and weather data as inputs. Here, we illustrate an approach for developing a dynamic modular gene-based model to simulate changes in main stem node numbers, time to first anthesis, and final node number on the main stem of common bean (Phaseolus vulgaris L.). In the modules, these crop characteristics are functions of relevant genes (quantitative trait loci (QTL)), the environment (E), and QTL × E interactions. The model was based on data from 187 recombinant inbred (RI) genotypes and the two parents grown at five sites (Citra, FL; Palmira, Colombia; Popayan, Colombia; Isabela Puerto Rico; and Prosper, North Dakota). The model consists of three dynamic QTL effect models for node addition rate (NAR, No. d− 1), daily rate of progress from emergence toward flowering (RF), and daily maximum main stem node number (MSNODmax), that were integrated to simulate main stem node number vs. time, and date of first flower using daily time steps. Model evaluation with genotypes not used in model development showed reliable predictions across all sites for time to first anthesis (R2 = 0.75) and main stem node numbers during the linear phase of node addition (R2 = 0.93), while prediction of the final main stem node number was less reliable (R2 = 0.27). The use of mixed-effects models to analyze multi-environment data from a wide range of genotypes holds considerable promise for assisting development of dynamic QTL effect models capable of simulating vegetative and reproductive development.

Comparative transcriptomics indicate changes in cell wall organization and stress response in seedlings during spaceflight

PREMISE OF THE STUDY Plants will play an important role in the future of space exploration as part of bioregenerative life support. Thus, it is important to understand the effects of microgravity and spaceflight on gene expression in plant development. METHODS We analyzed the transcriptome of Arabidopsis thaliana using the Biological Research in Canisters (BRIC) hardware during Space Shuttle mission STS-131. The bioinformatics methods used included RMA (robust multi-array average), MAS5 (Microarray Suite 5.0), and PLIER (probe logarithmic intensity error estimation). Glycome profiling was used to analyze cell wall composition in the samples. In addition, our results were compared to those of two other groups using the same hardware on the same mission (BRIC-16). KEY RESULTS In our BRIC-16 experiments, we noted expression changes in genes involved in hypoxia and heat shock responses, DNA repair, and cell wall structure between spaceflight samples compared to the ground controls. In addition, glycome profiling supported our expression analyses in that there was a difference in cell wall components between ground control and spaceflight-grown plants. Comparing our studies to those of the other BRIC-16 experiments demonstrated that, even with the same hardware and similar biological materials, differences in results in gene expression were found among these spaceflight experiments. CONCLUSIONS A common theme from our BRIC-16 space experiments and those of the other two groups was the downregulation of water stress response genes in spaceflight. In addition, all three studies found differential regulation of genes associated with cell wall remodeling and stress responses between spaceflight-grown and ground control plants.

Crop Modeling Approaches for Predicting Phenotype of Grain Legumes with Linkage to Genetic Information

In this chapter we introduce concepts on how mechanistic crop simulation models can be linked with genetic information to predict phenotype in different environments. There has been rapid advancement of genotyping along with continued improvement of mechanistic simulation models that predict dynamic daily (or faster) growth processes of crops in response to varying weather, soils, and management conditions. Crop models have genotype-specific-parameters (GSPs) that describe performance of different cultivars; nevertheless, those GSPs are empirical mathematical parameters that are estimated directly from field phenotyping data. There is great opportunity to link the modeled GSPs with genes (or QTLs) obtained from genotyping, so that phenotypic performance can be directly predicted from genotype. The largest challenge is the phenotyping needed to characterize the phenotypes that result from gene expression in different environments. Examples are given of phenotyping in a recombinant common bean study. Additional mechanisms and different GSPs may be needed in the crop models to achieve this goal. Since crop models are already programmed to account for weather, soils, and management effects, they are efficient tools in which hypothetical alleles of genes can be evaluated for multiple environments. Model simulations illustrate examples of genotype-by-environment (G × E) interactions, where a given allele (gene) for a trait may have either positive or negative effects on yield, depending on weather and management conditions. Examples of linkage of GSPs to genes are given for common bean, along with phenotypic outcomes of growth patterns observed to be very responsive to presence or absence of alleles of genes.

Development of a QTL-environment-based predictive model for node addition rate in common bean

Key messageThis work reports the effects of the genetic makeup, the environment and the genotype by environment interactions for node addition rate in an RIL population of common bean. This information was used to build a predictive model for node addition rate.AbstractTo select a plant genotype that will thrive in targeted environments it is critical to understand the genotype by environment interaction (GEI). In this study, multi-environment QTL analysis was used to characterize node addition rate (NAR, node day− 1) on the main stem of the common bean (Phaseolus vulgaris L). This analysis was carried out with field data of 171 recombinant inbred lines that were grown at five sites (Florida, Puerto Rico, 2 sites in Colombia, and North Dakota). Four QTLs (Nar1, Nar2, Nar3 and Nar4) were identified, one of which had significant QTL by environment interactions (QEI), that is, Nar2 with temperature. Temperature was identified as the main environmental factor affecting NAR while day length and solar radiation played a minor role. Integration of sites as covariates into a QTL mixed site-effect model, and further replacing the site component with explanatory environmental covariates (i.e., temperature, day length and solar radiation) yielded a model that explained 73% of the phenotypic variation for NAR with root mean square error of 16.25% of the mean. The QTL consistency and stability was examined through a tenfold cross validation with different sets of genotypes and these four QTLs were always detected with 50–90% probability. The final model was evaluated using leave-one-site-out method to assess the influence of site on node addition rate. These analyses provided a quantitative measure of the effects on NAR of common beans exerted by the genetic makeup, the environment and their interactions.

A Predictive Model for Time-to-Flowering in the Common Bean Based on QTL and Environmental Variables

The common bean is a tropical facultative short-day legume that is now grown in tropical and temperate zones. This observation underscores how domestication and modern breeding can change the adaptive phenology of a species. A key adaptive trait is the optimal timing of the transition from the vegetative to the reproductive stage. This trait is responsive to genetically controlled signal transduction pathways and local climatic cues. A comprehensive characterization of this trait can be started by assessing the quantitative contribution of the genetic and environmental factors, and their interactions. This study aimed to locate significant QTL (G) and environmental (E) factors controlling time-to-flower in the common bean, and to identify and measure G × E interactions. Phenotypic data were collected from a biparental [Andean × Mesoamerican] recombinant inbred population (F11:14, 188 genotypes) grown at five environmentally distinct sites. QTL analysis using a dense linkage map revealed 12 QTL, five of which showed significant interactions with the environment. Dissection of G × E interactions using a linear mixed-effect model revealed that temperature, solar radiation, and photoperiod play major roles in controlling common bean flowering time directly, and indirectly by modifying the effect of certain QTL. The model predicts flowering time across five sites with an adjusted r-square of 0.89 and root-mean square error of 2.52 d. The model provides the means to disentangle the environmental dependencies of complex traits, and presents an opportunity to identify in silico QTL allele combinations that could yield desired phenotypes under different climatic conditions.

Testing of Greenhouse Cladding Materials for Space Environments

Bioregenerative Life Support Systems in the form of transparent, inflatable greenhouses present an economical and reliable solution for providing consumables to astronauts on long duration space missions. With NASAs goal to place human explorers on Mars, identification of cladding materials with appropriate optical and physical properties that can withstand the high ultraviolet radiation, low pressure, and low temperature Martian environment is necessary for greenhouse design. The objective of this study was to develop methods for evaluating the effects of simulated Mars environmental conditions on the transmissivity and mechanical strength of candidate greenhouse cladding materials. The University of Floridas Mars Simulation Chamber was utilized to expose material samples to simulated Mars environmental conditions. Changes in control versus exposed material sample transmissivities were measured using a spectroradiometer over a range of wavelengths from 200 to 800 nm and material peak yield stresses were determined using an Instron universal testing machine. Results indicated that, under Mars simulated environmental conditions for 42 Mars equivalent days, materials experienced a reduction in transmission in the photosynthetically active region and a decrease in material strength. In short, the methods developed in this study provide a means for evaluating the transmissivity and strength of candidate greenhouse cladding materials under Mars environmental conditions for the determination of their suitability in greenhouse design.