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The Genome Analysts – New Methods in Plant Breeding

Dr. Tsanko Gechev, scientific manager of CropStrengthen, in the greenhouse. Photo: Thomas Hölzel.

Dr. Tsanko Gechev, scientific manager of CropStrengthen, in the greenhouse. Photo: Thomas Hölzel.

How large can fruits get? How resistant are they to disease? How long can they survive during a drought? The information for all these traits is codified in a plant’s genome. Researchers are working to identify which genes are responsible for which traits and how they can be activated or deactivated. Molecular biologists at the University of Potsdam are primarily interested in genes that make plants more stress-tolerant.

To a layperson it may sound as if the researchers at the chair Molecular Biology have brought a bit of biodynamic gardening to the lab. Molecular biologist Tsanko Gechev is holding a little plastic bottle labeled Super Fifty, which contains a brown powder. This highly concentrated Ascophyllum nodosum seaweed extract is harvested on the Irish coast and processed into a powder by the company BioAtlantis. The company claims the concentrate has many positive effects on plant growth: a higher crop yield, stronger root growth, and a higher soil bacteria count. The compound is a so-called biostimulator or plant strengthener.

In the climate chamber, Dr. Gechev shows us why Super Fifty is being used in molecular biological research. Pots and pallets with plants of all age groups are tightly packed on shelves at a constant 21°C. Some show the first green of the rosette; others already have seeds on long stems. Arabidopsis thaliana – the common thale cress – is the plant geneticists’ “pet”. Its complete genome was mapped in 2000, and the functions of many of its genes are already known. It is therefore relatively easy for the researchers to determine which gene activities are influenced by a biostimulator.

Gechev is the scientific manager of the “CropStrengthen” project, in which the common thale cress meets Super Fifty. CropStrengthen, funded by the EU and industrial partners, is part of the European Industrial Doctorate Network (EID). As a Horizon 2020 project of the Marie Skłodowska-Curie Actions, it also supports young researchers. Five doctoral candidates of 180 applicants were chosen to research in CropStrengthen over the next four years. “Our goal is to find out which genes are responsible for an enhanced stress resistance in Arabidopsis thaliana and to then carry these results over to crops,” Gechev explains. For these examinations, the University of Potsdam is collaborating with two commercial partners – Ireland-based BioAtlantis Ltd. produces the biostimulants and Netherlands-based Enza Zaden breeds the crops.

Ivan Ivanov from Bulgaria is the first doctoral candidate who is working on his thesis within the program. The young molecular biologist will be researching in Potsdam over the next 18 months and then another 18 months at Enza Zaden. The advantages of this are obvious for him. At the university he will benefit from the researchers’ expertise and be able to study the latest biotechnological and biochemical methods as well as learn how to evaluate the mass of data with bioinformatics. At the commercial partner, he will learn about the relevance of his research in practical applications. “My employment chances after my doctoral studies are strong,” he underlines.

Bernd Müller-Röber, Professor of Molecular Biology at the University of Potsdam, pulls all the strings. “Plants cannot run away and have developed many mechanisms during evolution to cope with various environmental conditions,” he explains. Dry or wet conditions, too little or too much light, insufficient nutrients or damage due to caterpillars – plants react to the various challenges they face at a location, even if it is not immediately visible. The adaptations are usually invisible and take place at the metabolic and genetic level in the plant. It seems that biostimulants like Super Fifty help the plants to genetically adjust to stressors. They can better tolerate dry and cold periods and also continue to grow even if they lack nutrients. “We have not yet understood why,” Müller-Röber explains. “The key question is what stimulates plant growth.”

The researchers will analyze what happens in the plants at the molecular and biochemical level when treated with plant strengtheners. As a first step, Arabidopsis thaliana will be cultivated with and without biostimulants under both stress and optimal growth conditions. The molecular biologists will then analyze the plant’s genome. Do the resulting patterns of gene activity differ in the cultivated plants? Which genes are activated or deactivated? Which physiological processes does it influence? The researchers hope that this knowledge will later enable them to hybridize the genes for higher stress tolerance into vegetable crops like tomatoes and bell peppers through conventional breeding.

The highlight: Once the researchers have identified the relevant genes, they will be able to select those parents whose genome contains the desired sections. Their aim is to make successful breeding considerably more economical and faster because those hybrids with little promise at the genomic level can immediately be excluded. “Our aim is to develop diagnostic markers for breeding programs,” Müller-Röber explains. If we succeed, breeders will be able to look for the respective markers in the genome of the sprout and determine if it is worth further cultivating or breeding this plant. “There is no need for fields to grow the plants until their traits become visible; all initial screenings can be done in the lab,” Müller-Röber continues. This procedure is already being used when the genes for the desired traits are already known.

Such a gene is ATR7. The researchers have determined that it increases stress tolerance in the model plant Arabidopsis thaliana, although the physiological reasons for this are still unknown. This research aims to understand the functionality of ATR7 and to identify related genes in crops.

“We can save a lot of time, space, and money,” Müller-Röber emphasizes, “but we must not assume that the molecular analysis in the lab is sufficient.” The genome does not reveal everything. “The traits of a plant are ultimately the result of its interaction with the environment.” Tests in the fields and in the greenhouse are still necessary. “We are ultimately broadening possibilities.”

The Researchers

Prof. Bernd Müller-Röber studied biology and philosophy in Tübingen. Since 2000 he has been Professor of Molecular Biology at the University of Potsdam.

Contact

Universität Potsdam
Institut für Biochemie und Biologie
Karl-Liebknecht-Str. 24–25, 14476 Potsdam
E-Mail: bmr@uni-potsdam.nomorespam.de

Dr. Tsanko Gechev studied biology at the University of Plovdiv, Bulgaria. Since the beginning of 2015 he has been scientific manager of CropStrengthen.

Contact

E-Mail: gechev@uni-potsdam.nomorespam.de

The Project

“CropStrengthen” is part of the European Industrial Doctorate Network and a Marie Skłodowska-Curie Action funded by the European Union. The stress tolerance of crops will be enhanced using new methods of plant breeding and by identifying the respective genes.
Participating: University of Potsdam, Department of Molecular Biology, BioAtlantis Ltd., Ireland, Enza Zaden Beheer B.V., Netherlands
Duration: 2015–2018

Text: Heike Kampe, Translation: Susanne Voigt
Online-Editing: Agnes Bressa
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