umu.sePublications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
An integrated functional genomics and systems genetics analysis of leaf shape in Populus tremula 
Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. (Nathaniel Street)
Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. (Nathaniel Street)
Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. (Nathaniel Street)
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
Show others and affiliations
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Leaf shape is an important component of our relationship with the living world, representing a defining feature of how we recognise and classify plant species. There is extensive variation in the form and function of leaves within and between species. In the current study we utilised variation in leaf shape represented among individuals of a collection of Eurasian aspen (Populus tremula L.) sampled across Sweden and the remarkable extent of heterophylly present to establish morphological, cellular and transcriptional developmental time lines. We performed gene expression network and phenotypical regression analyses to identify genes of central importance or that were highly predictive of shape and size phenotypes during leaf development using a systems biology approach. We complemented this developmental study with a genome wide association study of leaf shape variation to identify single nucleotide polymorphisms associated with leaf shape and size, their genomic context and the biological role of associated genes. We then compared these association candidate genes to differentially expressed genes between groups of genotypes with highly contrasting leaf shapes, also considering whether there were expression quantitative trait loci associated with the genes. We demonstrate that our developmental gene expression series captured known biology for homologs of functionally characterised Arabidopsis thaliana genes and biological processes of importance during leaf development. We identified genes of high importance from the developmental series and natural variation analyses. These included genes with characterised functions in leaf development in addition to many novel candidates. Our systems genetics approach identified numerous genes supported by the developmental time series, phenotypic and expression association mapping and differential expression between phenotypic extremes. As such, we describe a rich resource for directing future functional characterisation studies and a comprehensive data resource characterising the role of gene expression during leaf development in aspen.

Keywords [en]
leaf shape, RNA-Sequencing, expression network, Populus tremula, natural variation, GWAS
National Category
Bioinformatics and Systems Biology Biochemistry and Molecular Biology
Research subject
Molecular Biology; Genetics
Identifiers
URN: urn:nbn:se:umu:diva-156461OAI: oai:DiVA.org:umu-156461DiVA, id: diva2:1289178
Available from: 2019-02-15 Created: 2019-02-15 Last updated: 2019-02-19
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)
Opponent
Supervisors
Available from: 2019-02-21 Created: 2019-02-18 Last updated: 2019-02-21Bibliographically approved

Open Access in DiVA

No full text in DiVA

Authority records BETA

Schiffthaler, BastianTerebieniec, Barbara KMähler, NiklasRobinson, Kathryn MMannapperuma, ChanakaJansson, StefanStreet, Nathaniel R

Search in DiVA

By author/editor
Schiffthaler, BastianTerebieniec, Barbara KMähler, NiklasRobinson, Kathryn MMannapperuma, ChanakaJansson, StefanStreet, Nathaniel R
By organisation
Umeå Plant Science Centre (UPSC)Department of Plant Physiology
Bioinformatics and Systems BiologyBiochemistry and Molecular Biology

Search outside of DiVA

GoogleGoogle Scholar

urn-nbn

Altmetric score

urn-nbn
Total: 265 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf