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  • 1.
    Bruxaux, Jade
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Zhao, Wei
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Hall, David
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Forestry Research Institute of Sweden (Skogforsk), Sävar, Sweden.
    Curtu, Alexandru Lucian
    Department of Silviculture, Transilvania University of Braşov, Braşov, Romania.
    Androsiuk, Piotr
    Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.
    Drouzas, Andreas D.
    Laboratory of Systematic Botany and Phytogeography, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece.
    Gailing, Oliver
    Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Germany.
    Konrad, Heino
    Department of Forest Biodiversity and Nature Conservation, Unit of Ecological Genetics, Austrian Research Centre for Forests (BFW), Vienna, Austria.
    Sullivan, Alexis R.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Semerikov, Vladimir
    Institute of Plant and Animal Ecology, Ural Division of Russian Academy of Sciences, Ekaterinburg, Russian Federation.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Scots pine – panmixia and the elusive signal of genetic adaptation2024In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137Article in journal (Refereed)
    Abstract [en]

    Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them.

    To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation.

    We found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expanding populations and minor impact of the last glacial maximum on historical population sizes. Genetic-environmental associations identified only a handful of single-nucleotide polymorphisms significantly linked to environmental gradients.

    The results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi-dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment.

  • 2.
    Hall, David
    Umeå University, Faculty of Science and Technology, Ecology and Environmental Science.
    Tracing selection and adaptation along an environmental gradient in Populus tremula2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The distribution of the expressed genotype is moved around in the population over time byevolution. Natural selection is one of the forces that act on the phenotype to change the patterns ofnucleotide variation underlying those distributions. How the phenotype changes over aheterogeneous environment describes the type of evolutionary force acting on this trait and thisshould be reflected in the variation at loci underlying this trait. While the variation in phenotypesand at the nucleotide level in a population indicates the same evolutionary force, it does notnecessarily mean that they are connected. In natural populations the continuous shifting of geneticmaterial through recombination events break down possible associations between loci facilitates theexamination of possible causal loci to single base pair differences in DNA-sequences. Connecting thegenotype and the phenotype thus provides an important step in the understanding the geneticarchitecture of complex traits and the forces that shape the observed patterns.This thesis examines the European aspen, Populus tremula, sampled from subpopulations overan extensive latitudinal gradient covering most of Sweden. Results show a clear geneticdifferentiation in the timing of bud set, a measure of the autumnal cessation of growth, betweendifferent parts of Sweden pointing at local adaptation. In the search for candidate genes thatunderlie the local adaptation found, most genes (25) in the photoperiodic gene network wereexamined for signals of selection. Genes in the photoperiodic network show an increase in theheterogeneity of differentiation between sampled subpopulations in Sweden. Almost half (12) of theexamined genes are under some form of selection. Eight of these genes show positive directionalselection on protein evolution and the gene that code for a photoreceptor, responsible for mediatingchanging light conditions to downstream targets in the network, has the hallmarks of a selectivesweep. The negative correlation between positive directional selection and synonymous diversityindicates that the majority of the photoperiod gene network has undergone recurrent selectivesweeps. A phenomenon that likely has occurred when P. tremula has readapted to the northern lightregimes during population expansion following retracting ice between periods of glaciations. Two ofthe genes under selection also have single nucleotide polymorphisms (SNP) that associate with budset, two in the PHYB2 gene and one in the LHY2 gene. Furthermore, there is an additional SNP inLHY1 that explain part of the variation in timing of bud set, despite the lack of a signal of selection atthe LHY1 gene. Together these SNPs explain 10-15% of the variation in the timing of bud set and 20-30% more if accounting for the positive co-variances between SNPs. There is thus rather extensiveevidence that genes in the photoperiod gene network control the timing of bud set, and reflect localadaptation in this trait.

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  • 3.
    Hall, David
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå Plant Science Centre, Department of Forest Genetics and Plant PhysiologySwedish University of Agricultural Sciences, Umeå, Sweden.
    Hallingbäck, Henrik R.
    Wu, Harry X.
    Estimation of number and size of QTL effects in forest tree traits2016In: Tree Genetics & Genomes, ISSN 1614-2942, E-ISSN 1614-2950, Vol. 12, no 6, article id 110Article in journal (Refereed)
    Abstract [en]

    Mapping the genetic architecture of forest tree traits is important in order to understand the evolutionary forces that have shaped these traits and to facilitate the development of genomic-based breeding strategies. We examined the number, size, and distribution of allelic effects influencing eight types of traits using 30 published mapping studies (linkage and association mapping) in forest trees. The sizes of allelic effects, measured as the phenotypic variance explained, generally showed a severely right-skewed distribution. We estimated the numbers of underlying causal effects (n(qtl)) for different trait categories by improving a method previously developed by Otto and Jones (Genetics 156: 2093-2107, 2000). Estimates of n(qtl) based on association mapping studies were generally higher (median at 643) than those based on linkage mapping (median at 33). Comparisons with simulated linkage and association mapping data suggested that the lower n(qtl) estimates for the linkage mapping studies could partly be explained by fewer causal loci segregating within the full-sib family populations normally used, but also by the cosegregation of causal loci due to limited recombination. Disease resistance estimates based on linkage mapping studies had the lowest median of four underlying effects, while growth traits based on association mapping had about 580 effects. Theoretically, the capture of 50% of the genetic variation would thus require a population size of about 200 for disease resistance in linkage mapping, while growth traits in association mapping would require about 25,000. The adequacy and reliability of the improved method was successfully verified by applying it to the simulated data.

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  • 4.
    Hall, David
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Ingvarsson, Pär
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Patterns of selection at the phytochrome A locus in European aspen (Populus tremula)Manuscript (preprint) (Other (popular science, discussion, etc.))
    Abstract [en]

    When a phenotype with a higher fitness arises in the population the underlying alleles are swept through the population until they reach fixation. The area surrounding the locus of the beneficial allele hitchhikes with the allele under selection, and the size of the area affected depends on the strength of selection. In Populus tremula a < 20kb region on linkage group 13 shows great reduction in synonymous diversity and an increase in rare and derived alleles as indicated by low negative values of Tajima's D and Fay and Wu's H. There is also an increase in associations between allleles at SNP sites in this region. We find that the sweep peaks in exon 2 of the phytochrome A gene. PHYA has not only undergone rapid protein evolution, it also show higher divergence in P. tremula than other plants examined, where it is unusually conserved, further pointing to adaptive significance of the increased rate of protein evolution seen in P. tremula.

  • 5.
    Hall, David
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Luquez, Virginia
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Garcia, Maribel Victoria
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    St Onge, Kate R
    Department of Evolutionary Functional Genomics, Evolutionary Biology Centre, Uppsala University, Sweden.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ingvarsson, Pär
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Adaptive population differentiation in phenology across a latitudinal gradient in European aspen (Populus tremula, L.): a comparison of neutral markers, candidate genes and phenotypic traits2007In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 61, p. 2849-2860Article in journal (Refereed)
    Abstract [en]

    A correct timing of growth cessation and dormancy induction represents a critical ecological and evolutionary trade-off between survival and growth in most forest trees (Rehfeldt et al. 1999; Horvath et al. 2003; Howe et al. 2003). We have studied the deciduous tree European Aspen (Populus tremula) across a latitudinal gradient and compared genetic differentiation in phenology traits with molecular markers. Trees from 12 different areas covering 10 latitudinal degrees were cloned and planted in two common gardens. Several phenology traits showed strong genetic differentiation and clinal variation across the latitudinal gradient, with QST values generally exceeding 0.5. This is in stark contrast to genetic differentiation at several classes of genetic markers (18 neutral SSRs, 7 SSRs located close to phenology candidate genes and 50 SNPs from five phenology candidate genes) that all showed FST values around 0.015. We thus find strong evidence for adaptive divergence in phenology traits across the latitudinal gradient. However, the strong population structure seen at the quantitative traits is not reflected in underlying candidate genes. This result fit theoretical expectations that suggest that genetic differentiation at candidate loci is better described by FST at neutral loci rather than by QST at the quantitative traits themselves.

  • 6.
    Hall, David
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ma, Xiao-Fei
    Program in Evolutionary Functional Genomics, Evolutionary Biology Center, Uppsala University.
    Ingvarsson, Pär K
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Adaptive evolution of the Populus tremula photoperiod pathway2011In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 20, no 7, p. 1463-1474Article in journal (Refereed)
    Abstract [en]

    Environmental cues entrain the circadian clock, a core component of the photoperiod pathway in plants, to daily and seasonal changes. The circadian clock mediates input signals from light and temperature receptors to downstream target genes through feedback loops. Several studies have shown that a correct timing of the circadian system is a fitness advantage and genes in photoperiod network have been implied to evolve in response to the diversifying selection in heterogeneous environment. In an attempt to quantify the extent of the historical patterns of selection on genes in the photoperiod pathway in the widely distributed tree species European aspen (Populus tremula) we obtained sequences for twenty-five of the genes in the network and these genes were compared to patterns of nucleotide diversity in 77 randomly chosen genes from across the genome of P. tremula. We found a significant reduction in synonymous diversity in photoperiod genes while non-synonymous diversity was in line with data from control genes. A substantial fraction of the genes show signs of selection, with eight genes showing signs of rapid protein evolution. In contrast to our expectations, genes closely associated with the core circadian clock show rapid protein evolution despite their central position in the pathway. Furthermore, selection on non-synonymous mutations is negatively correlated with synonymous diversity across all genes, indicating the action of recurrent selective sweeps.

  • 7.
    Hall, David
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Olsson, Jenny
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Zhao, Wei
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Kroon, Johan
    The Forestry Research Institute of Sweden (Skogforsk), Uppsala, Sweden.
    Wennström, Ulfstand
    The Forestry Research Institute of Sweden (Skogforsk), Uppsala, Sweden.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Divergent patterns between phenotypic and genetic variation in Scots pine2021In: Plant Communications, E-ISSN 2590-3462, Vol. 2, no 1, article id 100139Article in journal (Refereed)
    Abstract [en]

    In boreal forests, autumn frost tolerance in seedlings is a critical fitness component because it determines survival rates during regeneration. To understand the forces that drive local adaptation in this trait, we conducted freezing tests in a common garden setting for 54 Pinus sylvestris (Scots pine) populations (>5000 seedlings) collected across Scandinavia into western Russia, and genotyped 24 of these populations (>900 seedlings) at >10 000 SNPs. Variation in cold hardiness among populations, as measured by QST, was above 80% and followed a distinct cline along latitude and longitude, demonstrating significant adaptation to climate at origin. In contrast, the genetic differentiation was very weak (mean FST 0.37%). Despite even allele frequency distribution in the vast majority of SNPs among all populations, a few rare alleles appeared at very high or at fixation in marginal populations restricted to northwestern Fennoscandia. Genotype–environment associations showed that climate variables explained 2.9% of the genetic differentiation, while genotype–phenotype associations revealed a high marker-estimated heritability of frost hardiness of 0.56, but identified no major loci. Very extensive gene flow, strong local adaptation, and signals of complex demographic history across markers are interesting topics of forthcoming studies on this species to better clarify signatures of selection and demography.

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  • 8.
    Hall, David
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). The Forestry Research Institute of Sweden (Skogforsk), Sävar, Sweden.
    Zhao, Wei
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Heuchel, Alisa
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Gao, Jie
    CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, Menglun, China.
    Wennström, Ulfstand
    The Forestry Research Institute of Sweden (Skogforsk), Sävar, Sweden.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The effect of gene flow on frost tolerance in Scots pine – Latitudinal translocation of genetic material2023In: Forest Ecology and Management, ISSN 0378-1127, E-ISSN 1872-7042, Vol. 544, article id 121215Article in journal (Refereed)
    Abstract [en]

    Extensive gene flow can be detrimental to local adaptation and similarly, forestry seed sources such as seed orchards can be heavily influenced by external pollination, especially if the orchard material has been translocated a great distance. Here we conducted a coordinated genotyping-phenotyping study to examine how external pollination events and fecundity variation in a Pinus sylvestris seed orchard influence the genetic composition and the seed-lots’ autumn frost hardiness when genetic material had been translocated 630 km south. The results were then compared to those of a in situ established seed orchard. We genotyped and phenotype >1000 seedlings from these orchards, and constructed their pedigrees and scored their autumn frost tolerance in a controlled climate chamber environment. The hardiness scores were compared with a reference of nine natural stands along a latitudinal cline. We find substantial variation in fecundity and external pollination over crop years, thus unpredictable genetic composition because the contribution of some orchard clones is high in one crop but low in another. We observed that seedlings produced by mating among orchard genotypes were less hardy than expected (corresponding to an origin of −0.6°N) but the opposite in externally pollinated seedlings (+0.3 to +0.7°N). The freeze damage levels reflect the origin of parental genotypes, but to a smaller degree than expected (13% lower than expected damage levels for externally pollinate seedlings and 21% greater damage levels for internally pollinates seedlings). These results suggest that orchard parents’ origins, mating composition and orchard local environment could all affect the seed crops’ quality and their climate adaptation. Seed orchard crops are the key to realize the gain in forestry from breeding efforts. However, genetic monitoring of seed crops is necessary to improve the performance of seed orchards further and adjust deployment areas of seed crops in a timely manner for a more dynamic forestry, considering climate change and biodiversity demands.

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  • 9.
    Hall, David
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Zhao, Wei
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Advanced Innovation Center for Tree Breeding by MolecularDesign; College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Wennström, Ulfstand
    Andersson Gull, Bengt
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Parentage and relatedness reconstruction in Pinus sylvestris using genotyping-by-sequencing2020In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 124, no 5, p. 633-646Article in journal (Refereed)
    Abstract [en]

    Estimating kinship is fundamental for studies of evolution, conservation, and breeding. Genotyping-by-sequencing (GBS) and other restriction based genotyping methods have become widely applied in these applications in non-model organisms. However, sequencing errors, depth, and reproducibility between library preps could potentially hinder accurate genetic inferences. In this study, we tested different sets of parameters in data filtering, different reference populations and eight estimation methods to obtain a robust procedure for relatedness estimation in Scots pine (Pinus sylvestris L.). We used a seed orchard as our study system, where candidate parents are known and pedigree reconstruction can be compared with theoretical expectations. We found that relatedness estimates were lower than expected for all categories of kinship estimated if the proportion of shared SNPs was low. However, estimates reached expected values if loci showing an excess of heterozygotes were removed and genotyping error rates were considered. The genetic variance-covariance matrix (G-matrix) estimation, however, performed poorly in kinship estimation. The reduced relatedness estimates are likely due to false heterozygosity calls. We analyzed the mating structure in the seed orchard and identified a selfing rate of 3% (including crosses between clone mates) and external pollen contamination of 33.6%. Little genetic structure was observed in the sampled Scots pine natural populations, and the degree of inbreeding in the orchard seed crop is comparable to natural stands. We illustrate that under our optimized data processing procedure, relatedness, and genetic composition, including level of pollen contamination within a seed orchard crop, can be established consistently by different estimators.

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  • 10.
    Heuchel, Alisa
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Hall, David
    The Forestry Research Institute of Sweden (Skogforsk).
    Almqvist, Curt
    The Forestry Research Institute of Sweden (Skogforsk).
    Wennström, Ulftstand
    The Forestry Research Institute of Sweden (Skogforsk).
    Persson, Torgny
    The Forestry Research Institute of Sweden (Skogforsk).
    Topgrafting as a tool in operational Scots pine breedingManuscript (preprint) (Other academic)
  • 11.
    Heuchel, Alisa
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Hall, David
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. The Forestry Research Institute of Sweden (Skogforsk).
    Hajek, Jörgen
    The Forestry Research Institute of Sweden (Skogforsk).
    Wennström, Ulfstand
    The Forestry Research Institute of Sweden (Skogforsk).
    Improved reforestation material of Scots pine in northern Sweden – is the superiority independent from soil preparation methods?Manuscript (preprint) (Other academic)
  • 12.
    Heuchel, Alisa
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Hall, David
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Zhao, Wei
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Gao, Jie
    CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China.
    Wennström, Ulfstand
    The Forestry Research Institute of Sweden (Skogforsk), Sävar, Sweden.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Genetic diversity and background pollen contamination in Norway spruce and Scots pine seed orchard crops2022In: Forestry Research, ISSN 2767-3812, Vol. 2, no 1, article id 8Article in journal (Refereed)
    Abstract [en]

    Seed orchards are the key link between tree breeding and production forest for conifer trees. In Sweden, Scots pine and Norway spruce seed orchards currently supply ca. 85% of seedlings used in annual reforestation. The functionality of these seed orchards is thus crucial for supporting long-term production gain and sustainable diversity. We conducted a large-scale genetic investigation of pine and spruce orchards across Sweden using genotyping-by-sequencing. We genotyped 3,300 seedlings/trees from six orchards and 10 natural stands to gain an overview of mating structure and genetic diversity in orchard crops. We found clear differences in observed heterozygosity (HO) and background pollen contamination (BPC) rates between species, with pine orchard crops showing higher HO and BPC than spruce. BPC in pine crops varied from 87% at young orchard age to 12% at mature age, wherease this rate ranged between 27%−4% in spruce crops. Substantial variance in parental contribution was observed in all orchards with 30%−50% parents contibuting to 80% of the progeny. Selfing was low (2%−6%) in all seed crops. Compared to natural stands, orchard crops had slightly lower HO but no strong signal of inbreeding. Our results provide valuable references for orchard management.

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  • 13.
    Ingvarsson, Pär
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Garcia, M. Victoria
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Luguez, Virginia
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Hall, David
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Multilocus patterns of nucleotide polymorphism and the demographic history of Populus tremula2008In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 180, no 1, p. 329-340Article in journal (Refereed)
    Abstract [en]

    We investigated the utility of association mapping to dissect the genetic basis of naturally occurring variation in bud phenology in European aspen (Populus tremula). With this aim, we surveyed nucleotide polymorphism in 13 fragments spanning an 80-kb region surrounding the phytochrome B2 (phyB2) locus. Although polymorphism varies substantially across the phyB2 region, we detected no signs for deviations from neutral expectations. We also identified a total of 41 single nucleotide polymorphisms (SNPs) that were subsequently scored in a mapping population consisting of 120 trees. We identified two nonsynonymous SNPs in the phytochrome B2 gene that were independently associated with variation in the timing of bud set and that explained between 1.5 and 5% of the observed phenotypic variation in bud set. Earlier studies have shown that the frequencies of both these SNPs vary clinally with latitude. Linkage disequilibrium across the region was low, suggesting that the SNPs we identified are strong candidates for being causally linked to variation in bud set in our mapping populations. One of the SNPs (T608N) is located in the “hinge region,” close to the chromophore binding site of the phyB2 protein. The other SNP (L1078P) is located in a region supposed to mediate downstream signaling from the phyB2 locus. The lack of population structure, combined with low levels of linkage disequilibrium, suggests that association mapping is a fruitful method for dissecting naturally occurring variation in Populus tremula.

  • 14.
    Ingvarsson, Pär
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Garci­a, Maribel
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Hall, David
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Luquez, Virginia
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Clinal variation in phyB2, a candidate gene for day-length-induced growth cessation and bud set, across a latitudinal gradient in European aspen (Populus tremula).2006In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 172, no 3, p. 1845-53Article in journal (Refereed)
    Abstract [en]

    The initiation of growth cessation and dormancy represents a critical ecological and evolutionary trade-off between survival and growth in most forest trees. The most important environmental cue regulating the initiation of dormancy is a shortening of the photoperiod and phytochrome genes have been implicated in short-day-induced bud set and growth cessation in Populus. We characterized patterns of DNA sequence variation at the putative candidate gene phyB2 in 4 populations of European aspen (Populus tremula) and scored single-nucleotide polymorphisms in an additional 12 populations collected along a latitudinal gradient in Sweden. We also measured bud set from a subset of these trees in a growth chamber experiment. Buds set showed significant clinal variation with latitude, explaining ~90% of the population variation in bud set. A sliding-window scan of phyB2 identified six putative regions with enhanced population differentiation and four SNPs showed significant clinal variation. The clinal variation at individual SNPs is suggestive of an adaptive response in phyB2 to local photoperiodic conditions. Three of four SNPs showing clinal variation were located in regions with excessive genetic differentiation, demonstrating that searching for regions of high genetic differentiation can be useful for identifying sites putatively involved in local adaptation.

  • 15.
    Ingvarsson, Pär
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Garcia, Maribel
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Luquez, Virginia
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Hall, David
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Nucleotide polymorphism and phenotypic associations within and around the phytochrome B2 Locus in European aspen (Populus tremula, Salicaceae).2008In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 178, no 4, p. 2217-26Article in journal (Refereed)
    Abstract [en]

    We investigated the utility of association mapping to dissect the genetic basis of naturally occurring variation in bud phenology in European aspen (Populus tremula). With this aim, we surveyed nucleotide polymorphism in 13 fragments spanning an 80-kb region surrounding the phytochrome B2 (phyB2) locus. Although polymorphism varies substantially across the phyB2 region, we detected no signs for deviations from neutral expectations. We also identified a total of 41 single nucleotide polymorphisms (SNPs) that were subsequently scored in a mapping population consisting of 120 trees. We identified two nonsynonymous SNPs in the phytochrome B2 gene that were independently associated with variation in the timing of bud set and that explained between 1.5 and 5% of the observed phenotypic variation in bud set. Earlier studies have shown that the frequencies of both these SNPs vary clinally with latitude. Linkage disequilibrium across the region was low, suggesting that the SNPs we identified are strong candidates for being causally linked to variation in bud set in our mapping populations. One of the SNPs (T608N) is located in the "hinge region," close to the chromophore binding site of the phyB2 protein. The other SNP (L1078P) is located in a region supposed to mediate downstream signaling from the phyB2 locus. The lack of population structure, combined with low levels of linkage disequilibrium, suggests that association mapping is a fruitful method for dissecting naturally occurring variation in Populus tremula.

  • 16.
    Luquez, Virginia
    et al.
    INFIVE, UNLP-CONICET, La Plata, Argentina.
    Hall, David
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Albrectsen, Benedicte
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Karlsson, Jan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ingvarsson, Pär
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Natural phenological variation in aspen (Populus tremula): the SwAsp collection2008In: Tree Genetics & Genomes, ISSN 1614-2942, Vol. 4, p. 279-292Article in journal (Refereed)
    Abstract [en]

    The genus Populus is currently the main model system for genetic, genomic, and physiological research in trees. Phenotypic variation in aspen (Populus tremula) populations growing in different environments across Sweden is expected to reflect genetic variation that is important for local adaptation. To analyze such natural phenotypic and genetic variation, the Swedish Aspen (SwAsp) Collection was established. Trees were taken from 12 different populations across Sweden, from 56° to 66° latitude north and planted in two common gardens in Ekebo (55.9°N) and Sävar (63.4°N). Data related to phenological and growth traits were collected during the second year of growth. Some traits like the date of bud set and leaf area duration showed strong clinal variation patterns with latitude in both field trials, but the date of bud flush did not change along a latitudinal cline. The phenological traits showed moderate within-populations heritabilities, although growth traits showed weaker clinal patterns and lower heritabilities than the phenological traits. This research forms the starting point for the development of the SwAsp collection, a resource facilitating analysis of the natural genetic variation in aspen, the elucidation of the structure and dynamics of aspen populations, and the future identification of the genes controlling adaptive traits using association mapping of selected candidate genes.

  • 17.
    Ma, Xiao-Fei
    et al.
    Program in Evolutionary Functional Genomics, Evolutionary Biology Center, Uppsala University.
    Hall, David
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    St. Onge, Katherine
    Program in Evolutionary Functional Genomics, Evolutionary Biology Center, Uppsala University.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ingvarsson, Pär K
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Genetic differentiation, clinal variation and phenotypic associations with growth cessation across the Populus tremula Photoperiodic Pathway2010In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 186, p. 1033-1044Article in journal (Refereed)
    Abstract [en]

    Perennial plants monitor seasonal changes through changes inenvironmental conditions such as the quantity and quality oflight. To ensure a correct initiation of critical developmentalprocesses, such as the initiation and cessation of growth, plantshave adapted to a spatially variable light regime and genesin the photoperiodic pathway have been implicated as likelysources for these adaptations. Here we examine genetic variationin genes from the photoperiodic pathway in Populus tremula (Salicaceae)for signatures diversifying selection in response to varyinglight regimes across a latitudinal gradient. We fail to identifyany loci with unusually high levels of genetic differentiationamong populations despite identifying four SNPs that show significantallele frequency clines with latitude. We do, however, observelarge covariance in allelic effects across populations for growthcessation, a highly adaptive trait in P. tremula. High covariancein allelic effects is a signature compatible with diversifyingselection along an environmental gradient. We also observe significantlyhigher heterogeneity in genetic differentiation among SNPs fromthe photoperiod genes than among SNPs from randomly chosen genes.This suggests that spatially variable selection could be affectinggenes from the photoperiod pathway even if selection is notstrong enough to cause individual loci to be identified as outliers.SNPs from three genes in the photoperiod pathway (PHYB2, LHY1,and LHY2) show significant associations with natural variationin growth cessation. Collectively these SNPs explain 10–15%of the phenotypic variation in growth cessation. Covariancesin allelic effects across populations help explain an additional5–7% of the phenotypic variation in growth cessation.

  • 18.
    Zhao, Wei
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Gao, Jie
    CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, Yunnan, China.
    Hall, David
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Forestry Research Institute of Sweden (Skogforsk), Sävar, Sweden..
    Andersson, Bea Angelica
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Bruxaux, Jade
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Tomlinson, Kyle
    Center for Integrative Conservation & Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephant, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, Yunnan, China.
    Drouzas, Andreas
    Laboratory of Systematic Botany and Phytogeography, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece.
    Suyama, Yoshihisa
    Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Adaptive radiation of the Eurasian Pinus species under pervasive gene flowManuscript (preprint) (Other academic)
1 - 18 of 18
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