| 1. |
- Rönnberg Wästljung, Ann-Christin, et al.
(author)
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Optimized utilization of Salix—Perspectives for the genetic improvement toward sustainable biofuel value chains
- 2022
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In: Global Change Biology Bioenergy. - : John Wiley and Sons Inc. - 1757-1693 .- 1757-1707. ; 14:10, s. 1128-144
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Journal article (peer-reviewed)abstract
- Bioenergy will be one of the most important renewable energy sources in the conversion from fossil fuels to bio-based products. Short rotation coppice Salix could be a key player in this conversion since Salix has rapid growth, positive energy balance, easy to manage cultivation system with vegetative propagation of plant material and multiple harvests from the same plantation. The aim of the present paper is to provide an overview of the main challenges and key issues in willow genetic improvement toward sustainable biofuel value chains. Primarily based on results from the research project “Optimized Utilization of Salix” (OPTUS), the influence of Salix wood quality on the potential for biofuel use is discussed, followed by issues related to the conversion of Salix biomass into liquid and gaseous transportation fuels. Thereafter, the studies address genotypic influence on soil carbon sequestration in Salix plantations, as well as on soil carbon dynamics and climate change impacts. Finally, the opportunities for plant breeding are discussed using willow as a resource for sustainable biofuel production. Substantial phenotypic and genotypic variation was reported for different wood quality traits important in biological (i.e., enzymatic and anaerobic) and thermochemical conversion processes, which is a prerequisite for plant breeding. Furthermore, different Salix genotypes can affect soil carbon sequestration variably, and life cycle assessment illustrates that these differences can result in different climate mitigation potential depending on genotype. Thus, the potential of Salix plantations for sustainable biomass production and its conversion into biofuels is shown. Large genetic variation in various wood and biomass traits, important for different conversion processes and carbon sequestration, provides opportunities to enhance the sustainability of the production system via plant breeding. This includes new breeding targets in addition to traditional targets for high yield to improve biomass quality and carbon sequestration potential. © 2022 The Authors.
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| 2. |
- Adler, Anneli, et al.
(author)
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Variation of growth and phenology traits in poplars planted in clonal trials in Northern Europe-implications for breeding
- 2021
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In: BioEnergy Research. - : Springer Science and Business Media LLC. - 1939-1234 .- 1939-1242. ; 14, s. 426-444
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Journal article (peer-reviewed)abstract
- The increased demand for wood to replace oil-based products with renewable products has lifted focus to the Baltic Sea region where the environment is favorable for woody biomass growth. The aim of this study was to estimate broad-sense heritabilities and genotype-by-environment (GxE) interactions in growth and phenology traits in six climatically different regions in Sweden and the Baltics. We tested the hypothesis that both bud burst and bud set have a significant effect on the early growth of selected poplar clones in Northern Europe. Provenance hybrids of Populus trichocarpa adapted to the Northern European climate were compared to reference clones with adaptation to the Central European climate. The volume index of stemwood was under low to medium genetic control with heritabilities from 0.22 to 0.75. Heritabilities for phenology traits varied between 0.31 and 0.91. Locally chosen elite clones were identified. GxE interactions were analyzed using pairwise comparisons of the trials. Three different breeding zones for poplars between the latitudes of 55 degrees N and 60 degrees N in the Baltic Sea Region were outlined. The studied provenance hybrids with origin from North America offer a great possibility to broaden the area with commercial poplar plantations in Northern Europe and further improve the collection of commercial clones to match local climates. We conclude that phenology is an important selection criterion after growth.
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| 3. |
- Almeida, Pedro, et al.
(author)
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Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion
- 2020
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In: BMC Biology. - : Springer Science and Business Media LLC. - 1741-7007. ; 18:1
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Journal article (peer-reviewed)abstract
- BackgroundSex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear.ResultsHere, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes.ConclusionsOur data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.
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| 4. |
- Apuli, Rami-Petteri, et al.
(author)
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The genetic basis of adaptation in phenology in an introduced population of Black Cottonwood (Populus trichocarpa, Torr. & Gray)
- 2021
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In: BMC Plant Biology. - : BioMed Central (BMC). - 1471-2229. ; 21
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Journal article (peer-reviewed)abstract
- Background: Entering and exiting winter dormancy present important trade-offs between growth and survival at northern latitudes. Many forest trees display local adaptation across latitude in traits associated with these phenology transitions. Transfers of a species outside its native range introduce the species to novel combinations of environmental conditions potentially requiring different combinations of alleles to optimize growth and survival. In this study, we performed genome wide association analyses and a selection scan in a P. trichocarpa mapping population derived from crossings between clones collected across the native range and introduced into Sweden. GWAS analyses were performed using phenotypic data collected across two field seasons and in a controlled phytotron experiment.Results: We uncovered 584 putative candidate genes associated with spring and autumn phenology traits as well as with growth. Many regions harboring variation significantly associated with the initiation of leaf shed and leaf autumn coloring appeared to have been evolving under positive selection in the native environments of P. trichocarpa. A comparison between the candidate genes identified with results from earlier GWAS analyses performed in the native environment found a smaller overlap for spring phenology traits than for autumn phenology traits, aligning well with earlier observations that spring phenology transitions have a more complex genetic basis than autumn phenology transitions.Conclusions: In a small and structured introduced population of P. trichocarpa, we find complex genetic architectures underlying all phenology and growth traits, and identify multiple putative candidate genes despite the limitations of the study population.
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| 5. |
- Berlin Kolm, Sofia, et al.
(author)
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Genetic diversity, population structure and phenotypic variation in European Salix viminalis L. (Salicaceae)
- 2014
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In: Tree Genetics & Genomes. - : Springer Science and Business Media LLC. - 1614-2942 .- 1614-2950. ; 10:6, s. 1595-1610
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Journal article (peer-reviewed)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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| 6. |
- Berlin Kolm, Sofia, et al.
(author)
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Genetics of phenotypic plasticity and biomass traits in hybrid willows across contrasting environments and years
- 2017
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In: Annals of Botany. - : Oxford University Press (OUP). - 0305-7364 .- 1095-8290. ; 120, s. 87-100
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Journal article (peer-reviewed)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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| 7. |
- Berlin Kolm, Sofia, et al.
(author)
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High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus
- 2010
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 11:1, s. 129-
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Journal article (peer-reviewed)abstract
- BACKGROUND: Salix (willow) and Populus (poplar) are members of the Salicaceae family and they share many ecological as well as genetic and genomic characteristics. The interest of using willow for biomass production is growing, which has resulted in increased pressure on breeding of high yielding and resistant clones adapted to different environments. The main purpose of this work was to develop dense genetic linkage maps for mapping of traits related to yield and resistance in willow. We used the Populus trichocarpa genome to extract evenly spaced markers and mapped the orthologous loci in the willow genome. The marker positions in the two genomes were used to study genome evolution since the divergence of the two lineages some 45 mya. RESULTS: We constructed two linkage maps covering the 19 linkage groups in willow. The most detailed consensus map, S1, contains 495 markers with a total genetic distance of 2477 cM and an average distance of 5.0 cM between the markers. The S3 consensus map contains 221 markers and has a total genetic distance of 1793 cM and an average distance of 8.1 cM between the markers. We found high degree of synteny and gene order conservation between willow and poplar. There is however evidence for two major interchromosomal rearrangements involving poplar LG I and XVI and willow LG Ib, suggesting a fission or a fusion in one of the lineages, as well as five intrachromosomal inversions. The number of silent substitutions were three times lower (median: 0.12) between orthologs than between paralogs (median: 0.37 - 0.41). CONCLUSIONS: The relatively slow rates of genomic change between willow and poplar mean that the genomic resources in poplar will be most useful in genomic research in willow, such as identifying genes underlying QTLs of important traits. Our data suggest that the whole-genome duplication occurred long before the divergence of the two genera, events which have until now been regarded as contemporary. Estimated silent substitution rates were 1.28 x 10-9 and 1.68 x 10-9 per site and year, which are close to rates found in other perennials but much lower than rates in annuals.
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| 8. |
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| 9. |
- Berlin Kolm, Sofia, et al.
(author)
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Polymorphism and divergence of two willow species, Salix viminalis L. and Salix schwerinii E. Wolf
- 2011
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In: G3. - : Oxford University Press (OUP). - 2160-1836. ; 1:5, s. 387-400
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Journal article (peer-reviewed)abstract
- We investigated species divergence, present and past gene flow, levels of nucleotide polymorphism, and linkage disequilibrium in two willows from the plant genus Salix. Salix belongs together with Populus to the Salicaceae family; however, most population genetic studies of Salicaceae have been performed in Populus, the model genus in forest biology. Here we present a study on two closely related willow species Salix viminalis and S. schwerinii, in which we have resequenced 33 and 32 nuclear gene segments representing parts of 18 nuclear loci in 24 individuals for each species. We used coalescent simulations and estimated the split time to around 600,000 years ago and found that there is currently limited gene flow between the species. Mean intronic nucleotide diversity across gene segments was slightly higher in S. schwerinii (πi = 0.00849) than in S. viminalis (πi = 0.00655). Compared with other angiosperm trees, the two willows harbor intermediate levels of silent polymorphisms. The decay of linkage disequilibrium was slower in S. viminalis compared with S. schwerinii, and we speculate that this is due to different demographic histories as S. viminalis has been partly domesticated in Europe.
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| 10. |
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| 11. |
- Berlin Kolm, Sofia, et al.
(author)
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QTL mapping of biomass and nitrogen economy traits in willows (Salix spp.) grown under contrasting water and nutrient conditions
- 2014
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In: Molecular Breeding. - : Springer Science and Business Media LLC. - 1380-3743 .- 1572-9788. ; 34, s. 1987-2003
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Journal article (peer-reviewed)abstract
- In order to efficiently grow Salix for biomass production in warmer climates, varieties with a desirable response to drought and nutrient-limiting conditions are needed. The main objective of this study was to investigate the genetic background of biomass production and nitrogen (N) economy in contrasting conditions of water and nutrient availability and to identify candidate genes with a putative function in the expression of the different traits. Quantitative trait loci (QTLs) analysis was conducted using data from 198 individuals of a back-cross population between S. viminalis and S. schwerinii grown in a greenhouse under three combinations of N and water supply. In total, 60 QTLs were identified for biomass and N economy traits in the different treatments. Most of the QTLs mapped to linkage groups II, III, VI, X, XIII and B. At linkage groups III, VI and X, QTLs for both N economy and biomass traits co-located. The phenotypic variation explained by each QTL varied from 7.7 to 41.9 % of the total variance. QTLs for N economy traits explained most of the variation. Gene ontology (GO) analyses, performed on QTL intervals for each trait and projected to the Populus trichocarpa genome, revealed that genomic intervals connected to 19 traits were enriched for at least one GO term. Candidate genes were selected among genes linked to the enriched GO terms. These results represent a first necessary step for additional mapping and functional studies and encourage the development of marker-assisted breeding of Salix varieties adapted to drier climates.
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| 12. |
- Fogelqvist, Johan, et al.
(author)
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Genetic and morphological evidence for introgression between three species of willows
- 2015
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In: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 15
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Journal article (peer-reviewed)abstract
- Background: Hybridization and introgression are said to occur relatively frequently in plants, and in particular among different species of willows. However, data on the actual frequency of natural hybridization and introgression is rare. Here, we report the first fine-scale genetic analysis of a contact zone shared between the three basket willow species, Salix dasyclados, S. schwerinii and S. viminalis in the vicinity of the Lake Baikal in Southern Siberia. Individuals were sampled in fourteen populations and classified as pure species or hybrids based on a set of morphological characters. They were then genotyped at 384 nuclear SNP and four chloroplast SSR loci. The STRUCTURE and NewHybrids softwares were used to estimate the frequency and direction of hybridization using genotypic data at the nuclear SNP loci. Results: As many as 19 % of the genotyped individuals were classified as introgressed individuals and these were mainly encountered in the centre of the contact zone. All introgressed individuals were backcrosses to S. viminalis or S. schwerinii and no F1 or F2 hybrids were found. The rest of the genotyped individuals were classified as pure species and formed two clusters, one with S. schwerinii individuals and the other with S. viminalis and S. dasyclados individuals. The two clusters were significantly genetically differentiated, with F-ST = 0.333 (0.282-0.382, p < 0.001). In contrast, for the chloroplast haplotypes, no genetic differentiation was observed as they were completely shared between the species. Based on morphological classification only 5 % of the individuals were classified as introgressed individuals, which was much less than what was detected using genotypic data. Conclusions: We have discovered a new willow hybrid zone with relatively high frequency of introgressed individuals. The low frequency of F1 hybrids indicates that ongoing hybridization is limited, which could be because of the presence of reproductive barriers or simply because the conditions are not favorable for hybridization. We further conclude that in order to get a complete picture of the species composition of a hybrid zone it is necessary to use a combination of morphological characters and genetic data from both nuclear and chloroplast markers.
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| 13. |
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| 14. |
- Ghelardini, Luisa, et al.
(author)
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Genetic architecture of spring and autumn phenology in Salix
- 2014
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In: BMC Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 14, s. 31-
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Journal article (peer-reviewed)abstract
- Background: In woody plants from temperate regions, adaptation to the local climate results in annual cycles of growth and dormancy, and optimal regulation of these cycles are critical for growth, long-term survival, and competitive success. In this study we have investigated the genetic background to growth phenology in a Salix pedigree by assessing genetic and phenotypic variation in growth cessation, leaf senescence and bud burst in different years and environments. A previously constructed linkage map using the same pedigree and anchored to the annotated genome of P. trichocarpa was improved in target regions and used for QTL analysis of the traits. The major aims in this study were to map QTLs for phenology traits in Salix, and to identify candidate genes in QTL hot spots through comparative mapping with the closely related Populus trichocarpa. Results: All traits varied significantly among genotypes and the broad-sense heritabilities ranged between 0.5 and 0.9, with the highest for leaf senescence. In total across experiment and years, 80 QTLs were detected. For individual traits, the QTLs explained together from 21.5 to 56.5% of the variation. Generally each individual QTL explained a low amount of the variation but three QTLs explained above 15% of the variation with one QTL for leaf senescence explaining 34% of the variation. The majority of the QTLs were recurrently identified across traits, years and environments. Two hotspots were identified on linkage group (LG) II and X where narrow QTLs for all traits co-localized. Conclusions: This study provides the most detailed analysis of QTL detection for phenology in Salix conducted so far. Several hotspot regions were found where QTLs for different traits and QTLs for the same trait but identified during different years co-localised. Many QTLs co-localised with QTLs found in poplar for similar traits that could indicate common pathways for these traits in Salicaceae. This study is an important first step in identifying QTLs and candidate genes for phenology traits in Salix.
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| 15. |
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| 16. |
- Ghelardini, Luisa, et al.
(author)
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Quantitative Trait Loci analysis of traits related to biomass production in willow (Salix spp.)
- 2010
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Conference paper (peer-reviewed)abstract
- Willow trees (Salix spp.) have received increasing attention during the last decades for the purpose of bio-energy production in Europe. Willows are especially suitable for biomass production by short rotation cultivation because of their fast growth and high capacity to resprout after coppicing. However, achieving high biomass yields with relatively low inputs of energy requires development of high-yielding cultivars both suitable for plantation in different environments and efficient in the use of available resources. Selection and breeding of biomass willows would largely benefit from the use of easily detectable genetic markers linked to genes underlying economically important traits. In this study we present the results of quantitative trait loci (QTLs) analysis performed on several traits that are important determinants of biomass production and promising targets for the breeding of biomass willows. We mapped QTLs for growth, resource-economy-related traits such as biomass allocation, water use efficiency, leaf area efficiency, leaf nitrogen content and leaf nitrogen efficiency, and phenology traits such as timing of bud burst, growth cessation, and leaf senescence, in an experimental cross of Salix viminalis L. and Salix schwerinii E. Wolf . In the QTL analysis we used a dense genetic linkage map that we have constructed for the same population. The map was built using SNP markers located within genes evenly distributed throughout the Populus trichocarpa genome and it is thus aligned to the poplar physical map. We found high degree of synteny and gene order conservation between the genomes of willow and poplar. The use of the map aligned to the poplar genome allowed us to search for annotated genes the regions of the poplar genome corresponding to the QTLs found in Salix and to identify candidate genes putatively involved in the control of these traits
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| 17. |
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| 18. |
- Hallingbäck, Henrik, et al.
(author)
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Association mapping in Salix viminalis L. (Salicaceae) - identification of candidate genes associated with growth and phenology
- 2016
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In: Global Change Biology Bioenergy. - : Wiley. - 1757-1693 .- 1757-1707. ; 8:3, s. 670-685
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Journal article (peer-reviewed)abstract
- Willow species (Salix) are important as short-rotation biomass crops for bioenergy, which creates a demand for faster genetic improvement and breeding through deployment of molecular marker-assisted selection (MAS). To find markers associated with important adaptive traits, such as growth and phenology, for use in MAS, we genetically dissected the trait variation of a Salix viminalis (L.) population of 323 accessions. The accessions were sampled throughout northern Europe and were established at two field sites in Pustnas, Sweden, and at Woburn, UK, offering the opportunity to assess the impact of genotype-by-environment interactions (GxE) on trait-marker associations. Field measurements were recorded for growth and phenology traits. The accessions were genotyped using 1536 SNP markers developed from phenology candidate genes and from genes previously observed to be differentially expressed in contrasting environments. Association mapping between 1233 of these SNPs and the measured traits was performed taking into account population structure and threshold selection bias. At a false discovery rate (FDR) of 0.2, 29 SNPs were associated with bud burst, leaf senescence, number of shoots or shoot diameter. The percentage of accession variation explained by these associations ranged from 0.3% to 4.4%, suggesting that the studied traits are controlled by many loci of limited individual impact. Despite this, a SNP in the EARLY FLOWERING 3 gene was repeatedly associated (FDR<0.2) with bud burst. The rare homozygous genotype exhibited 0.4-1.0 lower bud burst scores than the other genotype classes on a five-grade scale. Consequently, this marker could be promising for use in MAS and the gene deserves further study. Otherwise, associations were less consistent across sites, likely due to their small estimates and to considerable GxE interactions indicated by multivariate association analyses and modest trait accession correlations across sites (0.32-0.61).
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| 19. |
- Hallingbäck, Henrik, et al.
(author)
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Genome-wide association mapping uncovers sex-associated copy number variation markers and female hemizygous regions on the W chromosome in Salix viminalis
- 2021
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 22
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Journal article (peer-reviewed)abstract
- Background Sex chromosomes are in some species largely undifferentiated (homomorphic) with restricted sex determination regions. Homomorphic but different sex chromosomes are found in the closely related genera Populus and Salix indicating flexible sex determination systems, ideal for studies of processes involved in sex chromosome evolution. We have performed genome-wide association studies of sex and analysed sex chromosomes in a population of 265 wild collected Salix viminalis accessions and studied the sex determining locus. Results A total of 19,592 markers were used in association analyses using both Fisher's exact tests and a single-marker mixed linear model, which resulted in 48 and 41 sex-associated (SA) markers respectively. Across all 48 SA markers, females were much more often heterozygous than males, which is expected if females were the heterogametic sex. The majority of the SA markers were, based on positions in the S. purpurea genome, located on chromosome 15, previously demonstrated to be the sex chromosome. Interestingly, when mapping the genotyping-by-sequencing sequence tag harbouring the two SA markers with the highest significance to the S. viminalis genomic scaffolds, five regions of very high similarity were found: three on a scaffold that represents a part of chromosome 15, one on a scaffold that represents a part of chromosome 9 and one on a scaffold not anchored to the genome. Based on segregation differences of the alleles at the two marker positions and on differences in PCR amplification between females and males we conclude that females had multiple copies of this DNA fragment (chromosome 9 and 15), whereas males only had one (chromosome 9). We therefore postulate that the female specific sequences have been copied from chromosome 9 and inserted on chromosome 15, subsequently developing into a hemizygous W chromosome linked region. Conclusions Our results support that sex determination in S. viminalis is controlled by one locus on chromosome 15. The segregation patterns observed at the SA markers furthermore confirm that S. viminalis females are the heterogametic sex. We also identified a translocation from chromosome 9 to the W chromosome.
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| 20. |
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| 21. |
- Hallingbäck, Henrik, et al.
(author)
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Genome Wide Associations of Growth, Phenology, and Plasticity Traits in Willow [Salix viminalis (L.)]
- 2019
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In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 10
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Journal article (peer-reviewed)abstract
- The short rotation biomass crop willow (Salix genera) has been of interest for bioenergy but recently also for biofuel production. For a faster development of new varieties molecular markers could be used as selection tool in an early stage of the breeding cycle. To identify markers associated with growth traits, genome-wide association mapping was conducted using a population of 291 Salix viminalis accessions collected across Europe and Russia and a large set of genotyping-by-sequencing markers. The accessions were vegetatively propagated and planted in replicated field experiments, one in Southern Sweden and one in Central Sweden. Phenology data, including bud burst and leaf senescence, as well as different growth traits were collected and measured repeatedly between 2010 and 2017 at both field environments. A value of the plasticity for each accession was calculated for all traits that were measured the same year in both environments as the normalized accession value in one environment subtracted by the corresponding value in the other environment. Broad-sense accession heritabilities and narrow-sense chip heritabilities ranged from 0.68 to 0.95 and 0.45 to 0.99, respectively for phenology traits and from 0.56 to 0.85 and 0.24 to 0.97 for growth traits indicating a considerable genetic component for most traits. Population structure and kinship between accessions were taken into account in the association analyses. In total, 39 marker-trait associations were found where four were specifically connected to plasticity and interestingly one particular marker was associated to several different plasticity growth traits. Otherwise association consistency was poor, possibly due to accession by environment interactions which were demonstrated by the low structure adjusted accession correlations across environments (ranging from 0.40 to 0.58). However, one marker association with biomass fresh weight was repeatedly observed in the same environment over two harvest years. For some traits where several associations were found, the markers jointly explained over 20% of the accession variation. The result from this study using a population of unrelated accessions has given useful information about marker-trait associations especially highlighting marker-plasticity associations and genotype-by-environment interactions as important factors to take account of in future strategies of Salix breeding.
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| 22. |
- Höglund, Solveig, et al.
(author)
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A rare major plant QTL determines non-responsiveness to a gall-forming insect in willow
- 2012
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In: Tree Genetics & Genomes. - : Springer Science and Business Media LLC. - 1614-2942 .- 1614-2950. ; 8:5, s. 1051-1060
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Journal article (peer-reviewed)abstract
- Growth and defence are plant traits that determine attack success by sessile herbivorous insects. Models of plant resistance suggest induced resistance to be an especially important mechanism in growth-dominated plant species. Little is known, however, about the effects of absence of induced responses as an alternative resistance mechanism. Large genetically based intraspecific variation in resistance (neonate larval mortality) occurs in Salix viminalis against the gall midge Dasineura marginemtorquens. In certain resistant genotypes, larval mortality is associated with formation of necrotic lesions and biochemical changes commonly found in hypersensitive response (HR). More detailed studies, however, have shown that resistance can occur without HR symptoms. By means of a quantitative trait locus (QTL) analysis, this study tested whether (1) resistance is caused by the HR or (2) by the failure of the midge to initiate a gall (non-responsiveness). One QTL explained 68 and 18 % of the variation in resistance in the experimental population during 2 years of investigation. Co-location of QTLs for resistance and HR was found in only one of the years, i.e. when HR was suppressed. The data suggest that the mechanism of resistance involves non-responsiveness, implying that the insect starves to death due to lack of resources. Such symptomless defence may be more important than previously thought because it is difficult to observe in nature.
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| 23. |
- Höglund, Solveig, et al.
(author)
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Willow resistance to a galling insect is driven by a lack of induced susceptibility not an induced defense
- 2015
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In: Arthropod-Plant Interactions. - : Springer Science and Business Media LLC. - 1872-8855 .- 1872-8847. ; 9, s. 447-455
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Journal article (peer-reviewed)abstract
- Gall-forming insects need to manipulate host plant's growth to access food resources. Because of this intimate relationship, a hypersensitive response (HR) is thought to be an important plant defense mechanism to kill the insect before a gall is formed. Few data exist, however, that unambiguously demonstrate that HR is causally linked to resistance against galling insects. Variation in Salix viminalis resistance to the gall midge Dasineura marginemtorquens is governed by only a few genes. Although the HR is considered to be an important resistance mechanism, an earlier study based on quantitative trait locus (QTL) analysis of data sets in which resistance was expressed, has shown that larval mortality is related to a single locus in a genomic region that does not contain a locus for HR, thus challenging previous suppositions that resistance is causally linked to the expression of a HR. The present study aims to test whether or not a HR causes the observed variation in willow resistance to D. marginemtorquens. By increasing the number of markers in the genomic region of interest and reanalyzing the QTL, we have enhanced the level of resolution, so permitting a more conclusive analysis than has previously been possible. The analysis identifies two genomic regions responding to gall midge attack. Importantly, the locus for resistance (measured as neonate larval mortality) and the locus for the HR are located in different regions, strongly contradicting the induced defense hypothesis. The analysis found that resistance and susceptibility were highly correlated because the allele associated with resistance was also associated with an absence of galls. It is suggested that a lack of induced susceptibility, rather than induced defense, explains the 'resistance' of S. viminalis to D. marginemtorquens.
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| 24. |
- Martin, Thomas, et al.
(author)
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Identification of a Differentially Expressed TIR-NBS-LRR Gene in a Major QTL Associated to Leaf Rust Resistance in Salix
- 2016
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In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11
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Journal article (peer-reviewed)abstract
- An earlier identified major quantitative trait locus for resistance towards the willow leaf rust fungus Melampsora larici-epitea in a Salix viminalis x (S. viminalis x S. schwerinii) population was used to identify potential resistance genes to the rust pathogen. Screening a genomic bacterial artificial chromosome library with markers from the peak position of the QTL region revealed one gene with TIR-NBS-LRR (Toll Interleukin1 Receptor-Nucleotide Binding Site-Leucine-Rich Repeat) domain structure indicative of a resistance gene. The resistance gene analog was denoted RGA1 and further analysis revealed a number of non-synonymous single nucleotide polymorphisms in the LRR domain between the resistant and susceptible Salix genotypes. Gene expression levels under controlled conditions showed a significantly lower constitutive expression of RGA1 in the susceptible genotype. In addition, the susceptible genotype showed a significantly reduced expression level of the RGA1 gene at 24 hours post inoculation with M. larici-epitea. This indicates that the pathogen may actively suppress RGA1 gene expression allowing a compatible plant-pathogen interaction and causing infection.
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| 25. |
- Mohan Pawar, Prashant, et al.
(author)
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QTL Mapping of Wood FT-IR Chemotypes Shows Promise for Improving Biofuel Potential in Short Rotation Coppice Willow (Salix spp.)
- 2018
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In: BioEnergy Research. - : Springer Science and Business Media LLC. - 1939-1234 .- 1939-1242. ; 11, s. 351-363
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Journal article (peer-reviewed)abstract
- An increasing interest to convert lignocellulosic biomass into biofuels has highlighted the potential of using willows for this purpose, due to its fast growth in short rotation coppice systems. Here, we use a mapping population of 463 individuals of a cross between Salix viminalis and S. viminalis x S. schwerinii to investigate the genetic background of different wood chemical traits, information of importance for breeding towards different uses of wood. Furthermore, using a subset of the mapping population, the correlation between biogas production and chemical traits was investigated. The phenotyping of wood was carried by Furrier-transformed-Infrared spectrometry (FT-IR) and water content analysis. Quantitative trait loci (QTLs) analysis was used to identify regions in the genome of importance for the phenotypic variation of these chemical traits. We found 27 QTLs for various traits. On linkage group (LG) VI-1, QTLs for signals assigned to G-lignin, lignin, and the S/G ratio were collocated and on LG XIV we found a cluster of QTLs representing signals assigned to lignin, cellulose, hemicellulose, and water. The QTLs explained from 3.4 to 6.9% of the phenotypic variation indicating a quantitative genetic background where many genes influence the traits. For the biogas production, a positive and negative correlation was seen with the signals assigned to acetyl and lignin, respectively. This study represents a first step in the understanding of the genetic background of wood chemical traits for willows, information needed for complementary studies, mapping of important genes, and for breeding of varieties for biofuel production purposes.
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| 26. |
- Ohlsson, Jonas, et al.
(author)
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Co-digestion of salix and manure for biogas: importance of clone choice, coppicing frequency and reactor setup
- 2020
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In: Energies. - : MDPI AG. - 1996-1073. ; 13
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Journal article (peer-reviewed)abstract
- Animalmanure represents amajor source of renewable energy that can be converted into biogasusing anaerobic digestion. In order to most efficiently utilize this resource, it can be co-digested withenergy dense, high biomethanation potential feedstocks such as energy crops. However, such feedstockstypically require pretreatments which are not feasible for small-scale facilities.We investigated theuse of single-stage and the sequential co-digestion of comminuted but otherwise non-pretreated Salixwith animal manure, and further investigated the effects of coppicing frequency and clone choice onbiomethanation potential and the area requirements for a typical Swedish farm-scale anaerobic digesterusing Salix and manure as feedstock. In comparison with conventional single-stage digestion, sequentialdigestion increased the volumetric and specific methane production by 57% to 577 NmL L?1 d?1 and192 NmL (g volatile solids (VS))?1, respectively. Biomethanation potential was the highest for the twoyear-old shoots, although gains in biomass productivity suggest that every-third-year coppicing maybe a better strategy for supplying Salix feedstock for anaerobic digestion. The biomethane productionperformance of the sequential digestion of minimally pretreated Salix mirrors that of hydrothermallypretreated hardwoods and may provide an option where such pretreatments are not feasible.
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| 27. |
- Ohlsson, Jonas, et al.
(author)
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Genetic variation of biomass recalcitrance in a natural Salix viminalis (L.) population
- 2019
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In: Biotechnology for Biofuels. - : Springer Science and Business Media LLC. - 1754-6834. ; 12
-
Journal article (peer-reviewed)abstract
- BackgroundSalix spp. are high-productivity crops potentially used for lignocellulosic biofuels such as bioethanol. In general, pretreatment is needed to facilitate the enzymatic depolymerization process. Biomass resistance to degradation, i.e., biomass recalcitrance, is a trait which can be assessed by measuring the sugar released after combined pretreatment and enzymatic hydrolysis. We have examined genetic parameters of enzymatic sugar release and other traits related to biorefinery use in a population of 286 natural Salix viminalis clones. Furthermore, we have evaluated phenotypic and genetic correlations between these traits and performed a genomewide association mapping analysis using a set of 19,411 markers.ResultsSugar release (glucose and xylose) after pretreatment and enzymatic saccharification proved highly variable with large genetic and phenotypic variations, and chip heritability estimates (h(2)) of 0.23-0.29. Lignin syringyl/guaiacyl (S/G) ratio and wood density were the most heritable traits (h(2)=0.42 and 0.59, respectively). Sugar release traits were positively correlated, phenotypically and genetically, with biomass yield and lignin S/G ratio. Association mapping revealed seven marker-trait associations below a suggestive significance threshold, including one marker associated with glucose release.ConclusionsWe identified lignin S/G ratio and shoot diameter as heritable traits that could be relatively easily evaluated by breeders, making them suitable proxy traits for developing low-recalcitrance varieties. One marker below the suggestive threshold for marker associations was identified for sugar release, meriting further investigation while also highlighting the difficulties in employing genomewide association mapping for complex traits.
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| 28. |
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| 29. |
- Pucholt, Pascal, et al.
(author)
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Genome-wide transcriptional and physiological responses to drought stress in leaves and roots of two willow genotypes
- 2015
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In: BMC Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 15
-
Journal article (peer-reviewed)abstract
- Background: Drought is a major environmental stress that can have severe impacts on plant productivity and survival. Understanding molecular mechanisms of drought responses is crucial in order to breed for drought adapted plant cultivars. The aim of the present study was to investigate phenotypic and transcriptional drought responses in two willow genotypes (520 and 592) originating from an experimental cross between S. viminalis x (S. viminalis x S. schwerinii). Willows are woody perennials in the Salicaceae plant family that are grown as bioenergy crops worldwide. Methods: An experiment was conducted where plants were exposed to drought and different eco-physiological parameters were assessed. RNA-seq data was furthermore generated with the Illumina technology from root tips and leaves from plants grown in drought and well-watered (WW) conditions. The RNA-seq data was assembled de novo with the Trinity assembler to create a reference gene set to which the reads were mapped in order to obtain differentially expressed genes (DEGs) between the drought and WW conditions. To investigate molecular mechanisms involved in the drought response, GO enrichment analyses were conducted. Candidate genes with a putative function in the drought response were also identified. Results: A total of 52,599 gene models were obtained and after filtering on gene expression (FPKM >= 1), 35,733 gene models remained, of which 24,421 contained open reading frames. A total of 5,112 unique DEGs were identified between drought and WW conditions, of which the majority were found in the root tips. Phenotypically, genotype 592 displayed less growth reduction in response to drought compared to genotype 520. At the transcriptional level, genotype 520 displayed a greater response in the leaves as more DEGs were found in genotype 520 compared to genotype 592. In contrast, the transcriptional responses in the root tips were rather similar between the two genotypes. A core set of candidate genes encoding proteins with a putative function in drought response was identified, for example MYBs and bZIPs as well as chlorophyll a/b binding proteins. Discussion: We found substantial differences in drought responses between the genotypes, both at the phenotypic and transcriptional levels. In addition to the genotypic variation in several traits, we also found indications for genotypic variation in trait plasticity, which could play a role in drought adaptation. Furthermore, the two genotypes displayed overall similar transcriptional responses in the root tips, but more variation in the leaves. It is thus possible that the observed phenotypic differences could be a result of transcriptional differences mostly at the leaf level. Conclusions: This study has contributed to a better general understanding of drought responses in woody plants, specifically in willows, and has implications for breeding research towards more drought adapted plants.
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| 30. |
- Pucholt, Pascal, et al.
(author)
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Single locus sex determination and female heterogamety in the basket willow (Salix viminalis L.)
- 2015
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In: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 114, s. 575-583
-
Journal article (peer-reviewed)abstract
- Most eukaryotes reproduce sexually and a wealth of different sex determination mechanisms have evolved in this lineage. Dioecy or separate sexes are rare among flowering plants but have repeatedly evolved from hermaphroditic ancestors possibly involving male or female sterility mutations. Willows (Salix spp.) and poplars (Populus spp.) are predominantly dioecious and are members of the Salicaceae family. All studied poplars have sex determination loci on chromosome XIX, however, the position differs among species and both male and female heterogametic system exists. In contrast to the situation in poplars, knowledge of sex determination mechanisms in willows is sparse. In the present study, we have for the first time positioned the sex determination locus on chromosome XV in S. viminalis using quantitative trait locus mapping. All female offspring carried a maternally inherited haplotype, suggesting a system of female heterogamety or ZW. We used a comparative mapping approach and compared the positions of the markers between the S. viminalis linkage map and the physical maps of S. purpurea, S. suchowensis and P. trichocarpa. As we found no evidence for chromosomal rearrangements between chromosome XV and XIX between S. viminalis and P. trichocarpa, it shows that the sex determination loci in the willow and the poplar most likely do not share a common origin and has thus evolved separately. This demonstrates that sex determination mechanisms in the Salicaceae family have a high turnover rate and as such it is excellent for studies of evolutionary processes involved in sex chromosome turnover.
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| 31. |
- Richards, Thomas, et al.
(author)
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Quantitative genetic architecture of adaptive phenology traits in the deciduous tree, Populus trichocarpa (Torr. And Gray)
- 2020
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In: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 125, s. 449-458
-
Journal article (peer-reviewed)abstract
- In a warming climate, the ability to accurately predict and track shifting environmental conditions will be fundamental for plant survival. Environmental cues define the transitions between growth and dormancy as plants synchronise development with favourable environmental conditions, however these cues are predicted to change under future climate projections which may have profound impacts on tree survival and growth. Here, we use a quantitative genetic approach to estimate the genetic basis of spring and autumn phenology inPopulus trichocarpato determine this species capacity for climate adaptation. We measured bud burst, leaf coloration, and leaf senescence traits across two years (2017-2018) and combine these observations with measures of lifetime growth to determine how genetic correlations between phenology and growth may facilitate or constrain adaptation. Timing of transitions differed between years, although we found strong cross year genetic correlations in all traits, suggesting that genotypes respond in consistent ways to seasonal cues. Spring and autumn phenology were correlated with lifetime growth, where genotypes that burst leaves early and shed them late had the highest lifetime growth. We also identified substantial heritable variation in the timing of all phenological transitions (h(2) = 0.5-0.8) and in lifetime growth (h(2) = 0.8). The combination of additive variation and favourable genetic correlations in phenology traits suggests that populations of cultivated varieties of P. Trichocarpa may have the capability to adapt their phenology to climatic changes without negative impacts on growth.
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| 32. |
- Rönnberg Wästljung, Ann-Christin, et al.
(author)
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Phenotypic plasticity in Populus trichocarpa clones across environments in the Nordic-Baltic region
- 2022
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In: Scandinavian Journal of Forest Research. - : Informa UK Limited. - 0282-7581 .- 1651-1891. ; 37, s. 1-5
-
Journal article (peer-reviewed)abstract
- Transition towards a bio-based society requires large amounts of woody biomass to be converted into biofuels and biomaterials. Populus species are good candidates for growth in short rotations, but there is a lack of climate-adapted plant material suitable for growth at the high latitudes of the Nordic-Baltic region. Here we studied the growth and phenology traits in 63 Populus trichocarpa clones earlier preliminary selected for growth at northern latitudes, in three different field sites; i.e. in central Sweden, eastern and western Latvia. The material showed moderate broad sense heritabilities, with high values for phenology traits, indicating opportunities for selection. Genotype x environment (g x e) interaction was identified for all traits, but the phenotypic correlation between pairs of sites provided more detailed information indicating the strength of the g x e interaction. The between-clone variation in plasticity was high, and we identified some clones showing a high and stable performance across the three sites. These clones are of particular interest for the commercial deployment and future breeding of Populus material for the Nordic-Baltic region.
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| 33. |
- Samils, Berit, et al.
(author)
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QTL mapping of resistance to leaf rust in Salix
- 2011
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In: Tree Genetics and Genomes. - : Springer Science and Business Media LLC. - 1614-2942 .- 1614-2950. ; 7, s. 1219-1235
-
Journal article (peer-reviewed)abstract
- Genetic mapping of quantitative trait loci (QTL) for resistance to Melampsora leaf rust was performed in two willow families: the progeny from a backcross between Salix viminalis and a hybrid S. viminalis x Salix schwerinii (population S(1)), and the F(1) progeny of a cross between two S. viminalis (population S(3)). Disease levels were scored in the field for three consecutive years. In the laboratory, five different rust strains were sprayed onto leaf disks and the following resistance components were scored: latent period, diameter and number of uredinia, and flecking. One major QTL and 14 smaller were identified in the S(1) host population. One rust strain, that represents a Melampsora form with limited incidence on S. viminalis, showed lower aggressiveness to the S(1) host population together with a different pattern in QTLs. In the S(3) host population, we detected 13 QTLs for rust resistance, of which two were located to the same genomic regions as those found for the S(1) population. We showed that the strongest QTL co-segregated with a gene homologous to a known Toll/interleukin receptor-nucleotide binding site-leucine-rich repeat resistance gene in poplar. The importance of the identified QTLs is discussed in relation to breeding for durable resistance.
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| 34. |
- Weih, Martin, et al.
(author)
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Optimizing nitrogen economy under drought: increased leaf nitrogen is an acclimation to water stress in willow (Salix spp.)
- 2011
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In: Annals of Botany. - : Oxford University Press (OUP). - 0305-7364 .- 1095-8290. ; 108, s. 1347-1353
-
Journal article (peer-reviewed)abstract
- Conclusions It is concluded that N-uptake efficiency and leaf N efficiency are important traits to improve growth under drought. Increased leaf N content (area basis) is an acclimation to optimize N economy under drought. The leaf N content is an interesting trait for breeding of willow bioenergy crops in a climate change future. In contrast, leaf biomass allocation is a less interesting breeding target to improve yield under drought.
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| 35. |
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| 36. |
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| 37. |
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| 38. |
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