| 1. |
- 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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| 2. |
- Berlin Kolm, Sofia, et al.
(författare)
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High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus
- 2010
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 11:1, s. 129-
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Tidskriftsartikel (refereegranskat)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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| 3. |
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| 4. |
- Berlin Kolm, Sofia, et al.
(författare)
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Polymorphism and divergence of two willow species, Salix viminalis L. and Salix schwerinii E. Wolf
- 2011
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Ingår i: G3. - : Oxford University Press (OUP). - 2160-1836. ; 1:5, s. 387-400
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Tidskriftsartikel (refereegranskat)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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| 5. |
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| 6. |
- Berlin Kolm, Sofia, et al.
(författare)
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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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Ingår i: Molecular Breeding. - : Springer Science and Business Media LLC. - 1380-3743 .- 1572-9788. ; 34, s. 1987-2003
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Tidskriftsartikel (refereegranskat)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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| 7. |
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| 8. |
- Ghelardini, Luisa, et al.
(författare)
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Genetic architecture of spring and autumn phenology in Salix
- 2014
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Ingår i: BMC Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 14, s. 31-
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Tidskriftsartikel (refereegranskat)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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| 9. |
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| 10. |
- Ghelardini, Luisa, et al.
(författare)
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Quantitative Trait Loci analysis of traits related to biomass production in willow (Salix spp.)
- 2010
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Konferensbidrag (refereegranskat)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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| 11. |
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| 12. |
- Höglund, Solveig, et al.
(författare)
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A rare major plant QTL determines non-responsiveness to a gall-forming insect in willow
- 2012
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Ingår i: Tree Genetics & Genomes. - : Springer Science and Business Media LLC. - 1614-2942 .- 1614-2950. ; 8:5, s. 1051-1060
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Tidskriftsartikel (refereegranskat)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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| 13. |
- Samils, Berit, et al.
(författare)
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QTL mapping of resistance to leaf rust in Salix
- 2011
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Ingår i: Tree Genetics and Genomes. - : Springer Science and Business Media LLC. - 1614-2942 .- 1614-2950. ; 7, s. 1219-1235
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Tidskriftsartikel (refereegranskat)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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| 14. |
- Weih, Martin, et al.
(författare)
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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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Ingår i: Annals of Botany. - : Oxford University Press (OUP). - 0305-7364 .- 1095-8290. ; 108, s. 1347-1353
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Tidskriftsartikel (refereegranskat)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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