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Publications (10 of 13) Show all publications
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: 2023-11-06Bibliographically approved
Bai, B., Schiffthaler, B., van der Horst, S., Willems, L., Vergara, A., Karlström, J., . . . Hanson, J. (2023). SeedTransNet: a directional translational network revealing regulatory patterns during seed maturation and germination. Journal of Experimental Botany, 74(7), 2416-2432
Open this publication in new window or tab >>SeedTransNet: a directional translational network revealing regulatory patterns during seed maturation and germination
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2023 (English)In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 74, no 7, p. 2416-2432Article in journal (Refereed) Published
Abstract [en]

Seed maturation is the developmental process that prepares the embryo for the desiccated waiting period before germination. It is associated with a series of physiological changes leading to the establishment of seed dormancy, seed longevity, and desiccation tolerance. We studied translational changes during seed maturation and observed a gradual reduction in global translation during seed maturation. Transcriptome and translatome profiling revealed specific reduction in the translation of thousands of genes. By including previously published data on germination and seedling establishment, a regulatory network based on polysome occupancy data was constructed: SeedTransNet. Network analysis predicted translational regulatory pathways involving hundreds of genes with distinct functions. The network identified specific transcript sequence features suggesting separate translational regulatory circuits. The network revealed several seed maturation-associated genes as central nodes, and this was confirmed by specific seed phenotypes of the respective mutants. One of the regulators identified, an AWPM19 family protein, PM19-Like1 (PM19L1), was shown to regulate seed dormancy and longevity. This putative RNA-binding protein also affects the translational regulation of its target mRNA, as identified by SeedTransNet. Our data show the usefulness of SeedTransNet in identifying regulatory pathways during seed phase transitions.

Place, publisher, year, edition, pages
Oxford University Press, 2023
Keywords
Arabidopsis thaliana, mRNA regulation, ribosome, seed germination, seed maturation, translatome profiling
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-209153 (URN)10.1093/jxb/erac394 (DOI)000885655900001 ()36208446 (PubMedID)2-s2.0-85160085758 (Scopus ID)
Funder
Bio4EnergySwedish National Infrastructure for Computing (SNIC)
Available from: 2023-06-20 Created: 2023-06-20 Last updated: 2023-06-20Bibliographically approved
Curci, P. L., Zhang, J., Mähler, N., Seyfferth, C., Mannapperuma, C., Diels, T., . . . Vandepoele, K. (2022). Identification of growth regulators using cross-species network analysis in plants. Plant Physiology, 190(4), 2350-2365
Open this publication in new window or tab >>Identification of growth regulators using cross-species network analysis in plants
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2022 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 190, no 4, p. 2350-2365Article in journal (Refereed) Published
Abstract [en]

With the need to increase plant productivity, one of the challenges plant scientists are facing is to identify genes that play a role in beneficial plant traits. Moreover, even when such genes are found, it is generally not trivial to transfer this knowledge about gene function across species to identify functional orthologs. Here, we focused on the leaf to study plant growth. First, we built leaf growth transcriptional networks in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and aspen (Populus tremula). Next, known growth regulators, here defined as genes that when mutated or ectopically expressed alter plant growth, together with cross-species conserved networks, were used as guides to predict novel Arabidopsis growth regulators. Using an in-depth literature screening, 34 out of 100 top predicted growth regulators were confirmed to affect leaf phenotype when mutated or overexpressed and thus represent novel potential growth regulators. Globally, these growth regulators were involved in cell cycle, plant defense responses, gibberellin, auxin, and brassinosteroid signaling. Phenotypic characterization of loss-of-function lines confirmed two predicted growth regulators to be involved in leaf growth (NPF6.4 and LATE MERISTEM IDENTITY2). In conclusion, the presented network approach offers an integrative cross-species strategy to identify genes involved in plant growth and development.

Place, publisher, year, edition, pages
Oxford University Press, 2022
National Category
Botany Plant Biotechnology
Identifiers
urn:nbn:se:umu:diva-201619 (URN)10.1093/plphys/kiac374 (DOI)000844537500001 ()35984294 (PubMedID)2-s2.0-85143141934 (Scopus ID)
Funder
The Research Council of Norway, 287465
Available from: 2022-12-14 Created: 2022-12-14 Last updated: 2022-12-14Bibliographically approved
Gandla, M. L., Mähler, N., Escamez, S., Skotare, T., Obudulu, O., Möller, L., . . . Jönsson, L. J. (2021). Overexpression of vesicle-associated membrane protein PttVAP27-17 as a tool to improve biomass production and the overall saccharification yields in Populus trees. Biotechnology for Biofuels, 14(1), Article ID 43.
Open this publication in new window or tab >>Overexpression of vesicle-associated membrane protein PttVAP27-17 as a tool to improve biomass production and the overall saccharification yields in Populus trees
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2021 (English)In: Biotechnology for Biofuels, ISSN 1754-6834, E-ISSN 1754-6834, Vol. 14, no 1, article id 43Article in journal (Refereed) Published
Abstract [en]

Background: Bioconversion of wood into bioproducts and biofuels is hindered by the recalcitrance of woody raw material to bioprocesses such as enzymatic saccharification. Targeted modification of the chemical composition of the feedstock can improve saccharification but this gain is often abrogated by concomitant reduction in tree growth.

Results: In this study, we report on transgenic hybrid aspen (Populus tremula × tremuloides) lines that showed potential to increase biomass production both in the greenhouse and after 5 years of growth in the field. The transgenic lines carried an overexpression construct for Populus tremula × tremuloides vesicle-associated membrane protein (VAMP)-associated protein PttVAP27-17 that was selected from a gene-mining program for novel regulators of wood formation. Analytical-scale enzymatic saccharification without any pretreatment revealed for all greenhouse-grown transgenic lines, compared to the wild type, a 20–44% increase in the glucose yield per dry weight after enzymatic saccharification, even though it was statistically significant only for one line. The glucose yield after enzymatic saccharification with a prior hydrothermal pretreatment step with sulfuric acid was not increased in the greenhouse-grown transgenic trees on a dry-weight basis, but increased by 26–50% when calculated on a whole biomass basis in comparison to the wild-type control. Tendencies to increased glucose yields by up to 24% were present on a whole tree biomass basis after acidic pretreatment and enzymatic saccharification also in the transgenic trees grown for 5 years on the field when compared to the wild-type control.

Conclusions: The results demonstrate the usefulness of gene-mining programs to identify novel genes with the potential to improve biofuel production in tree biotechnology programs. Furthermore, multi-omic analyses, including transcriptomic, proteomic and metabolomic analyses, performed here provide a toolbox for future studies on the function of VAP27 proteins in plants.

Place, publisher, year, edition, pages
BioMed Central, 2021
Keywords
Bioprocessing, Growth, Metabolomics, Populus, Proteomics, Transcriptomics, VAMP, VAMP-associated protein, VAP27, Vesicle-associated membrane protein
National Category
Plant Biotechnology
Identifiers
urn:nbn:se:umu:diva-180984 (URN)10.1186/s13068-021-01895-0 (DOI)000620931600002 ()2-s2.0-85100873005 (Scopus ID)
Available from: 2021-03-05 Created: 2021-03-05 Last updated: 2023-11-06Bibliographically approved
Christie, N., Mannapperuma, C., Ployet, R., van der Merwe, K., Mähler, N., Delhomme, N., . . . Myburg, A. A. (2021). qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE). BMC Bioinformatics, 22(1), Article ID 595.
Open this publication in new window or tab >>qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE)
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2021 (English)In: BMC Bioinformatics, E-ISSN 1471-2105, Vol. 22, no 1, article id 595Article in journal (Refereed) Published
Abstract [en]

Background: Affordable high-throughput DNA and RNA sequencing technologies are allowing genomic analysis of plant and animal populations and as a result empowering new systems genetics approaches to study complex traits. The availability of intuitive tools to browse and analyze the resulting large-scale genetic and genomic datasets remain a significant challenge. Furthermore, these integrative genomics approaches require innovative methods to dissect the flow and interconnectedness of biological information underlying complex trait variation. The Plant Genome Integrative Explorer (PlantGenIE.org) is a multi-species database and domain that houses online tools for model and woody plant species including Eucalyptus. Since the Eucalyptus Genome Integrative Explorer (EucGenIE) is integrated within PlantGenIE, it shares genome and expression analysis tools previously implemented within the various subdomains (ConGenIE, PopGenIE and AtGenIE). Despite the success in setting up integrative genomics databases, online tools for systems genetics modelling and high-resolution dissection of complex trait variation in plant populations have been lacking.

Results: We have developed qtlXplorer (https://eucgenie.org/QTLXplorer) for visualizing and exploring systems genetics data from genome-wide association studies including quantitative trait loci (QTLs) and expression-based QTL (eQTL) associations. This module allows users to, for example, find co-located QTLs and eQTLs using an interactive version of Circos, or explore underlying genes using JBrowse. It provides users with a means to build systems genetics models and generate hypotheses from large-scale population genomics data. We also substantially upgraded the EucGenIE resource and show how it enables users to combine genomics and systems genetics approaches to discover candidate genes involved in biotic stress responses and wood formation by focusing on two multigene families, laccases and peroxidases.

Conclusions: qtlXplorer adds a new dimension, population genomics, to the EucGenIE and PlantGenIE environment. The resource will be of interest to researchers and molecular breeders working in Eucalyptus and other woody plant species. It provides an example of how systems genetics data can be integrated with functional genetics data to provide biological insight and formulate hypotheses. Importantly, integration within PlantGenIE enables novel comparative genomics analyses to be performed from population-scale data.

Place, publisher, year, edition, pages
BioMed Central, 2021
Keywords
Co-expression, Database, eQTL, Eucalyptus, EucGenIE, Genome browser, Online resource, qtlXplorer, Systems genetics, ‘Omics integration
National Category
Genetics Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:umu:diva-190864 (URN)10.1186/s12859-021-04514-9 (DOI)000730565000001 ()34911434 (PubMedID)2-s2.0-85121369417 (Scopus ID)
Available from: 2021-12-29 Created: 2021-12-29 Last updated: 2024-01-17Bibliographically approved
Müller, N. A., Kersten, B., Leite Montalvão, A. P., Mähler, N., Bernhardsson, C., Bräutigam, K., . . . Fladung, M. (2020). A single gene underlies the dynamic evolution of poplar sex determination. [Letter to the editor]. Nature Plants, 6(6), 630-637
Open this publication in new window or tab >>A single gene underlies the dynamic evolution of poplar sex determination.
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2020 (English)In: Nature Plants, ISSN 2055-0278, Vol. 6, no 6, p. 630-637Article in journal, Letter (Refereed) Published
Abstract [en]

Although hundreds of plant lineages have independently evolved dioecy (that is, separation of the sexes), the underlying genetic basis remains largely elusive. Here we show that diverse poplar species carry partial duplicates of the ARABIDOPSIS RESPONSE REGULATOR 17 (ARR17) orthologue in the male-specific region of the Y chromosome. These duplicates give rise to small RNAs apparently causing male-specific DNA methylation and silencing of the ARR17 gene. CRISPR–Cas9-induced mutations demonstrate that ARR17 functions as a sex switch, triggering female development when on and male development when off. Despite repeated turnover events, including a transition from the XY system to a ZW system, the sex-specific regulation of ARR17 is conserved across the poplar genus and probably beyond. Our data reveal how a single-gene-based mechanism of dioecy can enable highly dynamic sex-linked regions and contribute to maintaining recombination and integrity of sex chromosomes.

Place, publisher, year, edition, pages
Springer Nature, 2020
National Category
Evolutionary Biology Botany
Identifiers
urn:nbn:se:umu:diva-182078 (URN)10.1038/s41477-020-0672-9 (DOI)000537029600001 ()32483326 (PubMedID)
Available from: 2021-04-08 Created: 2021-04-08 Last updated: 2021-04-08Bibliographically approved
Mähler, N., Schiffthaler, B., Robinson, K. M., Terebieniec, B. K., Vucak, M., Mannapperuma, C., . . . Street, N. R. (2020). Leaf shape in Populus tremula is a complex, omnigenic trait. Ecology and Evolution, 10(21), 11922-11940
Open this publication in new window or tab >>Leaf shape in Populus tremula is a complex, omnigenic trait
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2020 (English)In: Ecology and Evolution, E-ISSN 2045-7758, Vol. 10, no 21, p. 11922-11940Article in journal (Refereed) Published
Abstract [en]

Leaf shape is a defining feature of how we recognize and classify plant species. Although there is extensive variation in leaf shape within many species, few studies have disentangled the underlying genetic architecture. We characterized the genetic architecture of leaf shape variation in Eurasian aspen (Populus tremula L.) by performing genome‐wide association study (GWAS) for physiognomy traits. To ascertain the roles of identified GWAS candidate genes within the leaf development transcriptional program, we generated RNA‐Seq data that we used to perform gene co‐expression network analyses from a developmental series, which is publicly available within the PlantGenIE resource. We additionally used existing gene expression measurements across the population to analyze GWAS candidate genes in the context of a population‐wide co‐expression network and to identify genes that were differentially expressed between groups of individuals with contrasting leaf shapes. These data were integrated with expression GWAS (eQTL) results to define a set of candidate genes associated with leaf shape variation. Our results identified no clear adaptive link to leaf shape variation and indicate that leaf shape traits are genetically complex, likely determined by numerous small‐effect variations in gene expression. Genes associated with shape variation were peripheral within the population‐wide co‐expression network, were not highly connected within the leaf development co‐expression network, and exhibited signatures of relaxed selection. As such, our results are consistent with the omnigenic model.

Place, publisher, year, edition, pages
John Wiley & Sons, 2020
Keywords
complex trait, GWAS, leaf shape, natural variation, omnigenic, Populus tremula
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:umu:diva-170641 (URN)10.1002/ece3.6691 (DOI)000578291300001 ()2-s2.0-85092478395 (Scopus ID)
Note

Originally included in thesis in manuscript form.

Available from: 2020-05-12 Created: 2020-05-12 Last updated: 2024-01-17Bibliographically approved
Christie, N., Mannapperuma, C., Ployet, R., Van der Merwe, K., Mähler, N., Delhomme, N., . . . Myburg, A. A. (2020). The Eucalyptus Genome Integrative Explorer: an online resource for systems genetics in forest tree species. The Plant Journal
Open this publication in new window or tab >>The Eucalyptus Genome Integrative Explorer: an online resource for systems genetics in forest tree species
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2020 (English)In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313XArticle in journal (Other academic) Accepted
Place, publisher, year, edition, pages
John Wiley & Sons, 2020
National Category
Other Computer and Information Science Other Biological Topics
Identifiers
urn:nbn:se:umu:diva-170113 (URN)
Available from: 2020-04-27 Created: 2020-04-27 Last updated: 2023-05-02
Obudulu, O., Mähler, N., Skotare, T., Bygdell, J., Abreu, I. N., Ahnlund, M., . . . Tuominen, H. (2018). A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of​ ​​Populus​​ ​trees. BMC Genomics, 19, Article ID 11.
Open this publication in new window or tab >>A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of​ ​​Populus​​ ​trees
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2018 (English)In: BMC Genomics, E-ISSN 1471-2164, Vol. 19, article id 11Article in journal (Refereed) Published
Abstract [en]

Background: Secretory Carrier-Associated Membrane Proteins (SCAMPs) are highly conserved 32–38 kDa proteins that are involved in membrane trafficking. A systems approach was taken to elucidate function of SCAMPs in wood formation of Populus trees. Phenotypic and multi-omics analyses were performed in woody tissues of transgenic Populus trees carrying an RNAi construct for Populus tremula x tremuloides SCAMP3 (PttSCAMP3;Potri.019G104000).

Results: The woody tissues of the transgenic trees displayed increased amounts of both polysaccharides and lignin oligomers, indicating increased deposition of both the carbohydrate and lignin components of the secondary cell walls. This coincided with a tendency towards increased wood density as well as significantly increased thickness of the suberized cork in the transgenic lines. Multivariate OnPLS (orthogonal projections to latent structures) modeling of five different omics datasets (the transcriptome, proteome, GC-MS metabolome, LC-MS metabolome and pyrolysis-GC/MS metabolome) collected from the secondary xylem tissues of the stem revealed systemic variation in the different variables in the transgenic lines, including changes that correlated with the changes in the secondary cell wall composition. The OnPLS model also identified a rather large number of proteins that were more abundant in the transgenic lines than in the wild type. Several of these were related to secretion and/or endocytosis as well as both primary and secondary cell wall biosynthesis.

Conclusions: Populus SCAMP proteins were shown to influence accumulation of secondary cell wall components, including polysaccharides and phenolic compounds, in the woody tissues of Populus tree stems. Our multi-omics analyses combined with the OnPLS modelling suggest that this function is mediated by changes in membrane trafficking to fine-tune the abundance of cell wall precursors and/or proteins involved in cell wall biosynthesis and transport. The data provides a multi-level source of information for future studies on the function of the SCAMP proteins in plant stem tissues.

Place, publisher, year, edition, pages
Springer Publishing Company, 2018
Keywords
Secretory Carrier-Associated Membrane Protein (SCAMP), Populus, Wood chemistry, Wood density, Biomass, Bioprocessing, Cork, Multi-omics
National Category
Cell Biology
Identifiers
urn:nbn:se:umu:diva-143890 (URN)10.1186/s12864-017-4411-1 (DOI)000419232000004 ()2-s2.0-85042468619 (Scopus ID)
Projects
Bio4Energy
Funder
Swedish Research Council Formas, 232-2009-1698Bio4Energy
Available from: 2018-01-12 Created: 2018-01-12 Last updated: 2024-01-17Bibliographically approved
Lin, Y.-C., Wang, J., Delhomme, N., Schiffthaler, B., Sundström, G., Zuccolo, A., . . . Street, N. R. (2018). Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen. Proceedings of the National Academy of Sciences of the United States of America, 115(46), E10970-E10978
Open this publication in new window or tab >>Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen
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2018 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 46, p. E10970-E10978Article in journal (Refereed) Published
Abstract [en]

The Populus genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily Populus trichocarpa (Torr. & Gray), which was the first tree with a whole-genome assembly. To further advance evolutionary and functional genomic analyses in Populus, we produced genome assemblies and population genetics resources of two aspen species, Populus tremula L. and Populus tremuloides Michx. The two aspen species have distributions spanning the Northern Hemisphere, where they are keystone species supporting a wide variety of dependent communities and produce a diverse array of secondary metabolites. Our analyses show that the two aspens share a similar genome structure and a highly conserved gene content with P. trichocarpa but display substantially higher levels of heterozygosity. Based on population resequencing data, we observed widespread positive and negative selection acting on both coding and noncoding regions. Furthermore, patterns of genetic diversity and molecular evolution in aspen are influenced by a number of features, such as expression level, coexpression network connectivity, and regulatory variation. To maximize the community utility of these resources, we have integrated all presented data within the PopGenIE web resource (PopGenIE.org).

Place, publisher, year, edition, pages
NATL ACAD SCIENCES, 2018
Keywords
genome assembly, natural selection, coexpression, population genetics, Populus
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-154950 (URN)10.1073/pnas.1801437115 (DOI)000449934400020 ()30373829 (PubMedID)2-s2.0-85056516875 (Scopus ID)
Available from: 2019-01-07 Created: 2019-01-07 Last updated: 2020-05-13Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-2673-9113

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