Optimizing genomic data generation methods and uncovering parent-of-origin effects in Pinus sylvestris

The Scots pine is one of the most important keystone species in Finland and across Eurasia. Its ability to adapt to diverse environments is based on the variation within its genetic blueprint, the genome. However, studying the Scots pine genome is exceptionally difficult because it is massive, roughly seven times larger than the human genome. Furthermore, it is packed with repetitive sequences and complex regulatory mechanisms that make precise gene analysis a major challenge. This dissertation developed methods to overcome these technical hurdles and investigated the evolutionary forces influencing the development of pine seeds.

The study developed and tested a method to focus on the most critical parts of the genome: the genes. Since a large portion of the pine genome consists of "extra" repetitive sequences, various blockers are used to prevent these distractions from appearing in the analysis. The results showed that in-house species-specific blockers improved the accuracy of the sequencing and reduced costs. This method offers a practical improvement for researching other species with large, poorly understood genomes.

The second part of the dissertation examined gene regulation within the pine seed, which provides a unique model for studying heredity. A pine seed consists of an embryo and the surrounding tissue called the megagametophyte, which carries genetic material only from the mother. The study investigated genomic imprinting, a phenomenon where a gene's activity depends on whether it was inherited from the father or the mother. Although clear evidence of imprinting was not found in this dataset, the dissertation provides the first systematic overview of imprinting in conifers.

Finally, the study compared evolutionary differences between various tissues. The results showed that natural selection prunes harmful mutations more effectively from genes that function only in the maternally inherited (haploid) tissue. This confirms a biological theory suggesting that harmful genetic variants become visible more easily and are eliminated when they lack a second gene copy to shield them. The findings of this dissertation help us understand the molecular adaptation of forest trees and provide essential tools for future forest breeding and the conservation of biodiversity.