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Publications (10 of 160) Show all publications
Mariën, B., Robinson, K. M., Jurca, M., Michelson, I. H., Takata, N., Kozarewa, I., . . . Eriksson, M. E. (2025). Nature's master of ceremony: The Populus circadian clock as orchestratot of tree growth and phenology. Npj biological timing and sleep, 2(1), Article ID 16.
Open this publication in new window or tab >>Nature's master of ceremony: The Populus circadian clock as orchestratot of tree growth and phenology
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2025 (English)In: Npj biological timing and sleep, E-ISSN 2948-281X, Vol. 2, no 1, article id 16Article in journal (Refereed) Published
Abstract [en]

Understanding the timely regulation of plant growth and phenology is crucial for assessing a terrestrial ecosystem's productivity and carbon budget. The circadian clock, a system of genetic oscillators, acts as 'Master of Ceremony' during plant physiological processes. The mechanism is particularly elusive in trees despite its relevance. The primary and secondary tree growth, leaf senescence, bud set, and bud burst timing were investigated in 68 constructs transformed into Populus hybrids and compared with untransformed or transformed controls grown in natural or controlled conditions. The results were analyzed using generalized additive models with ordered-factor-smooth interaction smoothers. This meta-analysis shows that several genetic components are associated with the clock. Especially core clock-regulated genes affected tree growth and phenology in both controlled and field conditions. Our results highlight the importance of field trials and the potential of using the clock to generate trees with improved characteristics for sustainable silviculture (e.g., reprogrammed to new photoperiodic regimes and increased growth).

Place, publisher, year, edition, pages
Springer Nature, 2025
Keywords
Biological techniques, Plant sciences
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-237715 (URN)10.1038/s44323-025-00034-4 (DOI)40206183 (PubMedID)
Funder
The Kempe FoundationsVinnovaKnut and Alice Wallenberg Foundation
Available from: 2025-04-15 Created: 2025-04-15 Last updated: 2025-04-15Bibliographically approved
Bag, P., Ivanov, A. G., Huner, N. P. & Jansson, S. (2025). Photosynthetic advantages of conifers in the boreal forest. Trends in Plant Science, 30(4), 409-423
Open this publication in new window or tab >>Photosynthetic advantages of conifers in the boreal forest
2025 (English)In: Trends in Plant Science, ISSN 1360-1385, E-ISSN 1878-4372, Vol. 30, no 4, p. 409-423Article, review/survey (Refereed) Published
Abstract [en]

Boreal conifers – the ‘Christmas trees’ – maintain their green needles over the winter by retaining their chlorophyll. These conifers face the toughest challenge in February and March, when subzero temperatures coincide with high solar radiation. To balance the light energy they harvest with the light energy they utilise, conifers deploy various mechanisms in parallel. These include, thylakoid destacking, which facilitates direct energy transfer from Photosystem II (PSII) to Photosystem I (PSI), and excess energy dissipation through sustained nonphotochemical quenching (NPQ). Additionally, they upregulate alternative electron transport pathways to safely reroute excess electrons while maintaining ATP production. From an evolutionary and ecological perspective, we consider these mechanisms as part of a comprehensive photosynthetic alteration, which enhances our understanding of winter acclimation in conifers and their dominance in the boreal forests.

Place, publisher, year, edition, pages
Elsevier, 2025
Keywords
alternative electron transport, conifers, direct energy transfer, flavodiiron proteins, nonphotochemical quenching (NPQ), photosystems
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-232503 (URN)10.1016/j.tplants.2024.10.018 (DOI)39580266 (PubMedID)2-s2.0-105001083406 (Scopus ID)
Funder
EU, Horizon 2020, 675006
Available from: 2024-12-02 Created: 2024-12-02 Last updated: 2025-04-30Bibliographically approved
Robinson, K. M., Schiffthaler, B., Liu, H., Rydman, S. M., Rendón-Anaya, M., Ahlgren Kalman, T., . . . Street, N. (2024). An improved chromosome-scale genome assembly and population genetics resource for populus tremula. Physiologia Plantarum, 176(5), Article ID e14511.
Open this publication in new window or tab >>An improved chromosome-scale genome assembly and population genetics resource for populus tremula
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2024 (English)In: Physiologia Plantarum, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 176, no 5, article id e14511Article in journal (Refereed) Published
Abstract [en]

Aspen (Populus tremula L.) is a keystone species and a model system for forest tree genomics. We present an updated resource comprising a chromosome-scale assem- bly, population genetics and genomics data. Using the resource, we explore the genetic basis of natural variation in leaf size and shape, traits with complex genetic architecture.

We generated the genome assembly using long-read sequencing, optical and high-density genetic maps. We conducted whole-genome resequencing of the Umeå Aspen (UmAsp) collection. Using the assembly and re-sequencing data from the UmAsp, Swedish Aspen (SwAsp) and Scottish Aspen (ScotAsp) collections we performed genome-wide association analyses (GWAS) using Single Nucleotide Polymorphisms (SNPs) for 26 leaf physiognomy phenotypes. We conducted Assay of Transposase Accessible Chromatin sequencing (ATAC-Seq), identified genomic regions of accessible chromatin, and subset SNPs to these regions, improving the GWAS detection rate. We identified candidate long non-coding RNAs in leaf samples, quantified their expression in an updated co-expression network, and used this to explore the functions of candidate genes identified from the GWAS.

A GWAS found SNP associations for seven traits. The associated SNPs were in or near genes annotated with developmental functions, which represent candidates for further study. Of particular interest was a !177-kbp region harbouring associations with several leaf phenotypes in ScotAsp.

We have incorporated the assembly, population genetics, genomics, and GWAS data into the PlantGenIE.org web resource, including updating existing genomics data to the new genome version, to enable easy exploration and visualisation. We provide all raw and processed data to facilitate reuse in future studies.

Place, publisher, year, edition, pages
John Wiley & Sons, 2024
Keywords
genome assembly, natural selection, co-expression, population genetics, Populus, aspen, GWAS, leaf physiognomy, leaf shape, leaf size, genetic architecture, ATAC-Seq, lncRNA
National Category
Bioinformatics and Computational Biology Genetics and Genomics
Identifiers
urn:nbn:se:umu:diva-229976 (URN)10.1111/ppl.14511 (DOI)001313686100001 ()39279509 (PubMedID)2-s2.0-85204093798 (Scopus ID)
Funder
Swedish Research Council, 2019-05476Swedish Research Council Formas, 2018-01644Vinnova, S111416L0710
Note

Supplementary figures and appendixes under Supporting information on article web page. 

Available from: 2024-09-23 Created: 2024-09-23 Last updated: 2025-04-24Bibliographically approved
Nanda, S., Shutova, T., Cainzos, M., Bag, P., Jansson, S. & Holzwarth, A. R. (2024). ChloroSpec: A new in vivo chlorophyll fluorescence spectrometer for simultaneous wavelength- and time-resolved detection. Physiologia Plantarum, 176(2), Article ID e14306.
Open this publication in new window or tab >>ChloroSpec: A new in vivo chlorophyll fluorescence spectrometer for simultaneous wavelength- and time-resolved detection
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2024 (English)In: Physiologia Plantarum, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 176, no 2, article id e14306Article in journal (Refereed) Published
Abstract [en]

Chlorophyll fluorescence is a ubiquitous tool in basic and applied plant science research. Various standard commercial instruments are available for characterization of photosynthetic material like leaves or microalgae, most of which integrate the overall fluorescence signals above a certain cut-off wavelength. However, wavelength-resolved (fluorescence signals appearing at different wavelengths having different time dependent decay) signals contain vast information required to decompose complex signals and processes into their underlying components that can untangle the photo-physiological process of photosynthesis. Hence, to address this we describe an advanced chlorophyll fluorescence spectrometer - ChloroSpec - allowing three-dimensional simultaneous detection of fluorescence intensities at different wavelengths in a time-resolved manner. We demonstrate for a variety of typical examples that most of the generally used fluorescence parameters are strongly wavelength dependent. This indicates a pronounced heterogeneity and a highly dynamic nature of the thylakoid and the photosynthetic apparatus under actinic illumination. Furthermore, we provide examples of advanced global analysis procedures integrating this three-dimensional signal and relevant information extracted from them that relate to the physiological properties of the organism. This conveniently obtained broad range of data can make ChloroSpec a new standard tool in photosynthesis research.

Place, publisher, year, edition, pages
John Wiley & Sons, 2024
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-223953 (URN)10.1111/ppl.14306 (DOI)001207485500001 ()38659135 (PubMedID)2-s2.0-85191196422 (Scopus ID)
Funder
The Kempe FoundationsSwedish Research CouncilKnut and Alice Wallenberg FoundationSwedish Foundation for Strategic Research
Available from: 2024-05-03 Created: 2024-05-03 Last updated: 2025-02-14Bibliographically approved
Bag, P., Shutova, T., Shevela, D., Lihavainen, J., Nanda, S., Ivanov, A. G., . . . Jansson, S. (2023). Flavodiiron-mediated O2 photoreduction at photosystem I acceptor-side provides photoprotection to conifer thylakoids in early spring. Nature Communications, 14(1), Article ID 3210.
Open this publication in new window or tab >>Flavodiiron-mediated O2 photoreduction at photosystem I acceptor-side provides photoprotection to conifer thylakoids in early spring
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2023 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 3210Article in journal (Refereed) Published
Abstract [en]

Green organisms evolve oxygen (O2) via photosynthesis and consume it by respiration. Generally, net O2 consumption only becomes dominant when photosynthesis is suppressed at night. Here, we show that green thylakoid membranes of Scots pine (Pinus sylvestris L) and Norway spruce (Picea abies) needles display strong O2 consumption even in the presence of light when extremely low temperatures coincide with high solar irradiation during early spring (ES). By employing different electron transport chain inhibitors, we show that this unusual light-induced O2 consumption occurs around photosystem (PS) I and correlates with higher abundance of flavodiiron (Flv) A protein in ES thylakoids. With P700 absorption changes, we demonstrate that electron scavenging from the acceptor-side of PSI via O2 photoreduction is a major alternative pathway in ES. This photoprotection mechanism in vascular plants indicates that conifers have developed an adaptative evolution trajectory for growing in harsh environments.

Place, publisher, year, edition, pages
Springer Nature, 2023
National Category
Biochemistry Molecular Biology Botany
Identifiers
urn:nbn:se:umu:diva-209538 (URN)10.1038/s41467-023-38938-z (DOI)001002562700001 ()37270605 (PubMedID)2-s2.0-85160880215 (Scopus ID)
Funder
EU, Horizon 2020, 675006Swedish Research Council, (2016-04894 aSwedish Research Council, 2021-05062Swedish Research Council, 2020-03809The Kempe Foundations, 2014Swedish Research Council Formas, 2015-00907Swedish Research Council Formas, 2021-01474Swedish Foundation for Strategic Research, FFF20- 0008Vinnova, 2016-00504Knut and Alice Wallenberg Foundation, 2016-0352Knut and Alice Wallenberg Foundation, 2020.0240Göran Gustafsson Foundation for Research in Natural Sciences and Medicine, BS2022-0021
Available from: 2023-06-13 Created: 2023-06-13 Last updated: 2025-02-20Bibliographically approved
Escamez, S., Robinson, K. M., Luomaranta, M., Gandla, M. L., Mähler, N., Yassin, Z., . . . Tuominen, H. (2023). Genetic markers and tree properties predicting wood biorefining potential in aspen (Populus tremula) bioenergy feedstock. Biotechnology for Biofuels and Bioproducts, 16(1), Article ID 65.
Open this publication in new window or tab >>Genetic markers and tree properties predicting wood biorefining potential in aspen (Populus tremula) bioenergy feedstock
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2023 (English)In: Biotechnology for Biofuels and Bioproducts, E-ISSN 2731-3654, Vol. 16, no 1, article id 65Article in journal (Refereed) Published
Abstract [en]

Background: Wood represents the majority of the biomass on land and constitutes a renewable source of biofuels and other bioproducts. However, wood is recalcitrant to bioconversion, raising a need for feedstock improvement in production of, for instance, biofuels. We investigated the properties of wood that affect bioconversion, as well as the underlying genetics, to help identify superior tree feedstocks for biorefining.

Results: We recorded 65 wood-related and growth traits in a population of 113 natural aspen genotypes from Sweden (https://doi.org/10.5061/dryad.gtht76hrd). These traits included three growth and field performance traits, 20 traits for wood chemical composition, 17 traits for wood anatomy and structure, and 25 wood saccharification traits as indicators of bioconversion potential. Glucose release after saccharification with acidic pretreatment correlated positively with tree stem height and diameter and the carbohydrate content of the wood, and negatively with the content of lignin and the hemicellulose sugar units. Most of these traits displayed extensive natural variation within the aspen population and high broad-sense heritability, supporting their potential in genetic improvement of feedstocks towards improved bioconversion. Finally, a genome-wide association study (GWAS) revealed 13 genetic loci for saccharification yield (on a whole-tree-biomass basis), with six of them intersecting with associations for either height or stem diameter of the trees.

Conclusions: The simple growth traits of stem height and diameter were identified as good predictors of wood saccharification yield in aspen trees. GWAS elucidated the underlying genetics, revealing putative genetic markers for bioconversion of bioenergy tree feedstocks.

Place, publisher, year, edition, pages
BioMed Central (BMC), 2023
Keywords
Bioenergy, Biomass, Biorefining, Feedstock recalcitrance, Forest feedstocks, Saccharification
National Category
Forest Science
Identifiers
urn:nbn:se:umu:diva-206938 (URN)10.1186/s13068-023-02315-1 (DOI)000967835900001 ()2-s2.0-85152632077 (Scopus ID)
Funder
Swedish Research Council Formas, 942-2015-84Swedish Research Council Formas, 2018-01381Knut and Alice Wallenberg Foundation, 2016.0341Knut and Alice Wallenberg Foundation, 2016.0352Vinnova, 2016-00504Bio4Energy
Available from: 2023-04-27 Created: 2023-04-27 Last updated: 2025-03-05Bibliographically approved
Lihavainen, J., Šimura, J., Bag, P., Fataftah, N., Robinson, K. M., Delhomme, N., . . . Jansson, S. (2023). Salicylic acid metabolism and signalling coordinate senescence initiation in aspen in nature. Nature Communications, 14(1), Article ID 4288.
Open this publication in new window or tab >>Salicylic acid metabolism and signalling coordinate senescence initiation in aspen in nature
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2023 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 4288Article in journal (Refereed) Published
Abstract [en]

Deciduous trees exhibit a spectacular phenomenon of autumn senescence driven by the seasonality of their growth environment, yet there is no consensus which external or internal cues trigger it. Senescence starts at different times in European aspen (Populus tremula L.) genotypes grown in same location. By integrating omics studies, we demonstrate that aspen genotypes utilize similar transcriptional cascades and metabolic cues to initiate senescence, but at different times during autumn. The timing of autumn senescence initiation appeared to be controlled by two consecutive “switches”; 1) first the environmental variation induced the rewiring of the transcriptional network, stress signalling pathways and metabolic perturbations and 2) the start of senescence process was defined by the ability of the genotype to activate and sustain stress tolerance mechanisms mediated by salicylic acid. We propose that salicylic acid represses the onset of leaf senescence in stressful natural conditions, rather than promoting it as often observed in annual plants.

Place, publisher, year, edition, pages
Springer Nature, 2023
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-212477 (URN)10.1038/s41467-023-39564-5 (DOI)001037322100027 ()37463905 (PubMedID)2-s2.0-85165262787 (Scopus ID)
Funder
Swedish Research CouncilSwedish Research Council FormasThe Kempe FoundationsSwedish Foundation for Strategic ResearchKnut and Alice Wallenberg FoundationVinnova
Available from: 2023-08-03 Created: 2023-08-03 Last updated: 2025-04-24Bibliographically approved
Arshad, R., Saccon, F., Bag, P., Biswas, A., Calvaruso, C., Bhatti, A. F., . . . Büchel, C. (2022). A kaleidoscope of photosynthetic antenna proteins and their emerging roles. Plant Physiology, 189(3), 1204-1219
Open this publication in new window or tab >>A kaleidoscope of photosynthetic antenna proteins and their emerging roles
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2022 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 189, no 3, p. 1204-1219Article in journal (Refereed) Published
Abstract [en]

Photosynthetic light-harvesting antennae are pigment-binding proteins that perform one of the most fundamental tasks on Earth, capturing light and transferring energy that enables life in our biosphere. Adaptation to different light environments led to the evolution of an astonishing diversity of light-harvesting systems. At the same time, several strategies have been developed to optimize the light energy input into photosynthetic membranes in response to fluctuating conditions. The basic feature of these prompt responses is the dynamic nature of antenna complexes, whose function readily adapts to the light available. High-resolution microscopy and spectroscopic studies on membrane dynamics demonstrate the crosstalk between antennae and other thylakoid membrane components. With the increased understanding of light-harvesting mechanisms and their regulation, efforts are focusing on the development of sustainable processes for effective conversion of sunlight into functional bio-products. The major challenge in this approach lies in the application of fundamental discoveries in light-harvesting systems for the improvement of plant or algal photosynthesis. Here, we underline some of the latest fundamental discoveries on the molecular mechanisms and regulation of light harvesting that can potentially be exploited for the optimization of photosynthesis.

Place, publisher, year, edition, pages
Oxford University Press, 2022
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-194031 (URN)10.1093/plphys/kiac175 (DOI)000790909500001 ()35512089 (PubMedID)2-s2.0-85133103283 (Scopus ID)
Funder
EU, Horizon 2020, 675006
Available from: 2022-04-22 Created: 2022-04-22 Last updated: 2023-03-23Bibliographically approved
Fataftah, N., Edlund, E., Lihavainen, J., Bag, P., Björkén, L., Näsholm, T. & Jansson, S. (2022). Nitrate fertilization may delay autumn leaf senescence, while amino acid treatments do not. Physiologia Plantarum, 174(3), Article ID e13690.
Open this publication in new window or tab >>Nitrate fertilization may delay autumn leaf senescence, while amino acid treatments do not
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2022 (English)In: Physiologia Plantarum, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 174, no 3, article id e13690Article in journal (Refereed) Published
Abstract [en]

Fertilization with nitrogen (N)-rich compounds leads to increased growth but may compromise phenology and winter survival of trees in boreal regions. During autumn, N is remobilized from senescing leaves and stored in other parts of the tree to be used in the next growing season. However, the mechanism behind the N fertilization effect on winter survival is not well understood, and it is unclear how N levels or forms modulate autumn senescence. We performed fertilization experiments and showed that treating Populus saplings with inorganic nitrogen resulted in a delay in senescence. In addition, by using precise delivery of solutes into the xylem stream of Populus trees in their natural environment, we found that delay of autumn senescence was dependent on the form of N administered: inorganic N ((Formula presented.)) delayed senescence, but amino acids (Arg, Glu, Gln, and Leu) did not. Metabolite profiling of leaves showed that the levels of tricarboxylic acids, arginine catabolites (ammonium, ornithine), glycine, glycine-serine ratio and overall carbon-to-nitrogen (C/N) ratio were affected differently by the way of applying NO3− and Arg treatments. In addition, the onset of senescence did not coincide with soluble sugar accumulation in control trees or in any of the treatments. We propose that different regulation of C and N status through direct molecular signaling of NO3− and/or different allocation of N between tree parts depending on N forms could account for the contrasting effects of NO3− and tested here amino acids (Arg, Glu, Gln, and Leu) on autumn senescence.

Place, publisher, year, edition, pages
John Wiley & Sons, 2022
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-203158 (URN)10.1111/ppl.13690 (DOI)000798701400001 ()35460591 (PubMedID)2-s2.0-85132885123 (Scopus ID)
Funder
Swedish Research CouncilSwedish Research Council FormasKnut and Alice Wallenberg FoundationVinnova
Available from: 2023-01-16 Created: 2023-01-16 Last updated: 2023-01-16Bibliographically approved
Boussardon, C., Bag, P., Juvany, M., Šimura, J., Ljung, K., Jansson, S. & Keech, O. (2022). The RPN12a proteasome subunit is essential for the multiple hormonal homeostasis controlling the progression of leaf senescence. Communications Biology, 5(1), Article ID 1043.
Open this publication in new window or tab >>The RPN12a proteasome subunit is essential for the multiple hormonal homeostasis controlling the progression of leaf senescence
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2022 (English)In: Communications Biology, E-ISSN 2399-3642, Vol. 5, no 1, article id 1043Article in journal (Refereed) Published
Abstract [en]

The 26S proteasome is a conserved multi-subunit machinery in eukaryotes. It selectively degrades ubiquitinated proteins, which in turn provides an efficient molecular mechanism to regulate numerous cellular functions and developmental processes. Here, we studied a new loss-of-function allele of RPN12a, a plant ortholog of the yeast and human structural component of the 19S proteasome RPN12. Combining a set of biochemical and molecular approaches, we confirmed that a rpn12a knock-out had exacerbated 20S and impaired 26S activities. The altered proteasomal activity led to a pleiotropic phenotype affecting both the vegetative growth and reproductive phase of the plant, including a striking repression of leaf senescence associate cell-death. Further investigation demonstrated that RPN12a is involved in the regulation of several conjugates associated with the auxin, cytokinin, ethylene and jasmonic acid homeostasis. Such enhanced aptitude of plant cells for survival in rpn12a contrasts with reports on animals, where 26S proteasome mutants generally show an accelerated cell death phenotype.

Place, publisher, year, edition, pages
Nature Publishing Group, 2022
National Category
Botany Biochemistry Molecular Biology
Identifiers
urn:nbn:se:umu:diva-200406 (URN)10.1038/s42003-022-03998-2 (DOI)000862402500001 ()36180574 (PubMedID)2-s2.0-85139221413 (Scopus ID)
Funder
The Kempe FoundationsCarl Tryggers foundation , CTS2018-193Swedish Foundation for Strategic Research, FFF20-0008Knut and Alice Wallenberg FoundationVinnova
Available from: 2022-10-21 Created: 2022-10-21 Last updated: 2025-02-20Bibliographically approved
Projects
How do trees know it is autumn? [2009-05669_VR]; Umeå UniversityINFORMATIVE GENETICS MARKERS FOR TREES [2010-1450_Formas]; Umeå UniversityStructure and function of the proteins of the LHC family [2012-04755_VR]; Umeå UniversityHOW DO TREES KNOW IT IS AUTUMN? [2015-907_Formas]; Umeå UniversityHow do trees survive the winter? [2016-04894_VR]; Umeå University
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-7906-6891

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