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Browsing by Author "Koistinen, Ville"

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  • Koistinen, Ville (2024)
    Silver birch (Betula pendula) is both the third most commercially important, as well as abundant, tree in Finland. Faster growth is of interest from an industry, as well as climate change, perspective. In addition to higher biomass yield from a commercial point of view, faster growth in trees leads to absorption of more carbon dioxide, thus increasing their effect as a carbon sink to lessen the impact of climate change. By conducting a genome-wide association study, the aim of this thesis was to investigate the genetical background of B. pendula on three first-year growth traits: maximum height, maximum growth rate and time to cessation. Whole-genome sequencing data from 405 mother trees was used to provide a high-resolution genome-wide map for assessing genes associated with the three growth traits. A high-quality genotypic dataset of 5,727,473 single-nucleotide polymorphisms (SNP), which span across the whole genome, was established through rigorous filtering. Phenotypic data was estimated with a mixed linear model by best linear unbiased prediction from mother trees’ 7,266 seedlings, which were grown in a greenhouse under controlled conditions to monitor their height trajectories. Association testing was done as both a uni- and multivariate mixed linear model with the GEMMA algorithm. Overall, 16 unique suggestively significant SNPs were discovered among the three traits. Genes putatively associated with the SNPs were related to metabolic regulation and cell transportation processes, as well as biotic and abiotic stress. On each of the three traits, SNPs with the largest effects had around 5% deviation against the average phenotypic value, which could be considered a major effect for a polygenic trait. Only 4 out of the 16 suggestively associated SNPs were within gene regions, even though the putative genes themselves had also variants present abundantly in the dataset. This could suggest that the associated SNPs could be related to gene expression regulation, or they could be in linkage disequilibrium with multiple different genes, and thus be markers for combined effects of multiple genes on the focal trait. To validate the results, further studies such as gene editing on the associated genes, or a duplicated study on a different population, would be needed.