Biology subjects

Pyhäjärvi, T.

Publications and source records attributed to Pyhäjärvi, T..

7 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↗

bioRxiv2026

Using Maternally Inherited Haploid Tissue to Resolve Parental Alleles: Investigating Genomic Imprinting in Scots Pine (Pinus sylvestris)

Genomic imprinting is a rare epigenetic phenomenon in plants and animals, defined by parent-of-origin specific gene expression. Its molecular mechanisms and evolutionary significance remain incompletely understood. In this study, we investigated whether genomic imprinting occurs in Scots pine and, by extension, in other conifers to gain insight into the evolutionary origins of imprinting. We performed reciprocal crosses to assess imprinting in seed embryos and applied a unique approach that used exome-capture data from the haploid, maternally inherited megagametophyte tissue to identify maternal alleles, thereby allowing us to infer paternal alleles in the embryos of the same seeds. Our findings show that maternally inherited haploid megagametophyte tissue offers an effective strategy for resolving parental alleles in offspring while simultaneously removing extensive paralogous variation from the dataset. This framework is broadly applicable to other conifer species and to taxa that possess comparable maternally derived haploid tissues. No evidence of genomic imprinting was detected. Although the limited overlap between the exome-capture and RNA-sequencing datasets and the stringent paralog filtering reduced the amount of analyzable data considerably, the absence of detectable imprinting may also reflect genuinely weak or absent imprinting signals in conifers. We identified several limitations in this preliminary study and outline recommendations for future work to overcome them, and additional research will be necessary to determine whether genomic imprinting occurs in conifers

evolutionary biology↗

bioRxiv2025

The FORGENIUS genomic resources: new genotyping tools and genomic data for 23 forest tree species and their Genetic Conservation Units

Genetic diversity is a critical but often overlooked component of biological diversity. The European H2020 FORGENIUS project is precisely aimed at increasing the quality and quantity of genetic data to start monitoring the European network of forest Genetic Conservation Units (GCUs). A first step in this direction was developing standardized genomic resources for 23 forest tree species, spanning from rare and scattered (e.g., Abies nebrodensis and Torminalis glaberrima) to widespread, economically relevant ones (e.g., Fagus sylvatica, Picea abies and Pinus sylvestris). Here, we describe the development and application of targeted genotyping tools, primarily based on Single Primer Enrichment Technology (SPET), along with existing SNP arrays for the selected species. The SPET panels developed in FORGENIUS were designed to capture {square}10,000 loci per species, balancing species-specific and randomly distributed regions to ensure broad genome coverage and minimize ascertainment bias. Across 7,192 genotyped trees, we identified over 1.8 million single nucleotide polymorphisms (SNPs) covering approximately 50 Mb of DNA sequence. SPET panels demonstrated high genotyping efficiency and cross-species transferability, especially within genera such as Quercus and Abies. They represent a cost-effective, flexible, and scalable solution for population-level genetic assessments across diverse taxa, enabling standardized, genome-wide characterization of the GCU network. These resources not only promote the establishment of genetic monitoring, support genetically informed conservation strategies and improve our understanding of adaptive responses in European forests, but also enhance species delimitation and hybrid detection, and enable the characterization of phylogenetically related but previously underexplored species.

genomics↗

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↗

bioRxiv2020

Reproductive compensation and embryo competition drive the evolution of polyembryony

Simple polyembryony - where one gametophyte produces multiple embryos with different sires but the same maternal haplotype - is common among vascular plants. We show that together polyembryonys two benefits - "reproductive compensation" achieved by providing a backup for inviable embryos, and the opportunity to favor the fitter of surviving embryos, can favor the evolution of polyembryony. To do so, we develop an infinite-site, forward population genetics model to test how these factors can favor the evolution of polyembryony, and how these underlying benefits of polyembryony shape the genetic load under a range of biological parameters. While these two benefits are difficult to disentangle in nature, we construct variant models of polyembryony that either only include or only exclude the opportunity for reproductive compensation. We find that reproductive compensation strongly favors the evolution of polyembryony, and that polyembryony is favored much more weekly in its absence, suggesting that the benefit of a backup embryo is the force favoring polyembryony. Remarkably we find nearly identical results in cases in which mutations impact either embryo or post-embryonic fitness (no pleiotropy), and in cases in which mutations have identical fitness effects embryo or post-embryonic fitness (extreme pleiotropy). Finally, we find that the consequences of polyembryony depends on its function - polyembryony results in a decrease in mean embryonic fitness when acting as a mechanism of embryo compensation, and ultimately increases mean embryonic fitness when we exclude this potential benefit. Nature is, above all, profligate. Dont believe them when they tell you how economical and thrifty nature is. - Annie Dillard 1974.

evolutionary biology↗

bioRxiv2020

Model guided trait-specific co-expression network estimation as a new perspective for identifying molecular interactions and pathways

A wide variety of parametric approaches and co-expression networks have been developed for finding gene-by-gene interactions underlying complex traits from expression data. However, a little is known about the practical correspondence and synergistic potential of these different schemes. We provide a framework for parallel consideration of parametric interaction models with quantitative traits and co-expression networks based on a previously uncharacterized link between them. Resulting trait-specific co-expression network estimation method 1) serves to enhance the interpretation of biological networks in a more parametric sense and 2) exploits the underlying parametric model itself in the estimation process. It is tailored for simultaneous identification and classification of molecular interactions and pathways regulating complex traits by accounting for common characteristics of genetic architectures due to which the mainstream methods often lack efficiency. A remarkable advance over the state-of-art methods is illustrated theoretically and through comprehensive simulated scenarios. In particular, prognostically important novel findings in acute myeloid leukemia analysis demonstrate the methods immediate practical relevance. Author summaryHere we built up a mathematically justified bridge between parametric approaches and co-expression networks that have become prevalent for identifying molecular interactions underlying complex traits. We first shared our concern that methodological improvements around these schemes adjusting only their power and scalability are bounded by more fundamental scheme-specific limitations. Subsequently, our theoretical results were exploited to overcome these limitations to find gene-by-gene interactions neither of which can capture alone. We also aimed to illustrate theoretically and empirically how this framework enables the interpretation of co-expression networks in a more parametric sense to achieve systematic insights into complex biological processes more reliably. The main procedure was fit for various types of biological applications and high-dimensional data to cover the area of systems biology as broadly as possible. In particular, we chose to illustrate the methods applicability for gene-profile based risk-stratification in cancer research using public acute myeloid leukemia datasets.

systems biology↗

bioRxiv2019

Long-term reciprocal gene flow in wild and domestic geese reveals complex domestication history

Hybridization has frequently been observed between wild and domestic species and can substantially impact genetic diversity of both counterparts. Geese show some of the highest levels of interspecific hybridization across all bird orders, and two of the goose species in genus Anser have been domesticated providing excellent opportunity for joint study of domestication and hybridization. Until now, knowledge on the details of the goose domestication process has come from archaeological findings and historical writings supplemented with few studies based on mitochondrial DNA. Here, we used genome-wide markers to make the first genome-based inference of the timing of European goose domestication. We also analyzed the impact of hybridization on the genome-wide genetic variation in current populations of the European domestic goose and its wild progenitor: the greylag goose (Anser anser). Our dataset consisted of 58 wild greylags sampled around Eurasia and 75 domestic geese representing 14 breeds genotyped for 33,527 single nucleotide polymorphisms. Demographic reconstruction and clustering analysis suggested that divergence between wild and domestic geese around 5,300 generations ago was followed by long-term genetic exchange, and that greylag populations have 3.2-58.0% admixture proportions with domestic geese, with distinct geographic patterns. Surprisingly, many modern European breeds share considerable (> 10%) ancestry with Chinese domestic geese that is derived from the swan goose Anser cygnoid. We show that domestication process can progress despite continued and pervasive gene flow from the wild form.\n\nSignificance StatementReproductive isolation between conspecific wild and domestic populations is a cornerstone of the domestication process, yet gene flow between such wild and domestic populations has been frequently documented. European domestic geese and their wild progenitor (greylags) co-occur and can hybridize and we show that they represent a particularly persuasive case where wild and domestic populations are not isolated gene pools. Our study makes a first genome-based estimate of goose domestication, which up to now has mostly relied on archaeological findings and historical writings. We show ongoing gene flow between greylags and European domestic geese following domestication, but we also observe a surprisingly large contribution of Chinese domestic geese (a separate species) to the genetic make-up of European domestic geese.

evolutionary biology↗