| 1. |
- Barcala, Maximiliano Estravis, et al.
(författare)
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Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species
- 2024
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Ingår i: The Plant Journal. - 0960-7412 .- 1365-313X. ; 117:3, s. 944-955
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Tidskriftsartikel (refereegranskat)abstract
- Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype–environment and genotype–phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.
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| 2. |
- Berlin Kolm, Sofia, et al.
(författare)
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Genetic diversity, population structure and phenotypic variation in European Salix viminalis L. (Salicaceae)
- 2014
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Ingår i: Tree Genetics & Genomes. - : Springer Science and Business Media LLC. - 1614-2942 .- 1614-2950. ; 10:6, s. 1595-1610
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Tidskriftsartikel (refereegranskat)abstract
- To investigate the potential of association genetics for willow breeding, Salix viminalis germplasm was assembled from UK and Swedish collections (comprising accessions from several European countries) and new samples collected from nature. A subset of the germplasm was planted at two sites (UK and Sweden), genotyped using 38 SSR markers and assessed for phenological and biomass traits. Population structure, genetic differentiation (F-ST) and quantitative trait differentiation (Q(ST)) were investigated. The extent and patterns of trait adaptation were assessed by comparing F-ST and Q(ST) parameters. Of the 505 genotyped diploid accessions, 27 % were not unique. Genetic diversity was high: 471 alleles was amplified; the mean number of alleles per locus was 13.46, mean observed heterozygosity was 0.55 and mean expected heterozygosity was 0.62. Bayesian clustering identified four subpopulations which generally corresponded to Western Russia, Western Europe, Eastern Europe and Sweden. All pairwise F-ST values were highly significant (p<0.001) with the greatest genetic differentiation detected between the Western Russian and the Western European subpopulations (F-ST = 0.12), and the smallest between the Swedish and Eastern European populations (F-ST = 0.04). The Swedish population also had the highest number of identical accessions, supporting the view that S. viminalis was introduced into this country and has been heavily influenced by humans. Q(ST) values were high for growth cessation and leaf senescence, and to some extent stem diameter, but low for bud burst time and shoot number. Overall negative clines between longitudinal coordinates and leaf senescence, bud burst and stem diameter were also found.
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| 3. |
- Berlin Kolm, Sofia, et al.
(författare)
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Genetics of phenotypic plasticity and biomass traits in hybrid willows across contrasting environments and years
- 2017
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Ingår i: Annals of Botany. - : Oxford University Press (OUP). - 0305-7364 .- 1095-8290. ; 120, s. 87-100
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Tidskriftsartikel (refereegranskat)abstract
- Background and Aims Phenotypic plasticity can affect the geographical distribution of taxa and greatly impact the productivity of crops across contrasting and variable environments. The main objectives of this study were to identify genotype-phenotype associations in key biomass and phenology traits and the strength of phenotypic plasticity of these traits in a short-rotation coppice willow population across multiple years and contrasting environments to facilitate marker-assisted selection for these traits.Methods A hybrid Salix viminalis x (S. viminalis x Salix schwerinii) population with 463 individuals was clonally propagated and planted in three common garden experiments comprising one climatic contrast between Sweden and Italy and one water availability contrast in Italy. Several key phenotypic traits were measured and phenotypic plasticity was estimated as the trait value difference between experiments. Quantitative trait locus (QTL) mapping analyses were conducted using a dense linkage map and phenotypic effects of S. schwerinii haplotypes derived from detected QTL were assessed.Key Results Across the climatic contrast, clone predictor correlations for biomass traits were low and few common biomass QTL were detected. This indicates that the genetic regulation of biomass traits was sensitive to environmental variation. Biomass QTL were, however, frequently shared across years and across the water availability contrast. Phenology QTL were generally shared between all experiments. Substantial phenotypic plasticity was found among the hybrid offspring, that to a large extent had a genetic origin. Individuals carrying influential S. schwerinii haplotypes generally performed well in Sweden but less well in Italy in terms of biomass production.Conclusions The results indicate that specific genetic elements of S. schwerinii are more suited to Swedish conditions than to those of Italy. Therefore, selection should preferably be conducted separately for such environments in order to maximize biomass production in admixed S. viminalis x S. schwerinii populations.
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| 4. |
- Calleja-Rodriguez, Ainhoa, et al.
(författare)
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Analysis of phenotypic- and Estimated Breeding Values (EBV) to dissect the genetic architecture of complex traits in a Scots pine three-generation pedigree design
- 2019
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 462, s. 283-292
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Tidskriftsartikel (refereegranskat)abstract
- In forest tree breeding, family-based Quantitative Trait Loci (QTL) studies are valuable as methods to dissect the complexity of a trait and as a source of candidate genes. In the field of conifer research, our study contributes to the evaluation of phenotypic and predicted breeding values for the identification of QTL linked to complex traits in a three-generation pedigree population in Scots pine (Pinus sylvestris L.). A total of 11 470 open pollinated F-2-progeny trees established at three different locations, were measured for growth and adaptive traits. Breeding values were predicted for their 360 mothers, originating from a single cross of two grand-parents. A multilevel LASSO association analysis was conducted to detect QTL using genotypes of the mothers with the corresponding phenotypes and Estimated Breeding Values (EBV). Different levels of genotype-by-environment (G x E) effects among sites at different years, were detected for survival and height. Moderate-to-low narrow sense heritabilities and EBV accuracies were found for all traits and all sites. We identified 18 AFLPs and 12 SNPs to be associated with QTL for one or more traits. 62 QTL were significant with percentages of variance explained ranging from 1.7 to 18.9%. In those cases where the same marker was associated to a phenotypic or an ebvQTL, the ebvQTL always explained higher proportion of the variance, maybe due to the more accurate nature of Estimated Breeding Values (EBV). Two SNP-QTL showed pleiotropic effects for traits related with hardiness, seed, cone and flower production. Furthermore, we detected several QTL with significant effects across multiple ages, which could be considered as strong candidate loci for early selection. The lack of reproducibility of some QTL detected across sites may be due to environmental heterogeneity reflected by the genotype- and QTL-by-environment effects. (C) 2018 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license.
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| 5. |
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| 6. |
- Chen, Zhiqiang, et al.
(författare)
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Advantage of clonal deployment in Norway spruce (Picea abies (L.) H. Karst)
- 2020
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Ingår i: Annals of Forest Science. - : Springer Science and Business Media LLC. - 1286-4560 .- 1297-966X. ; 77
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Tidskriftsartikel (refereegranskat)abstract
- Key message There is considerable genetic gain of tree volume from clonal deployment in Norway spruce (Picea abies(L.) H. Karst) and clonal deployment will have at least 50% more or double genetic gain than the seedling deployment. Context Genetic parameters and genetic gains for wood quality and growth traits were estimated in six large clonal progeny trials. Aims Develop the optimal clonal deployment strategy of Norway spruce in Sweden. Methods Wood quality and growth traits were measured in all clonal trials and additive and non-additive genetic variances are partitioned. Results Additive and non-additive genetic variances were equally important for growth traits while non-additive variance was small or not significant for wood quality trait. The genetic gain predicted for clonal deployment was greater than any of the other four deployment strategies. Selecting the top 1% of tested clones (clonal forestry) would have 48.4% and 134.6% more gain than the gain predicted for the seedling deployment of selected full-sib families and half-sib family (family forestry), respectively, at the same selection intensity. Conclusion This study highlights that testing of 30-40 clones per family would maximize the realized genetic gain for different clonal selection scenarios, either selecting the best ten or 20 clones without any co-ancestry restrictions or selecting the best single clone from each of the best ten or 20 families (e.g., co-ancestry restriction). Clonal mean selection and vegetative deployment are the most effective.
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| 7. |
- Cronberg, Nils, et al.
(författare)
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Mossor
- 2000
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Ingår i: Red list of Swedish species. - 9188506231 ; , s. 93-105
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 8. |
- Cronberg, Nils, et al.
(författare)
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Mossor
- 2005
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Ingår i: The 2005 Red List of Swedish species. - 9188506304 ; , s. 191-204
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Bokkapitel (populärvet., debatt m.m.)
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| 9. |
- Fundová, Irena, et al.
(författare)
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Genetic improvement of sawn-board shape stability in Scots pine (Pinus sylvestris L.)
- 2020
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Ingår i: Industrial Crops and Products. - : Elsevier BV. - 0926-6690 .- 1872-633X. ; 157
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Tidskriftsartikel (refereegranskat)abstract
- Adequate shape stability is a prerequisite for utilization of sawn boards in the building industry. This study investigated the possibility of indirect genetic improvement of Scots pine (Pinus sylvestris L.) sawn-board shape stability (specifically the bow, crook and twist) via selective breeding based on traits that can be non-destructively measured on standing trees. Relationships between shape stability and wood quality traits measured on logs and sawn boards were also determined. A total of 1896 standing trees from a 39-year-old Scots pine full-sib progeny test were non-destructively measured. A subset of 496 trees was harvested and sawn into 50 x 100 mm boards, the quality of which was assessed both non-destructively and destructively. Among the traits assessed on standing trees, grain angle (GRA) appeared to be the best predictor of sawn-board twisting and crooking (r(A) = 0.84 and 0.62, respectively). The individual-tree narrow-sense heritability (h(i)(2)) was moderate for twist and GRA (0.37 and 0.40, respectively), low for bow (0.21) and very low for crook (0.05). Selective breeding targeting lower GRA would result in lower twist and crook but could also increase sawn-board density, stiffness and strength.
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| 10. |
- Fundová, Irena, et al.
(författare)
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Genetic Improvement of Sawn-Board Stiffness and Strength in Scots Pine (Pinus sylvestris L.)
- 2020
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Ingår i: Sensors (Basel, Switzerland). - : MDPI AG. - 1424-8220. ; 20
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Tidskriftsartikel (refereegranskat)abstract
- Given an overall aim of improving Scots pine structural wood quality by selective tree breeding, we investigated the potential of non-destructive acoustic sensing tools to accurately predict wood stiffness (modulus of elasticity, MOE) and strength (modulus of rupture, MOR) of sawn boards. Non-destructive measurements of wood density (DEN), acoustic velocity (VEL) and MOE were carried out at different stages of wood processing chain (standing trees, felled logs and sawn boards), whilst destructively measured stiffness and strength served as benchmark traits. All acoustic based MOE and VEL estimates proved to be good proxies (r(A) > 0.65) for sawn-board stiffness while MOETREE, VELHIT and resistograph wood density (DENRES) measured on standing trees and MOELOG and VELFAK measured on felled logs well reflected board strength. Individual-tree narrow-sense heritability (hi2) for VEL, MOE and MOR were weak (0.05-0.26) but were substantially stronger for wood density (0.34-0.40). Moreover, additive genetic coefficients of variation for MOE and MOR were in the range from 5.4% to 9.1%, offering potential targets for exploitation by selective breeding. Consequently, selective breeding based on MOETREE, DENRES or stem straightness (STR) could improve several structural wood traits simultaneously.
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