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Spatially resolved transcriptome profiling in model plant species
Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
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2017 (English)In: Nature Plants, ISSN 2055-026X, Vol. 3, no 6, article id 17061Article in journal (Refereed) Published
Abstract [en]

Understanding complex biological systems requires functional characterization of specialized tissue domains. However, existing strategies for generating and analysing high-throughput spatial expression profiles were developed for a limited range of organisms, primarily mammals. Here we present the first available approach to generate and study highresolution, spatially resolved functional profiles in a broad range of model plant systems. Our process includes highthroughput spatial transcriptome profiling followed by spatial gene and pathway analyses. We first demonstrate the feasibility of the technique by generating spatial transcriptome profiles from model angiosperms and gymnosperms microsections. In Arabidopsis thaliana we use the spatial data to identify differences in expression levels of 141 genes and 189 pathways in eight inflorescence tissue domains. Our combined approach of spatial transcriptomics and functional profiling offers a powerful new strategy that can be applied to a broad range of plant species, and is an approach that will be pivotal to answering fundamental questions in developmental and evolutionary biology.

Place, publisher, year, edition, pages
Nature Publishing Group, 2017. Vol. 3, no 6, article id 17061
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:umu:diva-138048DOI: 10.1038/nplants.2017.61ISI: 000406036800002PubMedID: 28481330OAI: oai:DiVA.org:umu-138048DiVA, id: diva2:1130595
Available from: 2017-08-10 Created: 2017-08-10 Last updated: 2019-02-19Bibliographically approved
In thesis
1. Using systems genetics to explore the complexity of leaf shape variation in Populus tremula
Open this publication in new window or tab >>Using systems genetics to explore the complexity of leaf shape variation in Populus tremula
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Leaves are essential for sustaining humanity as they function as the energy and oxygen-producing organ of plants. Intensive research on physiological processes has contributed immensely to our understanding of the function of leaves. However, comparatively little is known about how leaf size and shape is determined. The aim of my PhD was to assay leaf shape variation among individuals of Populus tremula (European aspen) sampled across the distribution range of Sweden to characterize the genetic architecture underlying variation, including elucidating contributing molecular mechanisms.

In this PhD I employed an integrated systems genetics and systems biology approach to identify genetic components of variation and to assign biological function to these. We integrated population-wide data on leaf shape, gene expression and genome variation from a collection of P. tremula genotypes and used this to perform genome-wide association studies. We then integrated these results with a systems biology transcriptomics study of leaf development to provide developmental and biological context. We demonstrate that our developmental gene expression series captured known homologs of functionally characterized Arabidopsis thaliana genes and biological processes of importance during leaf development. In addition to these known genes of high importance, we also identified many novel candidate genes. Our systems genetics approach identified numerous genes with a potential role in leaf development that was supported by the developmental time series. From our association studies and population analyses we have shown that there are no large-effect loci contributing to variation in leaf shape and that highly ranked loci associated with leaf shape are primarily located in the regulatory regions of genes. Furthermore, we identified loci controlling variation in gene expression and sets of genes with significant differential expression between groups of genotypes with highly contrasting leaf shapes. We show that genes with significant associations influencing expression among genotypes are enriched in the periphery of the corresponding gene co-expression network and that they experience relaxed selective constraint. Taken together, these results suggest that leaf shape is a highly complex trait controlled by a large number of loci, each contributing only a small effect, that those loci likely act via modulation of gene expression and that they do not show signals of adaptive selection. In addition, we adapted and optimized the method of spatial transcriptomics for use in plant species. This method provides a transcriptome-wide in situ, spatially-resolved assay of transcript expression at high spatial resolution.

Place, publisher, year, edition, pages
Umeå: Umeå University, 2019. p. 60
Keywords
Populus, Arabidopsis, systems biology, systems genetics, spatial transcriptomics (ST), single nucleotide polymorphism (SNP), Genome wide associations study (GWAS), expression GWAS (eGWAS)
National Category
Bioinformatics and Systems Biology Genetics
Research subject
Molecular Biology
Identifiers
urn:nbn:se:umu:diva-156464 (URN)978-91-7601-879-8 (ISBN)
Public defence
2019-03-14, Lilla hörsalen, KB.E3.01, KBC-huset, Umeå, 10:00 (English)
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Available from: 2019-02-21 Created: 2019-02-18 Last updated: 2019-02-21Bibliographically approved

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Giacomello, StefaniaTerebieniec, Barbara K.Mannapperuma, ChanakaStreet, Nathaniel

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Giacomello, StefaniaTerebieniec, Barbara K.Mannapperuma, ChanakaStreet, Nathaniel
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Umeå Plant Science Centre (UPSC)Department of Plant Physiology
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