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A major locus controls local adaptation and adaptive life history variation in a perennial plant
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Life Sciences, Norwegian University of Life Science.
Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences.
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Stora Enso AB.
Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Background: The initiation of growth cessation and dormancy represent critical life-history trade-offs between survival and growth, and have important fitness effects in perennial plants. Such adaptive life history traits often show strong local adaptation along environmental gradients but despite their importance, the genetic architecture of these traits remains poorly understood.

Results: We integrate whole genome re-sequencing with environmental and phenotypic data from common garden experiments to investigate the genomic basis of local adaptation across a latitudinal gradient in European aspen (Populus tremula). We discover a single genomic region containing the PtFT2 gene that mediates local adaptation in the timing of bud set and that explains 65% of the observed genetic variation in bud set. This locus is the likely target of a recent selective sweep that originated right before or during colonization of northern Scandinavia following the last glaciation. Field and greenhouse experiments confirm that variation in PtFT2 gene expression affect the phenotypic variation in bud set that we observe in wild natural populations.

Conclusions: Our results reveal a major effect locus that determine the timing of bud set and that have facilitated rapid adaptation to shorter growing seasons and colder climates in European aspen. The discovery of a single locus explaining a substantial fraction of the variation in a key life history trait is remarkable given that such traits are generally considered to be highly polygenic. These findings provide a dramatic illustration of how loci of large-effect for adaptive traits can arise and be maintained over large geographical scales in natural populations.

Keywords [en]
Populus tremula, Local adaptation, Genomic basis, PtFT2, Adaptive traits, Selective sweep
National Category
Evolutionary Biology Genetics
Identifiers
URN: urn:nbn:se:umu:diva-145495OAI: oai:DiVA.org:umu-145495DiVA, id: diva2:1188304
Available from: 2018-03-07 Created: 2018-03-07 Last updated: 2018-06-09Bibliographically approved
In thesis
1. Genomic selection and genome-wide association studies to dissect quantitative traits in forest trees
Open this publication in new window or tab >>Genomic selection and genome-wide association studies to dissect quantitative traits in forest trees
2018 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The convergence of quantitative genetics of complex traits with genomic technologies is quickly becoming an innovative approach to explore fundamental genetic questions and also have practical consequences for implementations in tree breeding. In this thesis, I used genomic selection and genome-wide association studies (GWAS) to dissect the genetic basis of quantitative traits, i.e. growth, phenology and wood property traits. I also assessed the importance of dominance and epistatic effects in hybrid Eucalyptus. Both dominance and epistasis are important in hybrids, as they are the likely contributing to the genetic basis of heterosis. To successfully implement genomic selection models, several important factors have to be considered. I found that for a good model establishment, both the size and composition of the training population, as well as the number of SNPs to be important considered. Based on the optimal models, additive, dominance and epistasis genetic effects of growth and wood traits have been estimated to evaluate genetic parameters and how these influence the prediction accuracy, which can be used in selecting elite breeding individuals or clones. I also addressed the advantage of genotyping-based analyses by showing that we could accurately correct pedigree information errors. More importantly, genotyping-based analyses capture both Mendelian segregation variation within full-sib families and cryptic genetic links through unknown common ancestors, which are not available from traditional pedigree data. GWAS were used to analyse growth and phenology related traits. Using a single-trait GWAS method, we identified a region strongly associated with the timing of bud set in Populus tremula, a trait with high heritability. For the growth related traits, we found that a multi-traits GWAS approach was more powerful than single-trait analyses as it identified more associated SNPs in hybrid Eucalyptus. Moreover, many more novel associated SNPs were identified from considering over-dominance effects in the GWAS analyses. After annotating the associated SNPs I show that these functional candidate genes were related to growth and responding to abiotic and biotic stress. In summary, the results of genomic selection and GWAS provided a deeper understanding of the genetic backgrounds of quantitative traits in forest trees.

Place, publisher, year, edition, pages
Umeå: Umeå University, 2018. p. 38
Keywords
Genomic prediction, genome-wide association study, additive effects, dominance effects, epistasis effects, realized relationship matrix, Eucalyptus grandis, Eucalyptus urophylla
National Category
Genetics Evolutionary Biology Forest Science
Identifiers
urn:nbn:se:umu:diva-145497 (URN)978-91-7601-849-1 (ISBN)
Public defence
2018-04-06, Lilla hörsalen (KB.E3.01), KBC-byggnaden, Umeå, 10:00 (English)
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Supervisors
Available from: 2018-03-16 Created: 2018-03-07 Last updated: 2018-06-09Bibliographically approved

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Wang, JingTan, BiyueRobinson, Kathryn M.Michelson, Ingrid H.Scofield, Douglas G.Jansson, StefanStreet, Nathaniel R.Ingvarsson, Pär K.

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Wang, JingTan, BiyueRobinson, Kathryn M.Michelson, Ingrid H.Scofield, Douglas G.Jansson, StefanStreet, Nathaniel R.Ingvarsson, Pär K.
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Department of Ecology and Environmental SciencesDepartment of Plant Physiology
Evolutionary BiologyGenetics

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