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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).

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).

NORFAB: NORthern FABa

NORFAB (NORthern FABa) is a consortium of Northern hemisphere groups with key expertise in Faba beans who aim to develop sophisticated genomics-based plant breeding methods and provide access to germplasm with the relevant genetic diversity. NORFAB aims to improve the yield and quality of faba bean seeds in order to make them a competitive protein crop in northern European and Canadian/US northern prairie conditions. Research on Faba bean genomics and genetics will be developed using new genotyping and phenotyping methodologies and new hybrid approaches combining genomic selection with QTL mapping and gene introgression. The methods for genomics-based breeding will be developed by the university partners and implemented by the industry partners involved in the project. The approach will target multigene control of seed quality, content of protein, fiber and antinutritional factors along with agronomical traits.

The NORFAB project provides funding to Stig U. Andersen and Jens Stougaard through an  Innovation Fund Denmark Grand Solutions grant, 2016-2021.

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

ENSA: Engineering Nitrogen Symbiosis for Africa

The ENSA project involves ten international partners and aims 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. Now in the second phase, the project is focusing its efforts on engineering nodule organogenesis in cereals and establishing a framework of understanding to tackle the challenge of engineering bacterial infection. 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, Dugald Reid, Kasper R. Andersen, Simon Kelly 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)

NCHAIN: Forging stronger links in the organic nitrogen chain.

In agriculture, nitrogen (N) is an important macronutrient critical for plant yield. Without access to synthetic N fertilizers, many Danish organic farmers face a severe challenge in providing sufficient amounts of nitrogen for optimal crop yield. The main N contribution often comes from clover/grass swards, which both generate feed for livestock and provide N fertilization and soil improvement for successive crops in a crop rotation scheme. The N chain in this production system has four main links: 1) Symbiotic N2 fixation by rhizobia; 2) Transfer of fixed N to legume hosts (clover); 3) Transfer of fixed N to other plant species (grasses); 4) Transfer of plant N to cattle. Overall, the efficiency depends heavily on interspecies interactions between rhizobium/clover and clover/grass. The state of the art is to assume that rhizobia already present in the soil provide effective nitrogen fixation with all clover varieties: essentially, that genetic variation between rhizobia is insignificant or that optimal rhizobia for all clover varieties are present in all soils. In terms of plant interactions, it is assumed that the performance of clover and grass varieties determined in monoculture reflects their performance as mixed crops. We hypothesize that gains in N fixation and biomass yield can be obtained using genomic prediction of interspecies interactions, and we will test this hypothesis by capturing and analyzing genotype and phenotype data for rhizobium/clover/grass crops.

NCHAIN provides funding to Stig U. Andersen and is funded by the Innovation Fund Denmark, 2015 – 2020.

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

ProFaba: Developing improved Vicia faba breeding practices and varieties to drive domestic protein production in the European Union.

ProFaba aims to boost protein production in Europe by improving faba bean (Vicia faba) as a European protein crop, thereby contributing to a more balanced and protein-self-sufficient agricultural system. The project brings together experts in a variety of fields to tackle the main obstacles to faba bean success as a protein crop. Using a collaborative approach focusing on common resources, ProFaba will build a common reference and data repository for faba genome, genotype, and phenotype data, ensuring easy communication throughout the faba community. These resources will be leveraged by developing common diversity panels and breeding lines, phenotyped for agronomic traits in five European locations. This will allow deciphering the genomic architecture of faba traits, understanding genotype by environment interactions, and direct incorporation of this knowledge into active, predictive breeding programs through the participating breeders from Denmark, Germany, France and Spain.

ProFaba provides funding to Stig U. Andersen and is funded by the European Union's Horizon 2020 research and innovation program under grant agreement No [771134]. 2019 – 2022

For more information about this project, please contact Stig U Andersen (sua@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 – 2022.

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)

Section coordinator

Group leaders

Junior Group Leaders

Simon Kelly

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

Dugald Reid

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

Peer-reviewed publications

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