Digitala Vetenskapliga Arkivet

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 improved genome assembly of the European aspen 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.ORCID iD: 0000-0002-9771-467x
Show others and affiliations
(English)Manuscript (preprint) (Other academic)
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:umu:diva-170640OAI: oai:DiVA.org:umu-170640DiVA, id: diva2:1429850
Available from: 2020-05-12 Created: 2020-05-12 Last updated: 2020-05-14
In thesis
1. Embracing the data flood: integrating diverse data to improve phenotype association discovery in forest trees
Open this publication in new window or tab >>Embracing the data flood: integrating diverse data to improve phenotype association discovery in forest trees
2020 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Complex traits represent valuable research targets as many highly desirable properties of plants and animals (such as growth rate and height) fall into this group. However, associating biological markers with these traits is incredibly challenging, in part due to their small effect sizes. For the two species at the core of our research, European aspen (Populus tremula) and Norway spruce (Picea abies), association studies are even more challenging, primarily due to the fragmented state of their genome assemblies. These assemblies represent the gene space well, but poorly represented inter-genic regions hinder variant discovery and large scale association studies.

In this thesis, I present my work to improve association discovery of complex traits in forest trees. Firstly, to overcome the issues with assembly fragmentation, I have created an updated version of the P. tremula genome, which is highly contiguous and anchored in full chromosomes. To calculate the dense linkage map required to order and orient the aspen assembly, I developed "BatchMap", a parallel implementation of linkage mapping software. BatchMap has been successfully applied to several dense linkage maps, including aspen and Norway spruce, and was essential to the progress in improving the aspen genome assembly. Further, I developed seidr, which represents a starting point in multi-layer, network-based systems biology, an analysis technique with promising prospects for complex trait association analysis. As a case study, I applied some of the methods developed to the analysis of leaf shape in natural populations of European aspen, a complex, omnigenic trait.

The multi-layer model of systems biology and related analysis techniques offer promise in the analysis of complex traits, and this thesis represents a starting point toward an intricate, holistic model of systems biology that may help to unravel the overwhelmingly complicated nature of complex traits.

Place, publisher, year, edition, pages
Umeå: Umeå University, 2020. p. 83
Keywords
Systems Biology, Association Discovery, Genomics, Transcriptomics, Genome Assembly, Gene Networks, Forest Tree, Aspen, Spruce
National Category
Biological Sciences
Research subject
biology
Identifiers
urn:nbn:se:umu:diva-170643 (URN)978-91-7855-273-3 (ISBN)978-91-7855-274-0 (ISBN)
Public defence
2020-06-12, KBE303 - Stora hörsalen, Umeå, 10:00 (English)
Opponent
Supervisors
Note

2020-06-10: Errata spikblad - Ny tid för disputation. 

Available from: 2020-05-20 Created: 2020-05-13 Last updated: 2020-06-10Bibliographically approved

Open Access in DiVA

No full text in DiVA

Search in DiVA

By author/editor
Schiffthaler, Bastian
By organisation
Umeå Plant Science Centre (UPSC)Department of Plant Physiology
Biological Sciences

Search outside of DiVA

GoogleGoogle Scholar

urn-nbn

Altmetric score

urn-nbn
Total: 257 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