Biology subjects

Kramer, D. M.

Publications and source records attributed to Kramer, D. M..

14 recordsLinked to original sources

bioRxiv2026

From Field Photosynthesis to Genetic Architecture: Insights from the First Dedicated Photosynthesis Hackathon

Photosynthesis is among the most consequential yet genetically complex traits in crop plants, and translating its natural variation into actionable genomic targets remains a central challenge for breeding climate-resilient varieties. To start addressing this, researchers are generating increasingly large, multi-environment field photosynthesis datasets. Yet, these data have been structurally under-analysed since their inception. Here we report the outcomes of the first dedicated hackathon focused on computational mining of such field data held in Accra, Ghana, in March 2026. Bringing together data scientists, plant physiologists, geneticists, and breeders from Europe and Africa, these interdisciplinary teams used photosynthetic data collected with hand-held fluorometers to genome-wide marker data across four crop species: cowpea (Vigna unguiculata), barley (Hordeum vulgare), common bean (Phaseolus vulgaris), and potato (Solanum tuberosum). Despite using different species and methods, independent teams identified the same three key findings. First, mechanism-informed feature engineering and dynamic modelling recover genetic signals that are not detected or discarded in standard analysis pipelines, resulting in traits with improved heritability and meaningful associations with yield. Secondly, machine learning methods proved effective at uncovering genetic associations, with temporally resolved features substantially outperforming single time-point measurements. Third, raw chlorophyll fluorescence and absorbance traces consistently contained more information and predictive power than the extracted parameters currently used. A defining feature of this event was having experimentalists and data scientists working together, enabling AI approaches to be grounded in domain knowledge and biological mechanisms rather than relying on data alone.

plant biology↗

bioRxiv2026

Natural genetic variation reveals divergent transcriptomic responses to hyperoxia in two Chlamydomonas reinhardtii ecotypes

Green algae must continuously balance resource availability to maintain photosynthetic performance. The O2:CO2 ratio is a key determinant of their metabolic mode. Under hyperoxia or low CO2, many algae induce a carbon concentrating mechanism (CCM). In the model green alga Chlamydomonas reinhardtii, the CCM relies on a pyrenoid, a specialized microcompartment that elevates CO2 around rubisco. While ambient CO2 acclimation is well-studied, responses to hyperoxia remain poorly understood, despite its frequent occurrence in nature under high light. Using controlled bioreactors, we exposed two diverse Chlamydomonas ecotypes, CC1009 and CC2343, to 95% oxygen to analyze time-dependent, genome-wide transcriptomic and phenotypic changes. Both ecotypes induced CCM genes, but they exhibited distinct molecular and physiological phenotypes. The tolerant ecotype (CC1009) successfully adapted, developing a functional CCM with a structured starch sheath. Conversely, the sensitive ecotype (CC2343) suffered growth arrest and formed malformed pyrenoids. Transcriptomics revealed that CC1009 initiated a rapid initial response, upregulating chloroplast proteostasis and downregulating nucleotide metabolism. CC2343 showed a massive, delayed transcriptional response, downregulating genes coding for photosystems and tetrapyrrole biosynthesis. This unbiased transcriptomic approach identifies key candidate genes driving algal acclimation to hyperoxic stress in natural, high-light environments.

genomics↗

bioRxiv2025

Control of Chloroplast Integrity by the Jasmonate Signaling Pathway is Linked to Growth-Defense Balance

Chloroplasts play a central role in plant responses to environmental stress. Little is known, however, about how chloroplast homeostasis is maintained during stress responses that place high metabolic and bioenergetic demands on the cell. As a chloroplast-derived retrograde signal, jasmonate (JA) promotes broad-spectrum immunity by triggering the degradation of JAZ transcriptional repressors that act in the nucleus to control chloroplast metabolism. Here, we manipulated JAZ abundance to investigate how chloroplast integrity and function is maintained at high levels of defense. A jaz decuple mutant (jazD) lacking 10 of 13 JAZs exhibited strong growth-defense antagonism without loss of photosynthetic efficiency. Treatment of jazD with the JA-receptor agonist coronatine triggered rapid loss of chlorophyll and the turnover of chloroplast proteins and lipids, leading to the collapse of photosynthetic activity and cell death. These findings were supported by global transcript and metabolite profiling over a time course of coronatine treatment. Genetic screens identified MYC2 and the JAZ-destabilizing F-box protein, COI1, as positive regulators of coronatine-induced chloroplast dismantling in jazD plants. These results demonstrate how the progressive loss of JAZ repression drives a continuum of MYC2-dependent growth-defense tradeoffs, including disassembly of the photosynthetic apparatus as a terminal response. In highlighting the critical role for JAZ proteins in maintaining chloroplast integrity at high levels of defense, our results provide insight into the general mechanism by which jasmonate governs chloroplast metabolism to balance growth and stress responses. One sentence summaryThis study shows that the jasmonate-mediated leaf transition from growth- to defense-oriented metabolism culminates in the disassembly of the photosynthetic apparatus.

plant biology↗

bioRxiv2024

From Quantitative Trait Loci towards Mechanisms: Linkage Integration Hypothesis Testing (LIgHT) Sheds Light on the Mechanisms of Genetically Modulated Stress Tolerance

The goal of this work is to assess the mechanistic bases of natural genetic variations in plant responses of photosynthesis to stress. To achieve this goal, we devised the Linkage Integration Hypothesis Testing (LIgHT) approach, comparing chromosomal locations of quantitative trait loci (QTL) for multiple phenotypes to distinguish between hypothetical mechanisms. As a use case, we explored genetic variations in photosynthesis-related processes under chilling stress in recombinant inbred lines of cowpea (Vigna unguiculata L. Walp.). We focused on photosynthesis-related parameters measurable in high throughput and indicative of proposed chilling responses, including the states of photosystems I (PSI) and II (PSII), photoprotective nonphotochemical quenching, PSII photodamage, and nyctinastic leaf movements (NLM). The patterns of QTL linkages indicated chilling stress tolerance is genetically controlled by avoiding PSII photodamage rather than PSI damage or NLM. This model was validated in a separate experiment measuring the rates of PSII photodamage and repair. Additional linkages suggest that chilling-induced damage to PSII is controlled by the thylakoid proton motive force and redox state of PSII. This regulation is modulated by thylakoid fatty acid composition, as suggested in Hoh et al., 2022. We propose the LIgHT approach can be broadly applied to test mechanisms underlying genetic variations. HighlightThis work Introduces the Linkage Integration Hypothesis Testing (LIgHT) approach for mechanistic studies of natural variations, identifying photosynthetic regulatory mechanisms underlying natural variations to abiotic stresses by applying this approach.

plant biology↗

bioRxiv2024

Species wide inventory of Arabidopsis thaliana organellar variation reveals ample phenotypic variation for photosynthetic performance

Efforts to improve photosynthetic performance are increasingly employing natural genetic variation. However, genetic variation in the organellar genomes (plasmotypes) is often disregarded due to the difficulty of studying the plasmotypes and the lack of evidence that this is a worthwhile investment. Here, we systematically phenotyped plasmotype diversity using Arabidopsis thaliana as a model species. A reanalysis of whole genome resequencing data of 1,531 representative accessions shows that the genetic diversity amongst the mitochondrial genomes is eight times lower than amongst the chloroplast genomes. Plasmotype diversity of the accessions divides the species into two major phylogenetic clusters, within which highly divergent subclusters are distinguished. We combined plasmotypes from 60 A. thaliana accessions with the nuclear genomes (nucleotypes) of four A. thaliana accessions to create a panel of 232 novel cytonuclear genotypes (cybrids). The cybrid plants were grown in a range of different light and temperature conditions and phenotyped using high-throughput phenotyping platforms. Analysis of the phenotypes showed that several plasmotypes alone or in interaction with the nucleotypes have significant effects on photosynthesis, and that the effects are highly dependent on the environment. Moreover, we introduce Plasmotype Association Studies (PAS) as a novel method to reveal plasmotypic effects. Within A. thaliana, several organellar variants can influence photosynthetic phenotypes, which emphasizes the valuable role this variation has on improving photosynthetic performance. The increasing feasibility of producing cybrids in various species calls for further research into how these phenotypes may support breeding goals in crop species. Significance statementPhotosynthesis is one of the few crop traits that has been largely unaddressed which can contribute to increasing crop yield potential. Exploiting genetic variation within organellar genomes presents a promising, yet untapped resource to improve photosynthesis. However, the extent of organellar variation and its impact on photosynthesis within a species remains largely unknown. Using Arabidopsis thaliana as a model species, we revealed highly divergent clusters of organellar variation. We constructed 232 novel combinations of species representative organellar and nuclear genomes, referred to as cybrids. High-throughput phenotyping of these cybrids revealed that organellar variants can substantially impact photosynthesis in different environments. These findings indicate that organellar genomes may be a valuable resource for improving photosynthesis in crops.

plant biology↗

bioRxiv2022

The NDH complex reveals a trade-off that constrains maximising photosynthesis in Arabidopsis thaliana

The Green Revolution has resulted in major improvements in crop productivity, but left photosynthesis largely unimproved. Despite ample variation of photosynthetic performance in crops and their wild relatives, the photosynthetic capacity of elite breeding lines remains well below its theoretical maximum. As yield is often the primary selective trait, current plant breeding approaches result in photosynthetic trade-offs that prevent positive selection for photosynthetic performance itself. Currently, genetic variation for photosynthetic performance is seldomly validated at the genetic level, and as a result these photosynthetic trade-offs remain poorly understood. Here we reveal the physiological nature of a photosynthetic trade-off caused by the NAD(P)H dehydrogenase (NDH) complex. The use of an Arabidopsis thaliana cybrid panel revealed how a natural allele of the chloroplastic gene NAD(P)H-QUINONE OXIDOREDUCTASE SUBUNIT 6 - a subunit of the NDH complex - results in a faster recovery of photosystem II efficiency after a transition from high to low irradiances. This improvement is due to a reduction in NDH activity. Under low-light conditions this reduction in NDH activity has a neutral effect on biomass, while under highly fluctuating light conditions, including high irradiances, more NDH activity is favoured. This shows that while allelic variation in one gene can have beneficial effects on one aspect of photosynthesis, it can, depending on environmental conditions, have negative effects on other aspects of photosynthesis. As environmental conditions are hardly ever stable in agricultural systems, understanding photosynthetic trade-offs allows us to explore shifting photosynthetic performance closer to the theoretical maximum.

plant biology↗

bioRxiv2022

Plethora of QTLs found in Arabidopsis thaliana reveals complexity of genetic variation for photosynthesis in dynamic light conditions

The environments in which plant species evolved are now generally understood to be dynamic rather than static. Photosynthesis has to operate within these dynamic environments, such as sudden changes to light intensities. Plants have evolved photoprotection mechanisms that prevent damage caused by sudden changes to high light intensities. The extent of genetic variation within plants species to deal with these dynamic light conditions remains largely unexplored. Here we show that one accession of A. thaliana has a more efficient photoprotection mechanism in dynamic light conditions, compared to six other accessions. The construction of a doubled haploid population and subsequent phenotyping in a dynamically controlled high-throughput system reveals up to 15 QTLs for photoprotection. Identifying the causal gene underlying one of the major QTLs shows that an allelic variant of cpFtsY results in more efficient photoprotection under high and fluctuating light intensities. Further analyses reveal this allelic variant to be overprotecting, reducing biomass in a range of dynamic environmental conditions. This suggests that within nature, adaptation can occur to more stressful environments and that revealing the causal genes and mechanisms can help improve the general understanding of photosynthetic functioning. The other QTLs possess different photosynthetic properties, and thus together they show how there is ample intraspecific genetic variation for photosynthetic functioning in dynamic environments. With photosynthesis being one of the last unimproved components of crop yield, this amount of genetic variation for photosynthesis forms excellent input for breeding approaches. In these breeding approaches, the interactions with the environmental conditions should however be precisely assessed. Doing so correctly, allows us to tap into natures solution to challenging environmental conditions.

plant biology↗

bioRxiv2022

The dynamics of non-photochemical quenching and cyclic electron transport in A.thaliana exposed to harmonically oscillating light

In natural environments, plants are exposed to rapidly changing light. Maintaining photosynthetic efficiency while avoiding photodamage requires equally rapid regulation of photoprotective mechanisms. We asked what the operation frequency range of regulation is in which plants can efficiently respond to varying light. Chlorophyll fluorescence, P700, plastocyanin, and ferredoxin responses of wild-type Arabidopsis thaliana were measured in oscillating light of various frequencies. We also investigated the npq1 mutant lacking violaxanthin de-epoxidase, the npq4 mutant lacking PsbS-protein, and the mutants crr2-2, and pgrl1ab impaired in different pathways of the cyclic electron transport. The fastest was the PsbS-regulation responding to oscillation periods longer than 10s. Processes involving violaxanthin de-epoxidase dampened changes of chlorophyll fluorescence in oscillation periods of 2min or longer. Knocking out the PGRL1-PGR5 pathway strongly reduced variations of all monitored parameters, probably due to congestion in the electron transport. Incapacitating the NDH-like pathway only slightly changed the photosynthetic dynamics. Our observations are consistent with the assumption that non-photochemical quenching in slow light oscillations involves violaxanthin de-epoxidase to produce, presumably, a stationary, non-oscillating level of zeaxanthin. We interpret the observed dynamics of Photosystem I components as being formed in slow light oscillations partially by thylakoid remodeling that modulates the redox rates.

plant biology↗

bioRxiv2021

Light Potentials of Photosynthetic Energy Storage in the Field: What limits the ability to use or dissipate rapidly increased light energy?

The responses of plant photosynthesis to rapid fluctuations in environmental conditions are thought to be critical for efficient capture of light energy. Such responses are not well represented under laboratory conditions, but have also been difficult to probe in complex field environments. We demonstrate an open science approach to this problem that combines multifaceted measurements of photosynthesis and environmental conditions, and an unsupervised statistical clustering approach. In a selected set of data on mint (Mentha sp.), we show that the "light potential" for increasing linear electron flow (LEF) and nonphotochemical quenching (NPQ) upon rapid light increases are strongly suppressed in leaves previously exposed to low ambient PAR or low leaf temperatures, factors that can act both independently and cooperatively. Further analyses allowed us to test specific mechanisms. With decreasing leaf temperature or PAR, limitations to photosynthesis during high light fluctuations shifted from rapidly-induced NPQ to photosynthetic control (PCON) of electron flow at the cytochrome b6f complex. At low temperatures, high light induced lumen acidification, but did not induce NPQ, leading to accumulation of reduced electron transfer intermediates, a situation likely to induce photodamage, and represents a potential target for improving the efficiency and robustness of photosynthesis. Finally, we discuss the implications of the approach for open science efforts to understand and improve crop productivity.

plant biology↗

bioRxiv2021

The Induction of Pyrenoid Synthesis by Hyperoxia and its Implications for the Natural Diversity of Photosynthetic Responses in Chlamydomonas

In algae, it is well established that the pyrenoid, a component of the carbon-concentrating mechanism (CCM), is essential for efficient photosynthesis at low CO2. However, the signal that triggers the formation of the pyrenoid has remained elusive. Here, we show that, in Chlamydomonas reinhardtii, the pyrenoid is strongly induced by hyperoxia, even at high CO2 or bicarbonate levels. These results suggest that the pyrenoid can be induced by a common product of photosynthesis specific to low CO2 or hyperoxia. Consistent with this view, the photorespiratory by-product, H2O2, induced the pyrenoid, suggesting that it acts as a signal. Finally, we show evidence for linkages between genetic variations in hyperoxia tolerance, H2O2 signaling, and pyrenoid morphologies.

plant biology↗

bioRxiv2020

Inactivation of mitochondrial Complex I stimulates chloroplast ATPase in Physcomitrella (Physcomitrium patens).

While light is the ultimate source of energy for photosynthetic organisms, mitochondrial respiration is still fundamental for supporting metabolism demand during the night or in heterotrophic tissues. Respiration is also important for the metabolism of photosynthetically active cells, acting as a sink for excess reduced molecules and source of substrates for anabolic pathways. In this work, we isolated Physcomitrella (Physcomitrium patens) plants with altered respiration by inactivating Complex I of the mitochondrial electron transport chain by independent targeting of two essential subunits. Results show that the inactivation of Complex I causes a strong growth impairment even in fully autotrophic conditions in tissues where all cells are photosynthetically active. Complex I mutants show major alterations in the stoichiometry of respiratory complexes while the composition of photosynthetic apparatus was substantially unaffected. Complex I mutants showed altered photosynthesis with higher yields of both Photosystems I and II. These are the consequence of a higher chloroplast ATPase activity that also caused a smaller {Delta}pH formation across thylakoid membranes as well as decreased photosynthetic control on cytochrome b6f, possibly to compensate for a deficit in ATP supply relative to demand in Complex I mutants. These results demonstrate that alteration of respiratory activity directly impacts photosynthesis in P. patens and that metabolic interaction between organelles is essential in their ability to use light energy for growth.

plant biology↗

bioRxiv2018

Reciprocal cybrids reveal how organellar genomes affect plant phenotypes

Assessing the impact of variation in chloroplast and mitochondrial DNA (collectively termed the plasmotype) on plant phenotypes is challenging due to the difficulty in separating their effect from nuclear derived variation (the nucleotype). Haploid inducer lines can be used as efficient plasmotype donors to generate new plasmotype-nucleotype combinations (cybrids)(Ravi et al., 2014). We generated a panel comprising all possible cybrids of seven Arabidopsis thaliana accessions and extensively phenotyped these lines for 1859 phenotypes under stable and fluctuating conditions. We show that natural variation in the plasmotype results in additive as well as epistatic effects across all phenotypic categories. Plasmotypes which induce more additive phenotypic changes also cause more significant epistatic effects, suggesting a possible common basis for both additive and epistatic effects. On average epistatic interactions explained twice as much of the variance in phenotypes as additive plasmotype effects. The impact of plasmotypic variation was also more pronounced under fluctuating and stressful environmental conditions. Thus, the phenotypic impact of variation in plasmotypes is the outcome of multilevel Nucleotype X Plasmotype X Environment interactions and, as such, the plasmotype is likely to serve as a reservoir of variation which is only exposed under certain conditions. The production of cybrids using haploid inducers is a quick and precise method for assessing the phenotypic effects of natural variation in organellar genomes. It will facilitate efficient screening of unique nucleotype-plasmotype combinations to both improve our understanding of natural variation in nucleotype plasmotype interactions and identify favourable combinations to improve plant performance.

genetics↗

bioRxiv2018

OLIVER: A Tool for Visual Data Analysis on Longitudinal Plant Phenomics Data

There is a critical unmet need for new tools to analyze and understand \"big data\" in the biological sciences where breakthroughs come from connecting massive genomics data with complex phenomics data. By integrating instant data visualization and statistical hypothesis testing, we have developed a new tool called OLIVER for phenomics visual data analysis with a unique function that any user adjustment will trigger real-time display updates for any affected elements in the workspace. By visualizing and analyzing omics data with OLIVER, biomedical researchers can quickly generate hypotheses and then test their thoughts within the same tool, leading to efficient knowledge discovery from complex, multi-dimensional biological data. The practice of OLIVER on multiple plant phenotyping experiments has shown that OLIVER can facilitate scientific discoveries. In the use case of OLIVER for large-scale plant phenotyping, a quick visualization identified emergent phenotypes that are highly transient and heterogeneous. The unique circular heat map with false-color plant images also indicates that such emergent phenotypes appear in different leaves under different conditions, suggesting that such previously unseen processes are critical for plant responses to dynamic environments.

bioinformatics↗

bioRxiv2018

Loss of Peroxisomal Hydroxypyruvate Reductase Inhibits Triose Phosphate Isomerase but Stimulates Cyclic Photosynthetic Electron Flow and the Glc-6P-Phosphate Shunt

The oxygenation of ribulose 1,5-bisphosphate by Rubisco is the first step in photorespiration and reduces the efficiency of photosynthesis in C3 plants. Our recent data indicates that mutants in photorespiration have increased rates of photosynthetic cyclic electron flow around photosystem I. We investigated mutant lines lacking peroxisomal hydroxypyruvate reductase to determine if there are connections between 2-PG accumulation and cyclic electron flow. We found that 2-PG is a competitive inhibitor of triose phosphate isomerase (TPI), an enzyme in the Calvin-Benson cycle that converts glyceraldehyde 3-phosphate to dihydroxyacetone phosphate. This block in metabolism could be overcome if glyceraldehyde 3-phosphate is exported to the cytosol where the cytosolic triose phosphate isomerase could convert it to dihydroxyacetone phosphate. We found evidence that carbon is reimported as Glc-6P-phosphate forming a cytosolic bypass around the block of stromal TPI. However, this also stimulates a Glc-6P-phosphate shunt, which consumes ATP, which can be compensated by higher rates of cyclic electron flow.\n\nOnce Sentence SummaryTriose phosphate isomerase is inhibited in plants lacking hydroxypyruvate reductase 1 and this is overcome by exporting triose phosphate to the cytosol and importing Glc-6P, which stimulates a Glc-6P-phosphate shunt and cyclic electron flow.

plant biology↗