| 1. |
- Apuli, Rami-Petteri, et al.
(författare)
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Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen (Populus tremula)
- 2020
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Ingår i: G3. - : GENETICS SOCIETY AMERICA. - 2160-1836. ; 10:1, s. 299-309
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Tidskriftsartikel (refereegranskat)abstract
- The rate of meiotic recombination is one of the central factors determining genome-wide levels of linkage disequilibrium which has important consequences for the efficiency of natural selection and for the dissection of quantitative traits. Here we present a new, high-resolution linkage map for Populus tremula that we use to anchor approximately two thirds of the P. tremula draft genome assembly on to the expected 19 chromosomes, providing us with the first chromosome-scale assembly for P. tremula (Table 2). We then use this resource to estimate variation in recombination rates across the P. tremula genome and compare these results to recombination rates based on linkage disequilibrium in a large number of unrelated individuals. We also assess how variation in recombination rates is associated with a number of genomic features, such as gene density, repeat density and methylation levels. We find that recombination rates obtained from the two methods largely agree, although the LD-based method identifies a number of genomic regions with very high recombination rates that the map-based method fails to detect. Linkage map and LD-based estimates of recombination rates are positively correlated and show similar correlations with other genomic features, showing that both methods can accurately infer recombination rate variation across the genome. Recombination rates are positively correlated with gene density and negatively correlated with repeat density and methylation levels, suggesting that recombination is largely directed toward gene regions in P. tremula.
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| 2. |
- Apuli, Rami-Petteri, et al.
(författare)
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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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Ingår i: BMC Plant Biology. - : BioMed Central (BMC). - 1471-2229. ; 21
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Tidskriftsartikel (refereegranskat)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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| 3. |
- Bernhardsson, Carolina, et al.
(författare)
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Development of a highly efficient 50K single nucleotide polymorphism genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome resequencing and its transferability to other spruce species
- 2021
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Ingår i: Molecular Ecology Resources. - : John Wiley & Sons. - 1755-098X .- 1755-0998. ; 21:3, s. 880-896
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Tidskriftsartikel (refereegranskat)abstract
- Norway spruce (Picea abies L. Karst) is one of the most important forest tree species with significant economic and ecological impact in Europe. For decades, genomic and genetic studies on Norway spruce have been challenging due to the large and repetitive genome (19.6 Gb with more than 70% being repetitive). To accelerate genomic studies, including population genetics, genome-wide association studies (GWAS) and genomic selection (GS), in Norway spruce and related species, we here report on the design and performance of a 50K single nucleotide polymorphism (SNP) genotyping array for Norway spruce. The array is developed based on whole genome resequencing (WGS), making it the first WGS-based SNP array in any conifer species so far. After identifying SNPs using genome resequencing data from 29 trees collected in northern Europe, we adopted a two-step approach to design the array. First, we built a 450K screening array and used this to genotype a population of 480 trees sampled from both natural and breeding populations across the Norway spruce distribution range. These samples were then used to select high-confidence probes that were put on the final 50K array. The SNPs selected are distributed over 45,552 scaffolds from the P. abies version 1.0 genome assembly and target 19,954 unique gene models with an even coverage of the 12 linkage groups in Norway spruce. We show that the array has a 99.5% probe specificity, >98% Mendelian allelic inheritance concordance, an average sample call rate of 96.30% and an SNP call rate of 98.90% in family trios and haploid tissues. We also observed that 23,797 probes (50%) could be identified with high confidence in three other spruce species (white spruce [Picea glauca], black spruce [P. mariana] and Sitka spruce [P. sitchensis]). The high-quality genotyping array will be a valuable resource for genetic and genomic studies in Norway spruce as well as in other conifer species of the same genus.
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| 4. |
- Bernhardsson, Carolina, et al.
(författare)
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Variant Calling Using Whole Genome Resequencing and Sequence Capture for Population and Evolutionary Genomic Inferences in Norway Spruce (Picea Abies)
- 2020
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Ingår i: The Spruce Genome. - Switzerland : Springer Nature. - 9783030210014 - 9783030210007 ; , s. 9-36
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Bokkapitel (refereegranskat)abstract
- Advances in next-generation sequencing methods and the development of new statistical and computational methods have opened up possibilities for large-scale, high-quality genotyping in most organisms. Conifer genomes are large and are known to contain a high fraction of repetitive elements and this complex genome structure has bearings for approaches that aim to use next-generation sequencing methods for genotyping. In this chapter, we provide a detailed description of a workflow for variant calling using next-generation sequencing in Norway spruce (Picea abies). The workflow starts with raw sequencing reads and proceeds through read mapping to variant calling and variant filtering. We illustrate the pipeline using data derived from both whole-genome resequencing data and reduced representation sequencing. We highlight possible problems and pitfalls of using next-generation sequencing data for genotyping stemming from the complex genome structure of conifers and how those issues can be mitigated or eliminated.
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| 5. |
- Capador‐Barreto, Hernán D., et al.
(författare)
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Killing two enemies with one stone? : Genomics of resistance to two sympatric pathogens in Norway spruce
- 2021
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Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 30:18, s. 4433-4447
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Tidskriftsartikel (refereegranskat)abstract
- Trees must cope with the attack of multiple pathogens, often simultaneously during their long lifespan. Ironically, the genetic and molecular mechanisms controlling this process are poorly understood. The objective of this study was to compare the genetic component of resistance in Norway spruce to Heterobasidion annosum s.s. and its sympatric congener Heterobasidion parviporum. Heterobasidion root- and stem-rot is a major disease of Norway spruce caused by members of the Heterobasidion annosum species complex. Resistance to both pathogens was measured using artificial inoculations in half-sib families of Norway spruce trees originating from central to northern Europe. The genetic component of resistance was analysed using 63,760 genome-wide exome-capture sequenced SNPs and multitrait genome-wide associations. No correlation was found for resistance to the two pathogens; however, associations were found between genomic variants and resistance traits with synergic or antagonist pleiotropic effects to both pathogens. Additionally, a latitudinal cline in resistance in the bark to H. annosum s.s. was found; trees from southern latitudes, with a later bud-set and thicker stem diameter, allowed longer lesions, but this was not the case for H. parviporum. In summary, this study detects genomic variants with pleiotropic effects which explain multiple disease resistance from a genic level and could be useful for selection of resistant trees to both pathogens. Furthermore, it highlights the need for additional research to understand the evolution of resistance traits to multiple pathogens in trees.
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| 6. |
- Eklöf, Helena, et al.
(författare)
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Comparing the Effectiveness of Exome Capture Probes, Genotyping by Sequencing and Whole-Genome Re-Sequencing for Assessing Genetic Diversity in Natural and Managed Stands of Picea abies
- 2020
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Ingår i: Forests. - : MDPI. - 1999-4907 .- 1999-4907. ; 11:11
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Tidskriftsartikel (refereegranskat)abstract
- Conifer genomes are characterized by their large size and high abundance of repetitive material, making large-scale genotyping in conifers complicated and expensive. One of the consequences of this is that it has been difficult to generate data on genome-wide levels of genetic variation. To date, researchers have mainly employed various complexity reduction techniques to assess genetic variation across the genome in different conifer species. These methods tend to capture variation in a relatively small subset of a typical conifer genome and it is currently not clear how representative such results are. Here we take advantage of data generated in the first large-scale re-sequencing effort in Norway spruce and assess how well two commonly used complexity reduction methods, targeted capture probes and genotyping by sequencing perform in capturing genome-wide variation in Norway spruce. Our results suggest that both methods perform reasonably well for assessing genetic diversity and population structure in Norway spruce (Picea abies (L.) H. Karst.). Targeted capture probes were slightly more effective than GBS, likely due to them targeting known genomic regions whereas the GBS data contains a substantially greater fraction of repetitive regions, which sometimes can be problematic for assessing genetic diversity. In conclusion, both methods are useful for genotyping large numbers of samples and they greatly reduce the cost involved with genotyping a species with such a complex genome as Norway spruce.
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| 7. |
- Eklöf, Helena, 1989-
(författare)
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Genetic diversity and differentiation in natural and managed stands of Norway spruce (Picea abies)
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Being one of Sweden’s most important tree species, both as a keystone species and for the forest industry, it is important that we keep our stands of Norway spruce (Picea abies (L.) Karst.) as healthy as possible. With an unclear starting point of existing genetic diversity in natural forests we need to both evaluate what levels of natural diversity we have to begin with and how modern forestry practices might affect this. Previous studies have used relatively few markers to study this or similar situation before. We proved that both capture probes and genotyping by sequencing (GBS) show similar results in common diversity measurements and offers many SNPs, although capture probes showed slightly more diversity in the results, we choose to use PoolSeq and GBS together to examine a large number of planted and natural stands of Norwegian spruce in northern Sweden. In line with previous results on the subject we did not find any large differences between our young, planted forests and our old forests, suggesting that today’s re-planting methods have not affected the general diversity in different stands. However, we did find a difference in the variance of our summary statistics on a stand level between planted and old stands, an indicator that there is a possibility that forestry can cause long-term effects. This becomes even more important in the light of possible clonal deployment of Norway spruce. I believe that more research is needed over both larger geographical areas and with a focus on within stand variation. Using mitochondrial and chloroplast DNA to discern finer details of spatial distribution within stands and looking closer at the genotypic diversity within natural and planted stands. An effort should also be put into examine how these possible differences are affecting the rest of the ecosystem, living with and among Norway spruce.
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| 8. |
- Fataftah, Nazeer, et al.
(författare)
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GIGANTEA influences leaf senescence in trees in two different ways
- 2021
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Ingår i: Plant Physiology. - : Oxford University Press. - 0032-0889 .- 1532-2548. ; 187:4, s. 2435-2450
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Tidskriftsartikel (refereegranskat)abstract
- GIGANTEA (GI) genes have a central role in plant development and influence several processes. Hybrid aspen T89 (Populus tremula x tremuloides) trees with low GI expression engineered through RNAi show severely compromised growth. To study the effect of reduced GI expression on leaf traits with special emphasis on leaf senescence, we grafted GI-RNAi scions onto wild-type rootstocks and successfully restored growth of the scions. The RNAi line had a distorted leaf shape and reduced photosynthesis, probably caused by modulation of phloem or stomatal function, increased starch accumulation, a higher carbon-to-nitrogen ratio, and reduced capacity to withstand moderate light stress. GI-RNAi also induced senescence under long day (LD) and moderate light conditions. Furthermore, the GI-RNAi lines were affected in their capacity to respond to “autumn environmental cues” inducing senescence, a type of leaf senescence that has physiological and biochemical characteristics that differ from those of senescence induced directly by stress under LD conditions. Overexpression of GI delayed senescence under simulated autumn conditions. The two different effects on leaf senescence under LD or simulated autumn conditions were not affected by the expression of FLOWERING LOCUS T. GI expression regulated leaf senescence locally-the phenotype followed the genotype of the branch, independent of its position on the tree-and trees with modified gene expression were affected in a similar way when grown in the field as under controlled conditions. Taken together, GI plays a central role in sensing environmental changes during autumn and determining the appropriate timing for leaf senescence in Populus.
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| 9. |
- Müller, Niels A., et al.
(författare)
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A single gene underlies the dynamic evolution of poplar sex determination.
- 2020
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Ingår i: Nature Plants. - : Springer Nature. - 2055-0278 .- 2055-026X. ; 6:6, s. 630-637
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Tidskriftsartikel (refereegranskat)abstract
- Although hundreds of plant lineages have independently evolved dioecy (that is, separation of the sexes), the underlying genetic basis remains largely elusive. Here we show that diverse poplar species carry partial duplicates of the ARABIDOPSIS RESPONSE REGULATOR 17 (ARR17) orthologue in the male-specific region of the Y chromosome. These duplicates give rise to small RNAs apparently causing male-specific DNA methylation and silencing of the ARR17 gene. CRISPR–Cas9-induced mutations demonstrate that ARR17 functions as a sex switch, triggering female development when on and male development when off. Despite repeated turnover events, including a transition from the XY system to a ZW system, the sex-specific regulation of ARR17 is conserved across the poplar genus and probably beyond. Our data reveal how a single-gene-based mechanism of dioecy can enable highly dynamic sex-linked regions and contribute to maintaining recombination and integrity of sex chromosomes.
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| 10. |
- Panahabadi, Rahele, et al.
(författare)
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Genome-Wide Association Mapping of Mixed Linkage (1,3;1,4)-beta-Glucan and Starch Contents in Rice Whole Grain
- 2021
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Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- The glucan content of rice is a key factor defining its nutritional and economic value. Starch and its derivatives have many industrial applications such as in fuel and material production. Non-starch glucans such as (1,3;1,4)-beta-D-glucan (mixed-linkage beta-glucan, MLG) have many benefits in human health, including lowering cholesterol, boosting the immune system, and modulating the gut microbiome. In this study, the genetic variability of MLG and starch contents were analyzed in rice (Oryza sativa L.) whole grain, by performing a new quantitative analysis of the polysaccharide content of rice grains. The 197 rice accessions investigated had an average MLG content of 252 mu g/mg, which was negatively correlated with the grain starch content. A new genome-wide association study revealed seven significant quantitative trait loci (QTLs) associated with the MLG content and two QTLs associated with the starch content in rice whole grain. Novel genes associated with the MLG content were a hexose transporter and anthocyanidin 5,3-O-glucosyltransferase. Also, the novel gene associated with the starch content was a nodulin-like domain. The data pave the way for a better understanding of the genes involved in determining both MLG and starch contents in rice grains and should facilitate future plant breeding programs.
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