Plant Models at the GMI

Arabidopsis thaliana is a member of the cabbage family (Brassicaceae), an agriculturally important group that includes cabbage, turnip, radish, cauliflower, broccoli, and others. Despite its limited agricultural value, in the last decades, Arabidopsis has been a staple research model organism that has advanced plant science globally, giving rise to innovative concepts and methodologies for physiological, biochemical, genetic, and molecular research.  

Arabidopsis has a small and well-characterized genome, is easy to cultivate and manipulate indoors, has a short life cycle (6 weeks from germination to a mature plant) and produces a large number of seeds. All these characteristics make Arabidopsis an ideal research model organism. Arabidopsis also contains all the main structures found in flowering plants, including flowers, stems, apical meristems, and many more. This makes Arabidopsis an ideal model for studying flowering plants.

In addition, its simplicity has established Arabidopsis as a model to study molecular mechanisms that are more complex in other species, including animals. Thus, Arabidopsis has become a key model for evolutionary studies, giving important insights that can be applied to research in other organisms. 

Scientists at the GMI have used Arabidopsis to study topics as diverse as chromatin structure and function, autophagy, insect-induced gall formation and transposon silencing. Some of the major discoveries at the GMI wouldn’t have been possible without this fascinating plant.  

The Marí-Ordóñez group is using Arabidopsis and other plant models to study how small RNA molecules recognize and silence transposons in plants.

The group of Frédéric Berger is using Arabidopsis to study how chromatin structure affects DNA function. The group tries to identify the evolutionary origin and function of histone variants and histone remodelers in chromatin structure. They also study the cellular mechanisms that silence transposons in Arabidopsis. 

The research group led by Yan Ma is developing a new insect-plant interaction model using Arabidopsis and the swede midge (Contarinia nasturtii). With this model, the group will study which molecular pathways insects hijack to induce plants to form galls, which are complex structures used by insects for the nutrition and protection of their larvae. 

The group of Magnus Nordborg uses comparative genomics approaches in Arabidopsis and other plant models to investigate how genetic variation arises, and how it affects the genotype.

Aethionema arabicum is, like Arabidopsis, a member of the cabbage family. Aethionema originates from the Irano-Turanian region, where the summers are very warm and dry. These harsh conditions have required Aethionema to develop special strategies to survive. 

Fascinatingly, Aethionema is able to time its germination precisely so that seeds germinate at those times of the year when the conditions for seedling establishment are optimal. Researchers at the GMI discovered that seed germination of one Aethionema subspecies originating from Cyprus is inhibited by light. This is in contrast to Arabidopsis seeds, which require light for germination.

Seeds of Cyprus Aethionema measure the intensity and duration of light exposure to gain information about the day length and therefore about the season. This way, they avoid germinating during the harsh summer and opt instead for the more convenient spring or autumn.

Aethionema has also developed an interesting reproduction strategy called heterocarpy. Each Aethionema plant produces two different types of seeds at the same time, inside two types of fruits. Winged fruits contain a single seed that will fall close to the plant, while non-winged fruits contain multiple seeds that will be distributed far away. Aethionema has become an emerging model species for studying heterocarpy, which occurs also in other species.

Marchantia polymorpha is a common species of liverwort found on all continents except Antarctica. Marchantia and related liverworts are distant relatives of flowering plants. They last shared a common ancestor around half a billion years ago.

Studying these plants can help us understand the physiological, cellular, and developmental adaptations that enabled plants to conquer land. Indeed, Marchantia has been used as a model in biology since the 19th century and was instrumental in the discovery of heterochromatin, plant sex chromosomes, and more.

Marchantia has a relatively small and simple genome with around 20.000 genes. This simplicity makes functional studies more straightforward than with other models. In addition, Marchantia has a short life cycle with two distinct phases. In one of these phases, the Marchantia cells only contain one copy of genetic material, which facilitates the study of some genes. Knocking out the only copy of a gene provides clear phenotype correlations and allows for straightforward characterization of gene and protein functions.

Indeed, using Marchantia as a model simplifies the study of transcription and signaling factors and gives important insight into the transcriptional networks involved in acquiring new developmental and physiological traits during evolution.

Researchers in the Dagdas Lab at the GMI use Marchantia to study selective autophagy in plants, trying to identify novel autophagy regulators. The autophagy process is essential to maintain homeostasis in the plant cell, as well as to defend it against external aggressions.

The development of the full plant body of Marchantia is also a topic of study at the GMI. Researchers in the Dolan Lab are studying how cell polarity is established in the Marchantia spore, and how polarity influences the development of the different plant structures.

Lastly, the Irwin Lab uses Marchantia and other models to study horizontal gene transfer, the process by which a gene from one species can end up in another, and its role in plant evolution.

Chlamydomonas reinhardtii is a single-celled, green alga that scientists at the GMI use as a model organism to gain insight into fundamental biological processes that are common to many different plants. 

One of the key advantages of using Chlamydomonas as a model organism is that it is easy to grow and manipulate in the laboratory. Researchers can grow large numbers of Chlamydomonas cells quickly and inexpensively, either in a Petri dish filled with a nutrient-rich agar gel or in a container filled with a liquid medium. 

Chlamydomonas is a valuable model system that has contributed to our understanding of fundamental biological processes.  

For example, Chlamydomonas has been an instrumental model to study photosynthesis, a vital process that allows plants and algae to use sunlight to make food and oxygen, essential for life on Earth. In addition, Chlamydomonas can be used to study the effects of environmental stresses on cells.

Scientists at the Ramundo Lab expose Chlamydomonas cells to different levels of light or heat to investigate how the cells respond to these and other stimuli. This research can help us understand how different plants adapt to changing environmental conditions.

Duckweeds like Lemna minor and Spirodela polyrhiza, also known as water lentils, are very small plants that have adapted to an aquatic lifestyle. Indeed, they float on water, where they form extensive colonies. 

Duckweeds have an extremely high proliferation rate through clonal propagation. This, coupled with their small size and ease of manipulation made duckweeds one of the first plant research models, with the first experiments on Lemna minor being published in 1839.  

Although duckweed research has been less prevalent in the last decades, recent advances in genetic engineering have brought duckweeds back into the spotlight as a potential model organism. 

Duckweeds are a great model for biochemical studies as they can take up chemicals directly from the water. In the last years, duckweeds have been essential in elucidating the function and roles of key plant proteins, as well as important molecular pathways. 

The Marí-Ordóñez Lab at the GMI uses duckweeds as a model to study the molecular mechanisms of gene silencing in plants. The unique small RNA patterns and epigenetic features of duckweeds make them an excellent model to study this process.