Genome shows the adaptability of the pine

The pine (Pinus sylvestris) does not reach maturity instantly. Therefore, it is useful to be able to ask them at an early stage: “What will you be when you grow up?”. Individual pines will answer the question with their genes.

How the genome affects the features of an organism is especially interesting to cultivators. For forest trees such as pines, it is especially important to predict their growth and cultivation potential from their genes. Genetic methods accelerate the knowing of the phenotype of a pine by dozens of years, because it is possible to determine the properties of a full-grown pine from the DNA of the seed it grew from. The pines most suitable for cultivation can thus be selected as saplings.

The DNA of a seed can already help evaluate the properties of a full-grown pine.

”Studying the genetic background of properties is essential for the understanding of evolution”, says professor of genetics Outi Savolainen from the University of Oulu. Her research group is searching for sections in plant genomes, which differ between individuals.

Most of the differences between genomes of individual pines have hardly any effect on their phenotypes, the perceptible features of trees. However, different genetic variants may occasionally be directly responsible for different properties of individuals. These parts of the genome may help in the research of what effect natural selection has on the DNA level.

At the same time, researchers are looking at how prevalent, beneficial or detrimental each gene variant is. Studying gene variants is beneficial also in medicine, where it is crucial to be able to make disease risk evaluations on the basis of the genome.

Researchers are looking into how prevalent, beneficial or detrimental each gene variant is.

However, there are few properties with only one or two genes behind them, as most properties are affected by several genes. These properties are called quantitative properties. They do not contain separate categories, but they are constantly adapting properties such as human length and productivity of crops. Outi Savolainen and her partners in the Biocenter Oulu research project are looking into how many genes are participating in the determining of such traits.

Study of constantly adapting properties is necessary, for example, for nature conservation. “Species are often adapting to their living environments with properties whose forming is influenced by several genes. In nature conservation genetics, many such properties are studied, such as fitness and reproductive capability, whose genetic background is hard to work out”, say Savolainen. Her research group is trying to find genes which reveal how genetic differences between individuals affect such properties.

 

Adaptation to the North showing in genes

Finland is a great place to look into pine genomes. Pine is our most common tree, and it has been studied here more thoroughly than anywhere else. Previous knowledge is helping modern researchers in their field investigation and research planning.

”Combining valuable historical and new genomic data offers fantastic research opportunities. Old data makes it possible to conduct long-term experiments”, says Savolainen, who was two years old when some of the trees studied in the project were planted.

It is especially important to study how plants adapt to northern circumstances. The research project is looking for genes in pine and Arabidopsis lyrata, which have helped these species to adapt to our latitudes. Such genes must exist, because these plants came from the south. “Every single plant and animal species living here has come from somewhere else after the Ice Age. They are all immigrants”, says Savolainen.

“Every single plant and animal species living here has come from somewhere else after the Ice Age. They are all immigrants.”

Northern life forms have adapted not only to the climate but also to day lengths, which change according to time of year. Plants must follow day length to know when to grow. When pines are grown in comparable conditions, northern trees end their growth sooner than the southern ones.

”We already know that pines have different phenotypes in different parts of Europe”, says Academy researcher Tanja Pyhäjärvi. “We are hoping to get to the genetics behind the variability of pine features. Our aim is to understand the genetic background for adaptability.”

The project has looked into the topic by studying genetic changes which are behind the differences in growth between trees. The dissertation by Sonja Kujala showed that different genes are behind the temporal development of northern and central European pines. Observations such as this have to be taken into account both in the breeding of pines and in studying how organisms can adapt to the changing world.

The warming climate is making life more complicated also for plants in the north. “We aim to generate information on how forest trees could adapt to a changing environment. In other words, what is going to happen to species in the future”, says Savolainen.

Knowledge on the genetic background of adaptations can be applied when we think how organisms can adapt to climate change.

”In actual fact, not in the future, but now”, Savolainen specifies. “Terribly many organisms have genetically adapted to the north after the last ice age. We can apply the knowledge of the genetic background of adaptations when we think how organism can adapt to climate change.”

 

Tanja Pyhäjärvi, Outi Savolainen and Mikko Sillanpää go deep inside the bark of the pine in their research. Picture: Antti Miettinen

 

Gigantic data challenges statisticians

The project is studying entire genomes of plant species – in other words, all of their genetic information. “The enormous size of the pine genome poses a challenge for research. Previous genome studies have looked at species with a smaller genome”, says Pyhäjärvi.

With the development of technologies, it has become exponentially cheaper and cheaper to produce genomic research data. This has resulted in the accumulation of massive amounts of data. The data is now so large that traditional statistical methods cannot be applied to them. Transforming data into information requires specific kind of statistics and data processing.

We need new kinds of tools to make statistical methods work in analysing gigantic data. Our aim is to get more information out of the same data. Methodical leaps forward are crucial, because otherwise data will become unused. Professor of statistics Mikko Sillanpää says that a fast processing time for statistical analyses on a computer has become increasingly important.

We need new kinds of tools to make statistical methods work in analysing gigantic data.

The different sub-projects are closely interconnected. “Especially the advances in geonomics methods have imporved our chances of reaching our goals. The starting point for improving statistical methods is that there exists material they can be applied to. Analysis methods will develop when there is more material. We also need bioinformatics and calculation. They are all interconnected”, says Sillanpää.

Challenging genome research produces unique information. Savolainen ends with an illustration: “Years ago we got a good peek into the genome, when we crossed American and European Arabidopsis lyrata. We discovered that their hybrids reproduced poorly, but we had no idea why. In a more recent study it was discovered that the genome has parts where genes from different strains are completely incompatible. That was impossible to conclude earlier from external properties.”

 

Antti Miettinen, text

 

Last updated: 1.11.2017