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Looking for history in seed DNA

14 November 2014

The seeds in the glass jars are dead, but they have a story to tell. Due to the fact that DNA is protected by shells and cell walls researchers can now show a completely new picture of the evolution, history and spread of cultivated plants.

The seeds in the glass jars are dead, but they have a story to tell. Due to the fact that DNA is protected by shells and cell walls researchers can now show a completely new picture of the evolution, history and spread of cultivated plants.

Only 150 years ago, Nordic farmers were growing original varieties in their fields. They would take seeds from their own crop or exchange with the neighbouring farm.

What they did, half without realizing, was a simple form of plant breeding where the seeds that gave the best crops in the local climate were favoured and passed on, even to neighbouring countries.

“It was the latitudes that governed the spread, not national boundaries,” says Nils Forsberg, PhD student in the “Historical Seeds” research group at Linköping University.

He is a geneticist, and will soon be finishing his thesis about the history of barley cultivation as reflected by the DNA of 150-year-old seeds gathered from unique collections in Sweden, Norway and Finland. The large-scale analyses were carried out with the help of the James Hutton Institute in Scotland.

The Swedish collection consists of 4,000 specially-made glass jars with thousands of seeds in each – barley, oats, wheat and rye. It was first kept at the museum of the Royal Swedish Academy of Agriculture in Frescati in Stockholm, and is now at the Nordic Museum.

“It was only kept by chance,” says Matti Leino, agronomist and reader in genetics and plant breeding, who divides his time between Linköping University and the Nordic Museum.

The seed collection, which was regarded for decades as a shelf-warmer of no great value, has become a goldmine for research with the breakthroughs in DNA technology. The history of the seed varieties now give us interesting insights into the agriculture and trade of ages past, and can also be of significance for modern-day plant breeding. After a study on wheat, in which Reader Jenny Hagenblad was able to show that its nutritional content can be improved with the help of genes from old Nordic varieties, it is now the turn of barley. The study, which gave completely new insights into how original varieties spread geographically, was published in the autumn of 2014.

For hundreds of years barley was the most important seed variety in the world. Thanks to its ability to adapt to extreme climates and poor soil, it has been grown around the whole globe except the tropics, and has been used in baking bread, boiling porridge and brewing beer.

In northern Norway, barley has been grown north of the 70th parallel. The researchers’ genetic analyses show that the varieties are almost the same as those grown on the other side of the mountains in Finnish and Swedish Tornedalen. The conclusion is that the seeds spread over borders, beyond the control of the protectionist national authorities.

“The most amazing thing was that barleys from the same latitude in Sweden, Norway and Finland are much more similar than barleys from different latitudes inside Sweden,” Ms Hagenblad says.

Barley and wheat both have their origins around 10,000 years again in Mesopotamia, between the Euphrates and the Tigris in modern-day Iraq. The first rye cultivation was in Anatolia. Oats, which is the youngest of our seed varieties, were first cultivated in the Mediterranean region. In the next project, the seed researchers will be examining the history of oats in Sweden. Seeds from the late 1800s will be compared genetically with modern varieties. Which genes gave the best yield? Which of the variable genes in older varieties have been lost?

The researchers also want to try to break down the barriers and investigate whether it is possible to get information from archaeological material: seeds – unfortunately often burned – that have been found during excavations of old settlements. At one excavation of a 17th-century brewery in Gothenburg, a wooden barrel full of pig manure was found.

DNA researchers in protective clothing“In the pig manure there were residues of seeds which we took to our partners at the University of Warwick. There we succeeded in extracting DNA that we could ascertain came from barley,” Mr Forsberg says.

Ms Hagenblad hopes to be able to carry out the same analysis on archaeological material and on intact seeds.

“But it’s a difficult job, as DNA is damaged by burning or chemical degradation.”

Researchers who compare the genomes of Neanderthals and modern humans have it much easier, she explains. The cells with their DNA content lie protected in fossilised bone; animal genomes are smaller than that of plants and they have, to a great extent, already been investigated.

Mr Leino compares it with a jigsaw puzzle:

“When you want to put together the bits of the puzzle, for example the wheat genome, you have a huge amount of blue sky – bits you can’t see any difference between.”

If they manage to overcome the difficulties with their fundamental studies, dizzying questions will open up. Genetic analyses of seeds that are hundreds of years old would, for example, be able to show how crops have adapted to known climate change – useful knowledge in the face of future challenges.

Picture 2: 150 year old barley seed from Arjeplog
Picture 3: Nils Forsberg carries out DNA analyses in protective clothing.

The seeds in the glass jars are dead, but they have a story to tell. Due to the fact that DNA is protected by shells and cell walls researchers can now show a completely new picture of the evolution, history and spread of cultivated plants.

Plant seeds protect their genetic material against dehydration

When seeds from the thale cress Arabidopsis thaliana mature, their cell nuclei reduce in size and the chromatin condenses

Plant seeds represent a special biological system: They remain in a dormant state with a significantly reduced metabolism and are thus able to withstand harsh environmental conditions for extended periods. The water content of maturing seeds is lower than ten percent. Researchers from the Max Planck Institute for Plant Breeding Research in Cologne have now discovered that the genetic material in seeds becomes more compact and the nuclei of the seed cells contract when the seeds begin to mature. The seeds probably protect their genetic material against dehydration in this way.

Cell nucleus of a plant seed in a dormant state (left) and after germination (right). The DNA in the smaller nucleus (blue) is more tightly compacted than in the larger one (green: methylated DNA).

© MPI for Plant Breeding Research

Plants prepare for changing environmental conditions in the best possible way by developing dormant seeds. Seeds that mature in autumn, for example, have no problem surviving the harsh conditions of winter. And when the seeds encounter more pleasant external conditions in spring, they germinate and reboot their metabolism, which has been running at a low speed. In archaeological excavations, seeds have even been found that had survived for several thousand years and were still able to germinate.

Dry seeds represent a transitional stage between embryonic and seedling stages. During developmental transitions, the genes that control the new state must be activated while the genes for the “old” stage are silenced. The genes in the cell nucleus are surrounded by proteins. This complex – the chromatin – can be tightly or loosely packed. The degree of compactness of the chromatin regulates the activity of the genes: the more “open” the chromatin, the better the genes can be read.

It was not known up to now whether the reduced metabolic activity or low water content of seeds was linked with changes in the chromatin. The research team working with Wim Soppe from the Max Planck Institute for Plant Breeding Research has now shown in studies on the thale cress that the cell nuclei clearly contract during seed maturation and the chromatin compacts as part of this process. Both processes are reversed during germination. “The size of the nucleus is independent of the state of dormancy of Arabidopsis thaliana seeds,” says Soppe. Instead, the reduction of the nucleus is an active process, the function of which is to increase resistance to dehydration. Again, the condensation of the chromatin arises independently of the changes in the nucleus.

Thanks to the discoveries of the Cologne-based researchers it may be possible to protect other organisms against dehydration, as the mechanisms that regulate the organisation of the chromatin have undergone little or no change over the course of evolution.

<span style="background-color: transparent; color: #444444;">When seeds from the thale cress <em>Arabidopsis thaliana</em> mature, their cell nuclei reduce in size and the chromatin condenses</span>