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
Genomic selection and genome-wide association studies to dissect quantitative traits in forest trees
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Stora Enso AB.
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 [en]
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: urn:nbn:se:umu:diva-145497ISBN: 978-91-7601-849-1 (print)OAI: oai:DiVA.org:umu-145497DiVA, id: diva2:1188358
Public defence
2018-04-06, Lilla hörsalen (KB.E3.01), KBC-byggnaden, Umeå, 10:00 (English)
Opponent
Supervisors
Available from: 2018-03-16 Created: 2018-03-07 Last updated: 2018-07-19Bibliographically approved
List of papers
1. Evaluating the accuracy of genomic prediction of growth and wood traits in two Eucalyptus species and their F-1 hybrids
Open this publication in new window or tab >>Evaluating the accuracy of genomic prediction of growth and wood traits in two Eucalyptus species and their F-1 hybrids
Show others...
2017 (English)In: BMC Plant Biology, ISSN 1471-2229, E-ISSN 1471-2229, Vol. 17, article id 110Article in journal (Refereed) Published
Abstract [en]

Background: Genomic prediction is a genomics assisted breeding methodology that can increase genetic gains by accelerating the breeding cycle and potentially improving the accuracy of breeding values. In this study, we use 41,304 informative SNPs genotyped in a Eucalyptus breeding population involving 90 E. grandis and 78 E. urophylla parents and their 949 F-1 hybrids to develop genomic prediction models for eight phenotypic traits-basic density and pulp yield, circumference at breast height and height and tree volume scored at age three and six years. We assessed the impact of different genomic prediction methods, the composition and size of the training and validation set and the number and genomic location of SNPs on the predictive ability (PA). Results: Heritabilities estimated using the realized genomic relationship matrix (GRM) were considerably higher than estimates based on the expected pedigree, mainly due to inconsistencies in the expected pedigree that were readily corrected by the GRM. Moreover, the GRM more precisely capture Mendelian sampling among related individuals, such that the genetic covariance was based on the true proportion of the genome shared between individuals. PA improved considerably when increasing the size of the training set and by enhancing relatedness to the validation set. Prediction models trained on pure species parents could not predict well in F-1 hybrids, indicating that model training has to be carried out in hybrid populations if one is to predict in hybrid selection candidates. The different genomic prediction methods provided similar results for all traits, therefore either GBLUP or rrBLUP represents better compromises between computational time and prediction efficiency. Only slight improvement was observed in PA when more than 5000 SNPs were used for all traits. Using SNPs in intergenic regions provided slightly better PA than using SNPs sampled exclusively in genic regions. Conclusions: The size and composition of the training set and number of SNPs used are the two most important factors for model prediction, compared to the statistical methods and the genomic location of SNPs. Furthermore, training the prediction model based on pure parental species only provide limited ability to predict traits in interspecific hybrids. Our results provide additional promising perspectives for the implementation of genomic prediction in Eucalyptus breeding programs by the selection of interspecific hybrids.

Place, publisher, year, edition, pages
BioMed Central, 2017
Keywords
Genomic relationship, Genomic heritability, Two-generation, Genome annotation, High-density SNP-chip, Bayesian LASSO, GBLUP, rrBLUP
National Category
Evolutionary Biology Genetics
Identifiers
urn:nbn:se:umu:diva-138559 (URN)10.1186/s12870-017-1059-6 (DOI)000404909700001 ()28662679 (PubMedID)
Available from: 2017-09-13 Created: 2017-09-13 Last updated: 2018-06-09Bibliographically approved
2. Genomic relationships reveal significant dominance effects for growth in hybrid Eucalyptus
Open this publication in new window or tab >>Genomic relationships reveal significant dominance effects for growth in hybrid Eucalyptus
2018 (English)In: Plant Science, ISSN 0168-9452, E-ISSN 1873-2259, Vol. 267, p. 84-93Article in journal (Refereed) Published
Abstract [en]

Non-additive genetic effects can be effectively exploited in control-pollinated families with the availability of genome-wide markers. We used 41,304 SNP markers and compared pedigree vs. marker-based genetic models by analysing height, diameter, basic density and pulp yield for Eucalyptus urophylla x E.grandis control-pollinated families represented by 949 informative individuals. We evaluated models accounting for additive, dominance, and first-order epistatic interactions (additive by additive, dominance by dominance, and additive by dominance). We showed that the models can capture a large proportion of the genetic variance from dominance and epistasis for growth traits as those components are typically not independent. We also showed that we could partition genetic variances more precisely when using relationship matrices derived from markers compared to using only pedigree information. In addition, phenotypic prediction accuracies were only slightly increased by including dominance effects for growth traits since estimates of non-additive variances yielded rather high standard errors. This novel result improves our current understanding of the architecture of quantitative traits and recommends accounting for dominance variance when developing genomic selection strategies in hybrid Eucalyptus.

Keywords
Dominance Epistasis Predictive ability Breeding strategy Heritability
National Category
Forest Science Genetics
Research subject
Genetics
Identifiers
urn:nbn:se:umu:diva-145493 (URN)10.1016/j.plantsci.2017.11.011 (DOI)000424962600009 ()
Projects
Bio4Energy
Funder
Swedish Research Council
Available from: 2018-03-07 Created: 2018-03-07 Last updated: 2019-09-06Bibliographically approved
3. Multivariate genome-wide association identify loci for complex growth traits by considering additive and over-dominance effects in hybrid Eucalyptus
Open this publication in new window or tab >>Multivariate genome-wide association identify loci for complex growth traits by considering additive and over-dominance effects in hybrid Eucalyptus
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Genome-wide association studies are a powerful and widely used approach to decipher the genetic control of quantitative traits. One of the major challenges for traits in hybrid forest trees, such as hybrid Eucalyptus, is dissecting also non-additive effects for complex traits using a traditional linear mixed model. These non-additive effects, especially over-dominance effects, are one of most important hypotheses for the genetic basis of heterosis. In this study, we used a population including 949 F1 hybrids and their 174 parents, that were phenotyped for circumference at breast height and height at age of three years and six years, and also genotyped at 37,832 informative SNPs. Here we use and compare single-trait and multi-trait association models by accounting for additive and over-dominance effects, to evaluate genomic regions associated with the growth traits. For additive effect-based association model, nine significant SNPs were observed in multi-trait analyses, whereas only two unique SNPs were detected in single-trait analyses. These two SNPs were also identified in the multi-trait model. When evaluating over-dominance effects, 17 and 13 SNPs were identified from multi-trait and single-trait models, respectively. Moreover, more phenotypic variation can be explained by SNPs identified from multi-trait GWAS when including over-dominance effects. Overall, this study shows the added values of including over-dominance and considering multiple traits for identifying genomic regions that control traits of interest and that could contribute to heterosis in hybrids.

Keywords
Eucalyptus grandis, E. urophylla, heterosis, multivariate mixed linear model, univariate mixed linear model
National Category
Genetics Forest Science
Identifiers
urn:nbn:se:umu:diva-145494 (URN)
Available from: 2018-03-07 Created: 2018-03-07 Last updated: 2018-06-09Bibliographically approved
4. A major locus controls local adaptation and adaptive life history variation in a perennial plant
Open this publication in new window or tab >>A major locus controls local adaptation and adaptive life history variation in a perennial plant
Show others...
2018 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 19, article id 72Article in journal (Refereed) Published
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 then 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). A single genomic region containing the PtFT2 gene mediates local adaptation in the timing of bud set and 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 affects the phenotypic variation in bud set that we observe in wild natural populations.

Conclusions: Our results reveal a major effect locus that determines the timing of bud set and that has 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.

Place, publisher, year, edition, pages
BioMed Central, 2018
Keywords
Populus tremula, Local adaptation, Genomic basis, PtFT2, Adaptive traits, Selective sweep
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-150175 (URN)10.1186/s13059-018-1444-y (DOI)000434210500001 ()29866176 (PubMedID)
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Note

Originally included in thesis in manuscript form.

Available from: 2018-07-18 Created: 2018-07-18 Last updated: 2018-08-14Bibliographically approved

Open Access in DiVA

fulltext(1311 kB)276 downloads
File information
File name FULLTEXT01.pdfFile size 1311 kBChecksum SHA-512
f82a4bbe8e9947198702db7cadc1398eece6a2265a56a232784ffaa24c54c0d86eab75cbeffd518f238b1c658f522a1ec37522dc6b7ac0bfbda8d2d8cabf84d7
Type fulltextMimetype application/pdf
spikblad(165 kB)31 downloads
File information
File name SPIKBLAD01.pdfFile size 165 kBChecksum SHA-512
23d63aaacc6fd164f35544b2bb65f916779df7f5a12eff168b98296fe9150bf2d5b8f982ed81825d64e6272dae6ea6c6ad6e5bd86af3e63f836730b111d465c8
Type spikbladMimetype application/pdf

Authority records BETA

Tan, Biyue

Search in DiVA

By author/editor
Tan, Biyue
By organisation
Department of Ecology and Environmental Sciences
GeneticsEvolutionary BiologyForest Science

Search outside of DiVA

GoogleGoogle Scholar
Total: 276 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

isbn
urn-nbn

Altmetric score

isbn
urn-nbn
Total: 60205 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