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Embracing the data flood: integrating diverse data to improve phenotype association discovery in forest trees
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. (Nathaniel Street)ORCID-id: 0000-0002-9771-467x
2020 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
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.

Ort, förlag, år, upplaga, sidor
Umeå: Umeå University , 2020. , s. 83
Nyckelord [en]
Systems Biology, Association Discovery, Genomics, Transcriptomics, Genome Assembly, Gene Networks, Forest Tree, Aspen, Spruce
Nationell ämneskategori
Biologiska vetenskaper
Forskningsämne
biologi
Identifikatorer
URN: urn:nbn:se:umu:diva-170643ISBN: 978-91-7855-273-3 (tryckt)ISBN: 978-91-7855-274-0 (digital)OAI: oai:DiVA.org:umu-170643DiVA, id: diva2:1429905
Disputation
2020-06-12, KBE303 - Stora hörsalen, Umeå, 10:00 (Engelska)
Opponent
Handledare
Anmärkning

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

Tillgänglig från: 2020-05-20 Skapad: 2020-05-13 Senast uppdaterad: 2020-06-10Bibliografiskt granskad
Delarbeten
1. Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen
Öppna denna publikation i ny flik eller fönster >>Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen
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2018 (Engelska)Ingår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, nr 46, s. E10970-E10978Artikel i tidskrift (Refereegranskat) 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).

Ort, förlag, år, upplaga, sidor
NATL ACAD SCIENCES, 2018
Nyckelord
genome assembly, natural selection, coexpression, population genetics, Populus
Nationell ämneskategori
Genetik
Identifikatorer
urn:nbn:se:umu:diva-154950 (URN)10.1073/pnas.1801437115 (DOI)000449934400020 ()30373829 (PubMedID)2-s2.0-85056516875 (Scopus ID)
Tillgänglig från: 2019-01-07 Skapad: 2019-01-07 Senast uppdaterad: 2020-05-13Bibliografiskt granskad
2. BatchMap: A parallel implementation of the OneMap R package for fast computation of F-1 linkage maps in outcrossing species
Öppna denna publikation i ny flik eller fönster >>BatchMap: A parallel implementation of the OneMap R package for fast computation of F-1 linkage maps in outcrossing species
2017 (Engelska)Ingår i: PLOS ONE, E-ISSN 1932-6203, Vol. 12, nr 12, artikel-id e0189256Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

With the rapid advancement of high throughput sequencing, large numbers of genetic markers can be readily and cheaply acquired, but most current software packages for genetic map construction cannot handle such dense input. Modern computer architectures and server farms represent untapped resources that can be used to enable higher marker densities to be processed in tractable time. Here we present a pipeline using a modified version of OneMap that parallelizes over bottleneck functions and achieves substantial speedups for producing a high density linkage map (N = 20,000). Using simulated data we show that the outcome is as accurate as the traditional pipeline. We further demonstrate that there is a direct relationship between the number of markers used and the level of deviation between true and estimated order, which in turn impacts the final size of a genetic map.

Nationell ämneskategori
Genetik
Identifikatorer
urn:nbn:se:umu:diva-144110 (URN)10.1371/journal.pone.0189256 (DOI)000418564200037 ()29261725 (PubMedID)2-s2.0-85038843145 (Scopus ID)
Tillgänglig från: 2018-01-23 Skapad: 2018-01-23 Senast uppdaterad: 2023-03-24Bibliografiskt granskad
3. An improved genome assembly of the European aspen Populus tremula
Öppna denna publikation i ny flik eller fönster >>An improved genome assembly of the European aspen Populus tremula
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(Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
Nationell ämneskategori
Biologiska vetenskaper
Identifikatorer
urn:nbn:se:umu:diva-170640 (URN)
Tillgänglig från: 2020-05-12 Skapad: 2020-05-12 Senast uppdaterad: 2020-05-14
4. Leaf shape in Populus tremula is a complex, omnigenic trait
Öppna denna publikation i ny flik eller fönster >>Leaf shape in Populus tremula is a complex, omnigenic trait
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2020 (Engelska)Ingår i: Ecology and Evolution, E-ISSN 2045-7758, Vol. 10, nr 21, s. 11922-11940Artikel i tidskrift (Refereegranskat) 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.

Ort, förlag, år, upplaga, sidor
John Wiley & Sons, 2020
Nyckelord
complex trait, GWAS, leaf shape, natural variation, omnigenic, Populus tremula
Nationell ämneskategori
Bioinformatik och systembiologi
Identifikatorer
urn:nbn:se:umu:diva-170641 (URN)10.1002/ece3.6691 (DOI)000578291300001 ()2-s2.0-85092478395 (Scopus ID)
Anmärkning

Originally included in thesis in manuscript form.

Tillgänglig från: 2020-05-12 Skapad: 2020-05-12 Senast uppdaterad: 2024-01-17Bibliografiskt granskad
5. Enhanced ensemble gene networks in systems biology
Öppna denna publikation i ny flik eller fönster >>Enhanced ensemble gene networks in systems biology
(Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
Nationell ämneskategori
Bioinformatik och systembiologi
Identifikatorer
urn:nbn:se:umu:diva-170642 (URN)
Tillgänglig från: 2020-05-12 Skapad: 2020-05-12 Senast uppdaterad: 2020-05-14

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