| 1. |
- Avia, Komlan, et al.
(författare)
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Association of FLOWERING LOCUS T/TERMINAL FLOWER 1-like gene FTL2 expression with growth rhythm in Scots pine (Pinus sylvestris)
- 2014
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 204:1, s. 159-170
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the genetic basis of the timing of bud set, an important trait in conifers, is relevant for adaptation and forestry practice. In common garden experiments, both Scots pine (Pinus sylvestris) and Norway spruce (Picea abies) show a latitudinal cline in the trait. We compared the regulation of their bud set biology by examining the expression of PsFTL2, a Pinus sylvestris homolog to PaFTL2, a FLOWERING LOCUS T/TERMINAL FLOWER 1 (FT/TFL1)-like gene, the expression levels of which have been found previously to be associated with the timing of bud set in Norway spruce. In a common garden study, we analyzed the relationship of bud phenology under natural and artificial photoperiods and the expression of PsFTL2 in a set of Scots pine populations from different latitudes. The expression of PsFTL2 increased in the needles preceding bud set and decreased during bud burst. In the northernmost population, even short night periods were efficient to trigger this expression, which also increased earlier under all photoperiodic regimes compared with the southern populations. Despite the different biology, with few limitations, the two conifers that diverged 140 million yr ago probably share an association of FTL2 with bud set, pointing to a common mechanism for the timing of growth cessation in conifers.
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| 2. |
- Benavides, Raquel, et al.
(författare)
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The GenTree Leaf Collection : Inter- and intraspecific leaf variation in seven forest tree species in Europe
- 2021
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Ingår i: Global Ecology and Biogeography. - : John Wiley & Sons. - 1466-822X .- 1466-8238. ; 30:3, s. 590-597
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Tidskriftsartikel (refereegranskat)abstract
- Motivation Trait variation within species can reveal plastic and/or genetic responses to environmental gradients, and may indicate where local adaptation has occurred. Here, we present a dataset of rangewide variation in leaf traits from seven of the most ecologically and economically important tree species in Europe. Sample collection and trait assessment are embedded in the GenTree project (EU-Horizon 2020), which aims at characterizing the genetic and phenotypic variability of forest tree species to optimize the management and sustainable use of forest genetic resources. Our dataset captures substantial intra- and interspecific leaf phenotypic variability, and provides valuable information for studying the relationship between ecosystem functioning and trait variability of individuals, and the response and resilience of species to environmental changes. Main types of variable contained We chose morphological and chemical characters linked to trade-offs between acquisition and conservation of resources and water use, namely specific leaf area, leaf size, carbon and nitrogen content and their ratio, and the isotopic signature of stable isotope C-13 and N-15 in leaves. Spatial location and grain We surveyed between 18 and 22 populations per species, 141 in total, across Europe. Time period Leaf sampling took place between 2016 and 2017. Major taxa and level of measurement We sampled at least 25 individuals in each population, 3,569 trees in total, and measured traits in 35,755 leaves from seven European tree species, i.e. the conifers Picea abies, Pinus pinaster and Pinus sylvestris, and the broadleaves Betula pendula, Fagus sylvatica, Populus nigra and Quercus petraea. Software format The data files are in ASCII text, tab delimited, not compressed.
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| 3. |
- Fogelqvist, Johan, et al.
(författare)
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Cryptic population genetic structure : the number of inferred clusters depends on sample size
- 2010
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:2, s. 314-323
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Tidskriftsartikel (refereegranskat)abstract
- Clustering methods have been used extensively to unravel cryptic population genetic structure. We investigated the effect of the number of individuals sampled in each location on the resulting number of clusters. Our study was motivated by recent results in Arabidopsis thaliana: studies in which more than one individual was sampled per location apparently have led to a much higher number of clusters than studies where only one individual was sampled in each location, as is generally done in this species. We show, using computer simulations and microsatellite data in A. thaliana, that the number of sampled individuals indeed has a strong impact on the number of resulting clusters. This effect is smaller if the sampled populations have a hierarchical structure. In most cases, sampling 5-10 individuals per population should be enough. The results argue for abandoning the concept of 'accessions' in partially selfing organisms.
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| 4. |
- Karpale, Mikko, et al.
(författare)
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Activation of nuclear receptor PXR induces atherogenic lipids and PCSK9 through SREBP2-mediated mechanism
- 2021
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Ingår i: British Journal of Pharmacology. - : Macmillan Publishers Ltd.. - 0007-1188 .- 1476-5381. ; 178:12, s. 2461-2481
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND AND PURPOSE: Many drugs and environmental contaminants induce hypercholesterolemia and promote the risk of atherosclerotic cardiovascular disease. The mechanisms involved are poorly defined precluding efficient prediction and prevention. We tested the hypothesis that pregnane X receptor (PXR), a xenobiotic-sensing nuclear receptor, regulates the level of circulating atherogenic lipids in humans and utilized mouse experiments to identify the mechanisms involved.EXPERIMENTAL APPROACH: We performed serum NMR metabolomics in healthy volunteers administered rifampicin, a prototypical human PXR ligand, or placebo in a crossover setting. Furthermore, we used high-fat diet fed wildtype and PXR knockout mice to investigate the mechanisms and pathways mediating the PXR-induced alterations in cholesterol homeostasis.KEY RESULTS: Activation of PXR induced cholesterogenesis both in pre-clinical and clinical settings. In human volunteers, rifampicin increased IDL, LDL and total cholesterol and lathosterol-cholesterol ratio, a marker of cholesterol synthesis, suggesting increased cholesterol synthesis. Mechanistic studies in mice indicated that PXR activation launches widespread induction of the cholesterol synthesis genes including the rate-limiting Hmgcr and upregulates the intermediates in the Kandutsch-Russell cholesterol synthesis pathway in the liver. Additionally, PXR activation induced plasma PCSK9, a negative regulator of hepatic LDL uptake, in both mice and humans. We propose that these effects were mediated through increased proteolytic activation of SREBP2 in response to PXR activation.CONCLUSION AND IMPLICATIONS: PXR activation induces cholesterol synthesis and elevates LDL and total cholesterol in humans. The PXR-SREBP2 pathway is a novel regulator of the cholesterol and PCSK9 synthesis, and a molecular mechanism for drug- and chemical-induced hypercholesterolemia.
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| 5. |
- Kastally, Chedly, et al.
(författare)
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Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research
- 2022
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Ingår i: The Plant Journal. - : John Wiley & Sons. - 0960-7412 .- 1365-313X. ; 109:5, s. 1337-1350
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Tidskriftsartikel (refereegranskat)abstract
- Pinus sylvestris (Scots pine) is the most widespread coniferous tree in the boreal forests of Eurasia, with major economic and ecological importance. However, its large and repetitive genome presents a challenge for conducting genome-wide analyses such as association studies, genetic mapping and genomic selection. We present a new 50K single-nucleotide polymorphism (SNP) genotyping array for Scots pine research, breeding and other applications. To select the SNP set, we first genotyped 480 Scots pine samples on a 407 540 SNP screening array and identified 47 712 high-quality SNPs for the final array (called 'PiSy50k'). Here, we provide details of the design and testing, as well as allele frequency estimates from the discovery panel, functional annotation, tissue-specific expression patterns and expression level information for the SNPs or corresponding genes, when available. We validated the performance of the PiSy50k array using samples from Finland and Scotland. Overall, 39 678 (83.2%) SNPs showed low error rates (mean = 0.9%). Relatedness estimates based on array genotypes were consistent with the expected pedigrees, and the level of Mendelian error was negligible. In addition, array genotypes successfully discriminate between Scots pine populations of Finnish and Scottish origins. The PiSy50k SNP array will be a valuable tool for a wide variety of future genetic studies and forestry applications.
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| 6. |
- Kemi, Ulla, et al.
(författare)
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Role of vernalization and of duplicated Flowering Locus C in the perennial Arabidopsis lyrata
- 2013
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 197:1, s. 323-335
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Tidskriftsartikel (refereegranskat)abstract
- FLOWERING LOCUS C (FLC) is one of the main genes influencing the vernalization requirement and natural flowering time variation in the annual Arabidopsis thaliana. Here we studied the effects of vernalization on flowering and its genetic basis in the perennial Arabidopsis lyrata. Two tandemly duplicated FLC genes (FLC1 and FLC2) were compared with respect to expression and DNA sequence. The effect of vernalization on flowering and on the expression of FLC1 was studied in three European populations. The genetic basis of the FLC1 expression difference between two of the populations was further studied by expression quantitative trait locus (eQTL) mapping and sequence analysis. FLC1 was shown to have a likely role in the vernalization requirement for flowering in A. lyrata. Vernalization decreased its expression and the northern study populations showed higher FLC1 expression than the southern one. eQTL mapping between two of the populations revealed one eQTL affecting FLC1 expression in the genomic region containing the FLC genes. Most FLC1 sequence differences between the study populations were found in the promoter region and in the first intron. Variation in the FLC1 sequence may cause differences in FLC1 expression between late- and early-flowering A. lyrata populations.
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| 7. |
- Lascoux, Martin, et al.
(författare)
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Local adaptation in plants
- 2016
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Ingår i: Encyclopedia of Life Sciences. - : John Wiley & Sons. - 1476-9506.
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Tidskriftsartikel (refereegranskat)
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| 8. |
- Lascoux, Martin, et al.
(författare)
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Past demography in forest trees : what can we learn from nuclear DNA sequences that we do not already know?
- 2008
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Ingår i: Plant Ecology & Diversity. - : Informa UK Limited. - 1755-0874 .- 1755-1668. ; 1:2, s. 209-215
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Tidskriftsartikel (refereegranskat)abstract
- Acquiring nuclear DNA sequences in forest tree species is becoming easier as molecular tools are developing rapidly and we now have at our disposal an array of theoretical methods to carry out statistical inferences from multilocus sequence variation. In the present article we use results from two recent studies of nuclear DNA sequence polymorphism in Norway spruce (Picea abies) and Scots pine (Pinus sylvestris) to illustrate what additional insights to each species' history can be gained compared with classical phylogeographic studies based on chloroplast or mitochondrial DNA. The sampling schemes and statistical analyses used in these two studies were similar facilitating a comparison between them. In both cases we inferred the presence of a rather severe bottleneck predating the Last Glacial Maximum (∌18,000 years ago). This result is discussed in relation to recent reassessments of the fossil pollen record and to its implication for our understanding of adaptation. Finally we briefly outline some suggestions for future research.
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| 9. |
- Leinonen, Päivi H., et al.
(författare)
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Local adaptation in European populations of Arabidopsis lyrata (Brassicaceae)
- 2009
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Ingår i: American Journal of Botany. - : Wiley. - 0002-9122 .- 1537-2197. ; 96:6, s. 1129-1137
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Tidskriftsartikel (refereegranskat)abstract
- We studied local adaptation to contrasting environments usingan organism that is emerging as a model for evolutionary plantbiology—the outcrossing, perennial herb Arabidopsis lyratasubsp. petraea (Brassicaceae). With reciprocal transplant experiments,we found variation in cumulative fitness, indicating adaptivedifferentiation among populations. Nonlocal populations didnot have significantly higher fitness than the local population.Experimental sites were located in Norway (alpine), Sweden (coastal),and Germany (continental). At all sites after one year, thelocal population had higher cumulative fitness, as quantifiedby survival combined with rosette area, than at least one ofthe nonlocal populations. At the Norwegian site, measurementswere done for two additional years, and fitness differencespersisted. The fitness components that contributed most to differencesin cumulative fitness varied among sites. Relatively small rosettearea combined with a large number of inflorescences producedby German plants may reflect differentiation in life history.The results of the current study demonstrate adaptive populationdifferentiation in A. lyrata along a climatic gradient in Europe.The studied populations harbor considerable variation in severalcharacters contributing to adaptive population differentiation.The wealth of genetic information available makes A. lyrataa highly attractive system also for examining the functionaland genetic basis of local adaptation in plants.
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| 10. |
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