Biology subjects

Kärkkäinen, K.

Publications and source records attributed to Kärkkäinen, K..

3 recordsLinked to original sources

bioRxiv2026

Gene expression dynamics through time reveal low pleiotropy genes underlying local adaptation in silver birch (Betula pendula)

Understanding the molecular mechanisms underlying local adaptation in boreal trees is important for assessing their adaptive potential under climate change. The role of pleiotropy in polygenic local adaptation remains poorly understood. Here we studied growth and temporal transcriptomic responses to photoperiod in three photoperiod treatments in three populations of Betula pendula within a two-week time period to identify genes and co-expression networks underlying local adaptation and to estimate the level of pleiotropy in population specific gene expression. We used RNA sequencing to characterize the temporal transcriptomic responses which were analyzed with variance partitioning, differential gene expression and weighted co-expression network analyses. Photoperiod treatment and sampling time were the main drivers of gene expression variation both at the co-expression module and single gene level. The majority of circadian clock and flowering time genes exhibited striking similarity across populations. Nevertheless, we detected small but significant population effects in the temporal gene expression patterns which were concentrated on the periphery of the co-expression networks consistent with low pleiotropy effects. Our findings suggest that local adaptation to growing season length among populations exhibiting very low genetic differentiation along a latitudinal cline in B. pendula is likely polygenic and potentially governed through low pleiotropy genes.

evolutionary biology↗

bioRxiv2023

Transcriptome analysis reveals novel regulators of the Scots pine stilbene pathway

Stilbenes are developmentally induced metabolites in Scots pine heartwood where they have important role in protecting wood from decaying fungi. The stilbene pathway is also stress inducible, and ultraviolet (UV)-C radiation was among the first discovered artificial stress activators of the pathway. Many conditions that activate the pathway are known, but the specific transcriptional regulators and the biosynthetic enzyme responsible for activating the stilbene precursor cinnamate in the pathway are unknown. Here we describe the first large-scale transcriptomic analysis of pine needles in response to UV-C exposure and treatment with translational inhibitor cycloheximide, both activating the transcription of stilbene pathway genes, to uncover the candidates for the transcriptional regulation of the pathway and the cinnamate activating CoA ligase. We show that the regulation of pine stilbene pathway has shared features with grapevine stilbene pathway. In both species, the stilbene pathway was transcriptionally activated after UV-C treatment, protein phosphatase inhibitors and plant hormones ethylene and jasmonate. The pine stilbene synthase promoter retains its inducibility when transformed in plants that normally do not synthesize stilbenes. Pine stilbene synthase promoter was able to activate the expression of a reporter gene in Arabidopsis in response to UV-C exposure and phosphatase inhibitors, but not as response to plant hormone treatment. This indicates that stilbene synthase gene regulation occurs both via ancient stress-response pathway(s) but also via species specific regulators. With transcriptomic approach we identified candidate enzymes for cinnamate acting CoA ligase and transcription factors regulating the pathway.

plant biology↗

bioRxiv2021

Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research

Scots pine (Pinus sylvestris) is the most widespread coniferous tree in the boreal forests of Eurasia and has major economic and ecological importance. However, its large and repetitive genome presents a challenge for conducting genome-wide analyses such as association studies and genomic selection. We present a new 50K SNP genotyping array for Scots pine research, breeding programs, and other applications. To select the SNP set, we first genotyped 480 Scots pine samples on a 407 540 SNP screening array, and identified 47 712 high-quality SNPs for the final array (called PiSy50k). Here, we provide details of the design and testing, as well as allele frequency estimates from the discovery panel, functional annotation, tissue-specific expression patterns, and expression level information for the SNPs or corresponding genes, when available. We validated the performance of the PiSy50k array using samples from breeding populations from Finland and Scotland. Overall, 39 678 (83.2%) SNPs showed low error rates (mean = 0.92%). Relatedness estimates based on array genotypes were consistent with the expected pedigrees, and the amount of Mendelian error was negligible. In addition, array genotypes successfully discriminate Scots pine populations from different geographic origins. The PiSy50k array will be a valuable tool for future genetic studies and forestry applications. Significance statementScots pine is an evolutionary, economically and ecologically impressive coniferous species but its gigantic genome has limited studying e.g. the genetic basis of its functional trait variation. We have developed a genotyping array that facilitates Scots pine genetic research and linking its trait variation to genetic polymorphisms and gene expression levels across the genome.

genomics↗