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The True Secrets of the Purple False Brome
August 26, 2010   
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Prof. Robert Hasterok, a cytogeneticist at the University of Silesia’s Faculty of Biology and Environmental Protection in Katowice, talks to Ewa Dereń.

In February, the international science journal Nature reported that researchers had sequenced the genome of Brachypodium distachyon, a model grass species used for genetic research. You are one of the authors of the paper and were in charge of a stage of the sequencing process that was of key importance to the project’s success. Your work made it possible to match individual parts of the nuclear DNA of Brachypodium distachyon with specific regions in the plant’s chromosomes. You and your Ph.D. student Dominika Idziak were the only Poles among over 100 researchers from 45 research centers who formed an international consortium to study the Brachypodium distachyon genome. What makes this rather unimpressive grass species draw so much attention among scientists around the world?

Brachypodium distachyon, commonly called purple false brome, is a model grass that enables researchers to more easily and thoroughly study temperate cereals, such as wheat, barley, rye and oats. These grasses are one of the most important groups of domesticated plants.

The sequencing of the nuclear genome of Brachypodium is a big step towards intensified research on cereal grain species with improved immunity to infections, better adaptation to tough climate and higher yields. The research described in Nature may have a substantial impact on global science, especially when it comes to the question of what humankind will eat in the future.

Why do scientists need model grasses instead of just doing research directly on cereals such as wheat?

All the cereals I listed are very difficult as subjects of genetic research. Their genomes are big and their nuclei contain vast quantities of DNA, most of which are non-coding sequences that carry little or no information of significance to the economic value of cereal species. We are only interested in relatively short sequences, or genes, which encode for certain qualities of plants, such as flowering time, size of harvest, composition of nutrients in caryopses, which constitute the bulk of human food, tolerance of poor soil quality, resistance to drought and pathogens and so on. If we were to try and track down the genes in huge, complex genomes with many repeated sequences, the genes would be much more difficult to identify. It was thus vital to find a model organism related to cultivated grasses closely enough to make sure the repertoire and arrangement of genes was similar to that of temperate cereals. Apart from having a small nuclear genome with a low number of repeated DNA sequences and few chromosomes, the model plant would need to display a number of other characteristics such as small physical stature, a short life cycle, self-fertility, and uncomplicated growth requirements; and, most importantly, it should grow in the temperate climate. Brachypodium distachyon is native to the Mediterranean region and areas north of it, up to the southern border of Poland. It is a common plant species in Iran, Iraq and Turkey. It reaches a height of 20-30 centimeters, is easy to grow and its life cycle takes only three to four months, so that it produces a new generation of seeds within just a quarter of a year from sowing.

Brachypodium was first proposed as a model grass by Prof. John Draper at Aberystwyth University in Britain. You started researching the plant in his team, being the first and only Polish scientist to do so. How do you remember that experience?

When I first came to Aberystwyth University on a scholarship, I did not even know that Brachypodium distachyon existed. I had been analyzing the chromosomes of species of the Brassica (cabbage) genus and completing my doctoral thesis at the University of Silesia when I got the opportunity to go to a European academic center as part of the EU’s Tempus program, which enabled researchers to undertake short-term fellowships. I chose Aberystwyth because their field of research was closest to what I was doing at the time. My fellowship went well so I was invited to come on a 12-month scholarship, and needless to say, I accepted the offer. Aberystwyth was my first encounter with research on grasses. When my year at the university was coming to a close, I got an invitation from Prof. Draper’s research group and so began my adventure with Brachypodium.
You were the first team member to see the chromosomes of Brachypodium. Is that correct?

Several of my colleagues had been trying to spot them, but since the chromosomes were small and quite difficult to see, as we found out later, all attempts indeed failed for a long time. Since my earlier research focused on plant species with tiny chromosomes as well, in the end I succeeded in spotting Brachypodium chromosomes and then counting and measuring them. That happened midway through 2000. In the following year, the journal Plant Physiology printed our first significant publication with a full description of Brachypodium distachyon.

We then gradually tackled the Brachypodium chromosomes. In the meantime, I returned to the University of Silesia and, as a young Ph.D. degree holder without a research team, I studied Brachypodium on my own. I also continued to work with the research group at Aberystwyth University and things went on like that until January 2006, when a conference took place in San Diego, California, that became another turning point in the research on Brachypodium distachyon. It was there that the idea to sequence the Brachypodium distachyon genome came about. Every year, the Plant and Animal Genome conference in San Diego draws around 2,000 scientists who deal with genetics and molecular biology. In 2006, the conference became a meeting point for a wide group of people from different countries who worked on Brachypodium, but never worked together until that point, and each one of them was doing something different. The research lacked a common direction and coordination. We decided to do something together and one of the most obvious ideas was to sequence the genome.

What exactly did your team do to help make the sequencing of the Brachypodium distachyon genome a success?

The consortium reached a point where the researchers had developed sequence maps of the Brachypodium genome and, to cut a long story short, the maps now had to be assigned to individual chromosomes. However, in all the many teams which did the sequencing there was not a single expert capable of doing just that. In the meantime, my team had designed a set of special markers enabling us to precisely identify each of the five chromosomes and particular chromosome regions in the Brachypodium distachyon genome. Figuratively speaking, we had come up with a set of colorful tacks we could push into any chromosome to locate it. Those sequence maps needed such tacks and so our contribution to the research and the publication in Nature was the integration of maps developed through Brachypodium distachyon genome sequencing with individual chromosomes. Our method made it possible to determine the physical location of large regions of the Brachypodium genome assembled into so-called supercontigs in the chromosomes. The makers of the maps arranged the supercontigs according to certain criteria, but sometimes these arrangements contained various errors and our tacks helped eliminate at least some of those. In other words, our contribution was small but pivotal at that particular stage of research.

What else can be investigated when it comes to Brachypodium distachyon?

For the time being, the research community is only familiar with the sequence of the genome. This can be compared to knowing just the letters of the alphabet, which is far from being able to read and understand a whole book. We still know very little about the functional contents of the genome; we do not know what many of the Brachypodium genes are responsible for and how they interact with other genes and non-coding sequences. My team is actually less interested in these questions, because we work on chromosomes and not individual genes. The successful sequencing of the genome has clearly expanded research possibilities at the chromosome level as well. For example, we now have access to libraries of DNA sequences which we use to obtain sets of sequences that will enable us to literally “paint” entire chromosomes, assigning a different color to each chromosome and visualizing it by employing fluorescent microscopy. The technique makes it possible to visualize a number of key processes that occur in Brachypodium distachyon cell nuclei. Such visualization was for a long time completely unobtainable for plant chromosomes. Our “chromosome painting” is the second time the technique has ever been used in plant research. Unlike human or animal chromosomes, those in plants cannot be easily painted and the only plant for which it became possible a couple of years ago was Arabidopsis thaliana, a model species as well. Brachypodium distachyon is the second plant and the first one as far as grasses are concerned.

At the beginning of this year, the Ministry of Science and Higher Education provided us with a substantial research grant to further analyze the Brachypodium distachyon genome, chromosome painting in particular. As part of the grant, we have been working with British scientists at research centers in Norwich and Aberystwyth and new publications are under way. There is a total of perhaps a few hundred people around the world who research Brachypodium distachyon, but the number is growing rapidly. Around 150 people are credited as the authors of the project which led to the publication in Nature.

What is the practical side of Brachypodium distachyon genome sequencing?

Research of this kind builds a certain body of knowledge that seemingly has no practical application, but in science you can never tell what will find practical application and when. Sometimes one discovery can supply the missing piece of the puzzle, and all of a sudden it creates a whole new quality that nobody else would have thought of before. That way, looking at scientific research solely in terms of immediate practical applications is taking things far too simply. For example, many people ask us if Brachypodium distachyon is a cereal species. Well, it is a weed that cannot be utilized directly like wheat, maize or rice. However, the plant can be very useful when it becomes a model to enable faster and easier understanding of important cereals. So, as far as direct, practical applications of the Brachypodium research are concerned, there are none to speak of, but some research centers are working on this direct aspect. For example, my colleagues at Aberystwyth are researching the resistance of Brachypodium distachyon to different fungal infections. Many pathogens which are dangerous to rice and wheat can also infect Brachypodium, but some Brachypodium distachyon ecotypes are resistant to them. The research seeks to establish the differences between the susceptible and resistant ecotypes, aiming to understand what differences in the genome organization and the arrangement of genes are responsible for the susceptibility and resistance to a given pathogen and what defense mechanisms the plant activates to contain infections. Last but not least, the researchers want to see how their studies of the model organism’s susceptibility and resistance can translate into a real-life situation on a wheat field or other.

This kind of research is just one of several directions. Another investigates how Brachypodium distachyon could be used in biofuel production. The plant itself is not really useful as an energy plant, because it is too small, incomparably smaller than, for example, Miscanthus, also known as “elephant grass.” But as a model organism, it can be used to study certain metabolic routes that trigger faster and more efficient enzymatic hydrolysis of cellulose. Plants abound in cellulose, as it is a major component of the plant cell wall. It would not be easy to do, but theoretically, cellulose could be used to produce ethanol and other biofuels. Research on the process is under way and some of it involves Brachypodium.

What other fields of research does your department pursue?

Our staff also deal with the molecular cytogenetics of plants, a science that studies plant genomes at the chromosomal level. It combines cytology, genetics, molecular biology and, to a growing extent, digital image analysis and processing, because state-of-the-art processing of microscopic images is very important to ensure appropriate presentation and quantification of the findings.

My department researches several areas. Some of my colleagues analyze the structure of nuclear genome in plants in the context of physical mapping of diverse DNA sequences that make up the genome. This is what my research team does as well. Others assess the stability of genomes exposed to different mutagens. For example, they irradiate the seeds of a given plant species or expose it to all kinds of chemical agents. Then, they watch its chromosomes and their behavior during cell division, so as to identify any possible rearrangements such as translocation when a fragment of one chromosome “jumps” to another one.

The third major field of research at the department are analyses of epigenetic regulation in the genome, as it is called. Taking a step beyond studying just DNA sequences, this kind of research focuses on various chemical modifications of the chromatin that have an impact on the structure of the chromatin and, consequently, its functions.

For several years now, my team has conducting research thanks to continuing financial support from the Polish Ministry of Science and Higher Education.
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