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Plant Molecular Biology

Section for Plant Molecular Biology

Plant Molecular Biology

The section's activities focus on genetic, molecular and biochemical research in the model plant Lotus japonicus, as well as several crop plants.

The research seeks to elucidate and understand the mechanisms behind genetic control of signal transduction, cell differentiation, developmental processes, local adaptation, and plant-microbe interactions. Key research areas include symbiotic nitrogen fixation, plant perception of microbial signalling molecules, susceptibility to pathogens, and colonisation by symbiotic and endophytic bacteria/fungi.

The section has state-of-the-art facilities for plant cultivation in Aarhus and Påskehøjgaard, including tissue culture rooms, climate chambers and greenhouses. In addition to general competencies in genetics, genomics, molecular biology, biochemistry and structural biology,  the group has specialized knowledge in various types of microscopy, applied bioinformatics and genome sequencing.

The section has also built up a population of retrotransposon mutants in Lotus japonicus. The population of more than 130,000 plant lines is available as a resource (Lotus Base) for determining the function of genes using reverse genetics.

The section consists of groups investigating:

Research activities within the section are currently funded by grants from the Novo Nordisk Foundation, the European Research Council, Innovation Fund Denmark, the European Union, and the Independent Research Fund Denmark. In addition, the group participates in a project that is currently supported through a grant to the University of Cambridge by the Bill and Melinda Gates Foundation and the UK government’s Department for International Development (DFID).

Current projects in the Plant Molecular Biology section

InRoot: Molecular Mechanisms and Dynamics of Plant-Microbe Interactions at the Root-Soil Interface

Recent research on plants and their naturally associated microorganisms has laid the groundwork to look into new perspectives and concepts for understanding plant function, performance and growth under limited input conditions. These new perspectives will help to reduce the environmental footprint and have the potential to define breeding targets and develop applications through microbial interventions. InRoot links plant and bacterial genetics, protein chemistry, analytical chemistry and plant physiology with bacterial and plant population biodiversity studies and advanced modeling.

The overarching aim of InRoot is to establish knowledge and tools for the evidence-based development of new resilient crops and associated microbial interventions that will improve productivity, reduce the need for fertilizers and pesticides, and alleviate negative environmental impacts accompanying food production. In order to do this InRoot looks at both the plant and bacterial contributions to crop resiliency. InRoot is organized around six research area that combine the expertise available at the PM section to investigate the natural diversity, host controlled rhizosphere and endosphere interactions, root responses, plant physiology and advanced modeling in a tightly interconnected and iterative workflow.

The InRoot provides funding to all PIs at PM section for the period 2019-2025, and is supported by the Novo Nordisk Foundation as part of Novo Nordisk’s wider ‘Collaborative Crop Resilience Program’ (CCRP).

For more information about this project, see inroot.au.dk or contact Jens Stougaard (stougaard@mbg.au.dk).

RINFEC: The Roots of Infection

RINFEC aims to identify and characterize the plant and bacterial genes responsible for interactions between plant roots and soil bacteria. The hypothesis behind the project is that the intercellular infection mechanism used by symbiotic rhizobia is an evolutionary development of a mechanism(s) that already exists to regulate plant root interaction with endophytic bacteria living within plant roots. By characterizing this unexplored intercellular mode of infection in Lotus japonicus, we hope to uncover both the plant and bacterial genetics involved as well as the biochemical processor that controls these mechanisms.

RINFEC will exploit Lotus’ capacity to support either intercellular entry (conserved mode) or legume specific infection thread entry, dependent on the rhizobia encountered. This allows comparative investigations of these two infection modes in simple binary interactions with the same host. Given the exceptional ability of different rhizobia for intercellular endophytic colonization of non-legume roots this provides an unprecedented platform to identify mechanisms by which plants selectively enable a subset of bacteria to infect roots. RINFEC will pioneer novel plant and bacterial genetic methods, cell-layer transcriptomics, phospho-proteomics and advanced biochemistry to break new ground in understanding infection and soil microbe influences on plant performance under environmental stress conditions.

The RINFEC project is funded by an ERC Advanced Grant from the European Research Council and runs for 5 years, 2019-2024.

For more information about this project, please contact Jens Stougaard (stougaard@mbg.au.dk).

Enhancing nitrogen fixation of Rhizobium-legume symbiosis for sustainable agricultural production

Food security is one of the most complex challenges facing humanity. So far, the boost in crop production has been achieved mostly by the increased use of inorganic fertilizers, in particular nitrogen. Nowadays sustainable production is a central theme for agriculture and legumes are extremely instrumental for this. Legume plants form symbiotic interactions with soil nitrogen-fixing microbes called rhizobia, able to directly absorb atmospheric nitrogen. Legumes accommodate rhizobia in special organs, the root nodules, provide bacteria with carbon and receive fixed nitrogen in return. Although, root nodule symbiosis is one of the most productive nitrogen-fixing systems its efficiency can be highly variable. Driven by the question "What restricts its efficiency?" we aim to discover and characterise molecular mechanisms negatively regulating symbiotic nitrogen fixation. Hypothetically these mechanisms could be evolutionarily co-opted from plant immunity with new and specific roles in limiting nitrogen fixation. It means that genetic regulators of symbiosis efficiency can be identified by comparative phylogenetics and subsequently be removed using gene-editing technologies to enhance symbiotic performance in legume crops.

This project provides funding to Aleksandr Gavrin and is funded by the Novo Nordisk Foundation, 2022-2027.

For more information about this project, please contact Aleksandr Gavrin (agav@mbg.au.dk).

ENSA: Enabling Nutrient Symbioses in Agriculture

The ENSA project involves ten international partners. Originally titled "Engineering Nitrogen Symbiosis for Africa", the project aimed to use naturally occurring biological nitrogen fixation to provide nitrogen to crop plants in small-holder farms in sub-Saharan Africa. The first phase of ENSA focused on the early recognition steps that allow rhizobial perception. In the second phase, the project focused its efforts on engineering nodule organogenesis in cereals and establishing a framework of understanding to tackle the challenge of engineering bacterial infection. In 2022, ENSA successfully replicated the nutrient-acquiring process that naturally occurs in some plants, a crucial step in the eventual goal of reducing or eliminating the need for expensive inorganic fertilisers. Now in its third phase, ENSA has expanded and adopted the new title "Enabling Nutrient Symbioses in Agriculture" and will expand its focus on the acquisition of nutrients beyond nitrogen through symbiotic relationships with mycorrhizal fungi. Africa still remains the highest priority for ENSA, but the project aims to benefit agriculture more widely.

Within the ENSA project, members of Plant Molecular Biology section mainly work on: auxin, cytokinin and cell cycle regulation and organogenesis; LCO perception, signal transduction and rhizobial interactions; and genetics of infection and organogenesis. 

The ENSA project provides funding to Simona Radutoiu, Kasper R. Andersen, Stig Uggerhøj Andersen, and Jens Stouggard and is currently supported through a grant to the University of Cambridge by the Bill & Melinda Gates Foundation and UK government's Department for International Development (DFID).

For further details see ensa.ac.uk or contact Jens Stougaard (stougaard@mbg.au.dk)

Nanobody-driven signal modulation of symbiotic plants LysM receptors

This project provides funding to Kasper R. Andersen and is funded by the Independent Research Fund Denmark | Nature and Universe. 2019 – 2023.

For more information about this project, please contact Kasper Røjkjær Andersen (kra@mbg.au.dk).

Identifying functional determinants of specificity in receptor kinases signaling

In this project we use a structural approach in combination with phylogenetics of key plant lineages to predict and model candidates for immunity or symbiosis determinants of specificity (DoS) in CERK6 and NFR1 protein kinases. Their predicted function will be tested and outlined biochemically and in vivo in genetically characterized plant backgrounds. This strategy will enable us to decouple immunity and symbiosis at the molecular level and gain a mechanistic understanding of how similar kinases drive opposing pathways in the same cell leading to specific whole plant responses.

This project provides funding to Simona Radutoiu and Kasper R. Andersen and is funded by the Novo Nordisk Fonden, 2019 – 2022.

For more information about this project please contact Simona Radutoiu (radutoiu@mbg.au.dk) or Kasper Røjkjær Andersen (kra@mbg.au.dk)

Carbohydrate signalling during plant root microbiota establishment

Intensive agricultural systems can secure the necessary crop yields for food supply of a growing human population. However, they rely heavily on resources that have negative impacts on ecosystems. Research and exploitation of biologicals emerged as a sustainable alternative, but this approach is currently less efficient and therefore needs to be revisited and suitable alternatives identified. The current study combines genetics, metagenomics and (meta)transcriptomics strategies across two legumes and two cereal crops to determine the role of exopolysaccharide signaling for plant colonization by endophytic members of Burkholderiales and Rhizobiales. This is used as a genetic framework to identify bacterial pathways associated with recognition of bacterial exopolysaccharides. Together this will establish a toolbox for accessing the compatibility of soil microbes and evaluate microbial communities prior to their development as biologicals with beneficial effects on plant hosts.

This project provides funding to Simona Radutoiu and Simon Kelly and is funded by the Independent Research Fund Denmark | Nature and Universe. 2019 – 2022.

For more information about this project please contact Simona Radutoiu (radutoiu@mbg.au.dk)

Cryo-EM investigation of LysM receptors and calcium decoders governing plant-microbe interactions

Plants and microbes interact and form symbioses that benefit both organisms. Examples of this are nitrogen fixation by legume-bacteria symbiosis, phosphate supply by plant–fungi symbiosis and plant disease resilience facilitated by commensal bacteria. To ensure specific communication between microbes and plants, both a perception system and a decoding system have evolved to ensure that beneficial microbes can interact and colonize the plant while harmful microbes are denied access. This project seeks to understand in molecular detail how plants interpret microbes using receptors and calcium signal decoders. We will use a combination of protein biochemistry, biophysics and structural biology to understand the molecular mechanism of plant–microbe communications at atomic resolution. This knowledge will help guide our efforts to engineer plants to be less dependent on chemical fertilisers and pesticides but obtain these benefits from microbial associations instead.

This project is funded by the Carlsberg Foundation, 2021-2024.

For more information, contact Kasper Røjkjær Andersen (kra@mbg.au.dk).

IMFABA: Local and sustainable protein production with improved faba beans

Faba beans are widely adapted to different climates, but yield especially well under moist temperate conditions. In Denmark, they can play a major role in substituting for soy imports and there is strong interest from both farmers and grain merchants. IMFABA will realise the great potential of faba beans by improving yield stability and protein properties, taking advantage of the expertise and resources developed during the NORFAB project. Drought and heat stress greatly affect yield stability. Leaf stomatal density and canopy temperature will be screened in the NORFAB germplasm to identify genotypes with contrasting drought responses. Their stomatal conductance will be measured and the active root zone will be monitored using moisture sensors to identify mechanisms underlying drought tolerance. Protein content, amino acid composition and protein digestibility are major targets for improvement in order to match soybean-based feed. Seed protein content, storage protein diversity and feed value will be screened to develop markers and enable breeding crosses that lead to increased protein and methionine content, without compromising yield or seed size. In NORFAB, breeding efforts were initiated and inbred breeding lines were generated. IMFABA takes an important next step by selecting breeding lines for new synthetic varieties based on drought resistance and protein properties, while also providing a basis for continued improvement of these traits in future breeding programs.

This project provides funding to Stig Uggerhøj Andersen from the Green Development and Demonstration Programme (GUDP) 2021–2025.

For more information, please email Stig Uggerhøj Andersen (sua@mbg.au.dk).

SCARI: Single cell analysis of root hair infection

Rhizobia infect legume roots and induce formation of nitrogen fixing root nodules. Infection occurs through infection threads formed in root hairs in the outermost root cell layer, the epidermis. Plant genes responsive to rhizobium inoculation have been identified in transcriptomic studies, but specific data on the infection process are lacking, because the studies were based on mixed cell populations comprising only a small fraction of infected cells. SCARI will use rapid root epidermis protoplasting and microfluidics-based single-cell sequencing to specifically identify the transcriptional profiles of root hair cells where infection threads are forming. Combining this approach with natural variation in legume-rhizobium compatibility will provide an unprecedented high-resolution view of the transcriptional events required for infection and establish a new basis for understanding how the plant decides whether or not to allow infection to proceed at the individual cell level.

This project is funded by Danmarks Fri Forskningsfond / Independent Research Fund Denmark 2021–2024.

For more information about this project, contact Stig Uggerhøj Andersen (sua@mbg.au.dk).

FabuLOX: A Genomics-Driven Approach to Improving Faba Bean Food and Processing Utility through Reduced Lipoxygenase (LOX) Activity

We will address a key limit to food use of faba bean – lipid oxidation that generates unpalatable “beany” flavors – by targeting the key enzyme responsible, lipoxygenase (LOX). LOX catalyzes fatty acid oxidation to volatiles, especially in wet processes such as protein isolation and dough making. We will annotate the genes in the new faba bean genome sequence and, combined with gene expression data, identify the key LOX for knockout. Data generated from genome annotation will provide a basis for attacking other important goals in faba bean improvement, including disease resistance, abiotic stress tolerance, and interactions with nitrogen fixing rhizobia. Through our Nordic (NORFAB) and European (Suscrop PROFABA) networks, pre-competitive sharing of the genomic information we generate, applied to a common set of diverse faba bean lines, will ensure that Nordic and European breeders can address the key challenges faced by local growers to increase faba competitiveness to generate a more balanced and protein-self-sufficient agricultural system that takes full advantage of biological nitrogen fixation.

This project is funded by the Novo Nordisk Foundation 2021–2023.

For more information on this project, contact Stig Uggerhøj Andersen (sua@mbg.au.dk).

ZEN: Zero-vicine faba beans

Faba bean is a promising protein crop but accumulates large amounts of vicine and convince in seeds. These antinutrients can induce favism in ~4% of the world’s population afflicted by glucose-6-phosphate dehydrogenase deficiency. Faba bean varieties with reduced content of vicine and convicine are available, but the residual antinutrient content is cause for concern in the food industry. Our earlier work indicates that vicine and convicine are synthesized from overflow metabolites in the riboflavin (vitamin B2) biosynthetic pathway and that the degree of overflow is controlled by the GTP cyclohydrolase VC1. We predict that elimination of one or two enzymes in addition to VC1 will cause the riboflavin pathway to revert to its normal configuration, resulting in zero-vicine faba beans. ZEN will thereby eliminate a major obstacle for the use of locally and sustainably produced protein in the booming plant-based food industry.

This project is funded by Danmarks Fri Forskningsfond / Independent Research Fund Denmark 2022–2026.

For more information about this project, contact Stig Uggerhøj Andersen (sua@mbg.au.dk).

Root2Res: Root phenotyping and genetic improvement for rotational crops resilient to environmental change

As agricultural systems face more and more constraints due to climate change, identifying and developing new crop cultivars able to make production more resilient is a priority. In this context, root systems play a major role as an essential component of the tolerance against abiotic stress (water deficit or excess, nutrition deficiency) and for their contribution to carbon storage in soils. Addressing root traits for breeders, geneticists and agronomists is a real challenge that needs efficient tools: root phenotyping tools both in field and controlled conditions, genetic tools with a set of relevant markers and genetic resources and modelling tools to extrapolate the results in other environments and agricultural contexts.

This project is funded by the European Union (Grant no. 101060124) 2022–2027.

For more information, please see Root2Res or contact Stig Uggerhøj Andersen (sua@mbg.au.dk).

Customized biofertilizers for enhanced yield and earnings in high-protein crops

Current commercial rhizobia biofertilizers contain generic bacteria and perform erratically in different soil conditions. The aim of this project is to create a new generation of rhizobial biofertilizers by designing a solution that offers an optimal i) crop ii) soil and iii) biofertilizer match. Our approach consists of a unique rhizobial soil test followed by high-throughput identification of elite rhizobia in the legume of interest. The rhizobial formulation can be produced as a valuable product because it is a precise, predictable, and efficient biofertilizer.

This project is funded by Innovations Fund Denmark and VILLUM FONDEN 2023–2024.

For more information, contact Marcela Mendoza-Suárez (marcela@mbg.au.dk).


The agricultural impact on climate change can be mitigated by developing local sources of protein. The cultivation of important protein crops in Denmark is limited by dry periods; broad bean (hestebønne) and white clover are especially susceptible to drought. Red clover is another protein crop, but its low protein quality offers a further challenge.

The project’s objective is to reduce the agricultural carbon footprint by achieving a high and stable production of protein in Denmark with crops that are high in protein quality, low in environmental footprint, and are suitable to a climate with periods of drought. Research will identify differences in root development and drought tolerance of different types of broad bean and clovers. The results will be used directly by Danish breeders to choose crossing-parents for development of more robust types. Moreover, we will conduct protein quality analyses of the different red clover genotypes, which can be used to develop new varieties. We will also develop genetic markers for breeding by screening for genes related to differences in protein quality and root development.

The project also directly affects climate impact. By producing a higher yield and more local sources of protein, we can expect to reduce emissions by 83,000 tonnes of CO2 per year. Furthermore, we expect the project to increase the amount of land devoted to protein crops, which will further reduce emissions by 160–260,000 tonnes of CO2 per year.

This project is funded by Promilleafgiftsfonden for Landbrug and coordinated by SEGES. Partners are Aarhus University, University of Copenhagen, Sejet Plant Breeding, Nordic Seed and DLF.

For more information, contact Stig Uggerhøj Andersen (sua@mbg.au.dk).

Group leaders


Associate Professors

Assistant Professor


Stig Uggerhøj Andersen

Professor Department of Molecular Biology and Genetics - Plant Molecular Biology

Simona Radutoiu

Professor Department of Molecular Biology and Genetics - Plant Molecular Biology

Jens Stougaard

Head of Department ad interim, Professor Department of Molecular Biology and Genetics - Plant Molecular Biology

Associate Professor

Kasper Røjkjær Andersen

Associate Professor Department of Molecular Biology and Genetics - Plant Molecular Biology

Assistant Professor

Aleksandr Gavrin

Assistant Professor Department of Molecular Biology and Genetics - Plant Molecular Biology

Peer-reviewed publications

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