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Genomic relationships reveal significant dominance effects for growth in hybrid Eucalyptus
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Biomaterials Division, Stora Enso AB, SE-131 04, Nacka, Sweden.
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.

Place, publisher, year, edition, pages
2018. Vol. 267, p. 84-93
Keywords [en]
Dominance Epistasis Predictive ability Breeding strategy Heritability
National Category
Forest Science Genetics
Research subject
Genetics
Identifiers
URN: urn:nbn:se:umu:diva-145493DOI: 10.1016/j.plantsci.2017.11.011ISI: 000424962600009OAI: oai:DiVA.org:umu-145493DiVA, id: diva2:1188294
Funder
Swedish Research CouncilAvailable 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)
Opponent
Supervisors
Available from: 2018-03-16 Created: 2018-03-07 Last updated: 2018-07-19Bibliographically approved

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Tan, Biyue

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