| 71. |
- Tan, Biyue, et al.
(author)
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Multivariate genome-wide association identify loci for complex growth traits by considering additive and over-dominance effects in hybrid Eucalyptus
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Other publication (other academic/artistic)abstract
- 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.
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| 72. |
- Wang, Jing, et al.
(author)
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A major locus controls local adaptation and adaptive life history variation in a perennial plant
- 2018
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In: Genome Biology. - : BioMed Central. - 1465-6906 .- 1474-760X. ; 19
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Journal article (peer-reviewed)abstract
- 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.
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| 73. |
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| 74. |
- Wang, Xi, 1990-, et al.
(author)
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Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies)
- 2020
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In: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 12:2, s. 3803-3817
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Journal article (peer-reviewed)abstract
- Under the neutral theory, species with larger effective population size are expected to harbor higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin's paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere, and it consequently plays a major role in European forestry. Here, we use whole-genome resequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an corresponding enormous current population size, our analyses find that genetic diversity of P. abies is low across a number of populations (pi = 0.0049 in Central-Europe, pi = 0.0063 in Sweden-Norway, pi = 0.0063 in Finland). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterized by several reoccurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.
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| 75. |
- Wang, Xi, 1990-, et al.
(author)
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Quantifying adaptive evolution and the effects of natural selection across the Norway spruce genome
- 2023
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In: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 32:19, s. 5288-5304
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Journal article (peer-reviewed)abstract
- Detecting natural selection is one of the major goals of evolutionary genomics. Here, we sequence whole genomes of 34 Picea abies individuals and quantify the amount of selection across the genome. Using an estimate of the distribution of fitness effects, we show that negative selection is very limited in coding regions, while positive selection is rare in coding regions but very strong in non-coding regions, suggesting the great importance of regulatory changes in evolution of Norway spruce. Additionally, we found a positive correlation between adaptive rate with recombination rate and a negative correlation between adaptive rate and gene density, suggesting a widespread influence from Hill-Robertson interference to efficiency of protein adaptation in P. abies. Finally, the distinct population statistics between genomic regions under either positive or balancing selection with that under neutral regions indicated impact from selection to genomic architecture of Norway spruce. Further gene ontology enrichment analysis for genes located in regions identified as undergoing either positive or long-term balancing selection also highlighted specific molecular functions and biological processes in that appear to be targets of selection in Norway spruce.
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| 76. |
- Wang, Xi, 1990-
(author)
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The roles of demography and natural selection in shaping genome-wide variation of Norway spruce
- 2020
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Doctoral thesis (other academic/artistic)abstract
- Understanding the relative contribution of genetic drift, natural selection, and mutation to genetic variation, and quantifying adaptive evolution and the effects of natural selection in species are enduring goals of evolutionary genetics. Norway spruce (Picea abies) is one of the most important conifer species that dominates from both an ecological and economical point of view in many boreal ecosystems. Recently published reference genome of Norway spruce makes it possible to perform population genomic studies to understand the basis of genetic variation and evolutionary effects of natural selection in P. abies by using next-generation sequencing (NGS) data. We create an ultra-dense genetic linkage map for Norway spruce using sequence capture data. The consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6% of the validated gene models) that we have anchored to the 12 linkage groups (LGs). We also demonstrate, however, that approximately 3.8% of the anchored scaffolds and 1.6% of the gene models covered by the consensus map have likely assembly errors. By performing population genetic analyses using the genomic regions anchored to LGs, our genetic linkage map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.In order to understand how different evolutionary forces have shaped patterns of nucleotide diversity in Norway spruce, we perform population genomic analyses using whole-genome resequencing data. We find that genetic diversity is low across a number of populations in spite of a very wide geographic distribution of P. abies. The demographic history of several reoccurring bottlenecks with concomitant decreases in effective population size, the recurrent natural selection (both purifying and positive selection), and the low overall mutation rates seen in conifers, together make contribute to the loss of genome-wide nucleotide diversity in Norway spruce.We quantify adaptive evolution and the effects of natural selection across the Norway spruce whole genome. The results show that negative selection is very limited in coding regions, while positive selection is rare in coding regions but very strong in non-coding regions, suggesting the great importance of regulatory changes in evolutionary history of P. abies. We further find a positive correlation between adaptive rate with recombination rate and a negative correlation between adaptive rate and gene density, suggesting a widespread influence from Hill-Robertson interference to efficiency of protein adaptation in P. abies. The distinct population statistics between genomic regions under either positive or balancing selection with that under neutral regions indicate impact from natural selection to genomic architecture of Norway spruce.
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