New genomic tool for Scots pine research and breeding

In a recently published study, we developed a new genomic tool, PiSy50k, for use in Scots pine evolutionary research and forestry applications.  It is anticipated the tool will be important in tree breeding applications, such as when aiming to improve the important growth traits of the species via genomic selection, as well as for many other evolutionary and breeding purposes.

PiSy50k is a genotyping array that gives information on almost 50 000 single nucleotide polymorphisms (SNPs) spread around the genome. SNPs are nucleotide positions in DNA with more than one nucleotide variant in the species. SNP arrays have the big advantages over previously existing genomic tools that individual level genotype data can be gained quickly and handling of the data does not require a lot of bioinformatics work.

Scots pine. Credit: Alina Niskanen

Scots pine is a dominating species in the Northern Eurasian boreal forest ecosystem. It is also a major source of wood-based products. Conifer trees commonly have very large genomes, and the Scots pine is not an exception. The genome of Scots pine consists of 24 million base pairs (Gbp), which is about eight times the size of, e.g., the human genome. A large genome with a lot of repetitive regions is challenging to study. The new array is a great advance for Scots pine research, because it allows an easy and quick way of studying genome-wide variation in a large sample of trees. These genotyping results are very useful, for example, in exploring population differences and relatedness between individuals.

Generally, individuals from the same population share the same SNP variant more often than individuals from different populations. However, the Scots pine populations are genetically very similar. The similarity is caused by the species’ very wide distribution range and long-distance wind pollination that connects the populations through gene flow. Despite small genetic differences between the Scots pine populations, our new array has such a high resolution that we were able to separate tree individuals from Finland and Scotland using the genotyping results. We also used the array results to recognize parent-offspring relationships and build pedigrees in the Finnish breeding population.

You can read more about this research in the following paper:

Chedly Kastally, Alina K. Niskanen, Annika Perry, Sonja T. Kujala, Komlan Avia, Sandra Cervantes, Matti Haapanen, Robert Kesälahti, Timo A. Kumpula, Tiina M. Mattila, Dario I. Ojeda, Jaakko S. Tyrmi, Witold Wachowiak, Stephen Cavers, Katri Kärkkäinen, Outi Savolainen, Tanja Pyhäjärvi. Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research. The Plant Journal. (2021)

Top image: Scots pine. Credit: Tanja Pyhäjärvi

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