Biology subjects

Danila, F. R.

Publications and source records attributed to Danila, F. R..

4 recordsLinked to original sources

bioRxiv2026

C4 photosynthetic pathway fluxes in transgenic rice plants

Most land plants photosynthesize using the C3 pathway, in which ribulose bisphosphate carboxylase/oxygenase (Rubisco) fixes CO2 into 3-carbon acids. The C4 pathway, a biochemical CO2-concentrating mechanism that operates in the context of specialized leaf anatomy to concentrate CO2 around Rubisco, is more efficient. Introduction of the C4 pathway into the C3 crop rice could increase yield by 50%. Expression of five C4 enzymes in transgenic rice previously led to flux through the first step. However, there was no evidence for flux later in the cycle. Here we developed new transgenic rice lines and novel protocols to detect C4 cycle activity: CO2 fixation into C4 acids by carboxylation of a C3 compound, decarboxylation, refixation of CO2 by Rubisco, and regeneration of the C3 donor. We demonstrate that these four core C4 reactions are operating in rice, establishing the in vivo flux framework needed to progress towards a functional carbon-concentrating mechanism

plant biology↗

bioRxiv2025

A conserved stripe rust effector elicits variable resistance responses in wheat

Plant resistance (R) and pathogen avirulence (Avr) gene interactions are central to pathogen recognition and disease resistance in crops. Functional characterisation of recognised Avr effectors of Puccinia striiformis f. sp. tritici (Pst) lags other key fungal pathogens of wheat. Here, we used a wheat protoplast-based screen to identify Avr/R interactions via the proxy of effector-induced defence responses in a set of diverse wheat cultivars. We identified an Avr candidate, termed AvrPstB48, that triggers defence responses in 16 out of 24 cultivars tested. AvrPstB48 is hemizygous, and the Pst genome carries four divergent paralogs within a gene cluster. Analysis of these paralogs revealed partial redundancy in their ability to activate wheat defences and enabled us to identify a single amino acid in AvrPstB48 that is necessary but not sufficient for defence activation. Notably, the activation of defence signalling by AvrPstB48 in protoplasts did not directly correlate with disease outcomes. Whole-plant infection assays revealed that some cultivars which exhibited strong defence activation in the protoplast assay are susceptible to the Pst isolate Pst104E137A- from which AvrPstB48 is derived. Comparison of infection dynamics of two wheat cultivars that differ in their AvrPstB48 recognition capacity revealed a delay in disease progression in the recognising cultivar Avocet S compared to the non-recognising cultivar Morocco. While correlative only, our observations, combined with other recent reports, support a recognize-then-suppress model of plant-pathogen interaction where disease outcomes are driven not only by simple Avr/R interactions but also by pathogen effectors that suppress defence signalling downstream of effector recognition.

plant biology↗

bioRxiv2024

Automated and high throughput measurement of leaf stomatal traits in canola

BackgroundAutomating stomatal trait measurement has gained popularity because of their inherent importance for field phenotyping application as stomata are critical for both carbon capture and water use efficiency in plants. Such tool has been reported for rice, wheat, tomato, barley and oil palm. However, none exist yet for canola, which is an important economic and agronomic crop globally. ResultsWe developed a new toolkit called Stomatal Comprehensive Automated Neural Network or SCAN by combining the use of high-resolution portable digital microscopy with machine learning based on You Only Look Once algorithm (YOLOv8). Digital micrographs of leaf surfaces enter the SCAN pipeline, which includes stomata detection, stomata segmentation and stomatal pore segmentation models, to measure stomatal density, stomatal size and stomatal pore area, respectively. In addition to SCANs ability to measure leaf stomatal traits in canola at 89 to 94% accuracy, we also showed that SCAN can be used to predict stomatal density even in species not included in the training set such as Arabidopsis, tobacco, rice, wheat, maize and proso millet. SCAN was designed for the biological science community with the premise that users are not required to possess advanced programming capabilities to manage dependency prerequisites, execute the models, and integrate the analysis. This was achieved by packaging the models into a desktop application system that can be accessed offline. ConclusionOverall, SCAN provides a non-destructive, real-time, portable, and high-throughput measurement of leaf stomatal traits in canola. The minimised hardware requirement and user-friendly desktop application system make SCAN suitable for field phenotyping application.

plant biology↗

bioRxiv2020

A role for neutral variation in the evolution of C4 photosynthesis

Convergent trait evolution is a recurrent phenomenon in all domains of the tree of life. While some convergent traits are caused by simple sequence changes, many are associated with extensive changes to the sequence and regulation of large cohorts of genes. It is unknown how organisms traverse this expansive genotype space to assemble such complex convergent phenotypes. C4 photosynthesis is a paradigm of large-scale phenotypic convergence. Conceptual and mathematical models propose that C4 photosynthesis evolved from ancestral C3 photosynthesis through sequential adaptive changes. These adaptive changes could have been rapidly assembled if modifications to the activity and abundance of enzymes of the C4 cycle was neutral in C3 plants. This neutrality would enable populations of C3 plants to maintain genotypes with expression levels of C4 enzymes analogous to those in C4 species and thus enable rapid assembly of a functional C4 cycle from naturally occurring genotypes given shared environmental selection. Here we show that there is substantial natural variation in expression of genes encoding C4 cycle enzymes between natural accessions of the C3 plant Arabidopsis thaliana. We further show through targeted transgenic experiments in the C3 crop Oryza sativa, that high expression of the majority of C4 cycle enzymes in rice is neutral with respect to growth, development, biomass and photosynthesis. Thus, substantial variation in the abundance and activity of C4 cycle enzymes is permissible within the limits of operation of C3 photosynthesis and the emergence of component parts of this complex convergent trait can be facilitated by neutral variation.

plant biology↗