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Climate-Driven Adaptive Differentiation in Melia azedarach: Evidence from a Common Garden Experiment. Genes (Basel) 2022; 13:genes13111924. [DOI: 10.3390/genes13111924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/10/2022] [Accepted: 10/19/2022] [Indexed: 11/04/2022] Open
Abstract
Studies of local adaptation in populations of chinaberry (Melia azedarach L.) are important for clarifying patterns in the population differentiation of this species across its natural range. M. azedarach is an economically important timber species, and its phenotype is highly variable across its range in China. Here, we collected M. azedarach seeds from 31 populations across its range and conducted a common garden experiment. We studied patterns of genetic differentiation among populations using molecular markers (simple sequence repeats) and data on phenotypic variation in six traits collected over five years. Our sampled populations could be subdivided into two groups based on genetic analyses, as well as patterns of isolation by distance and isolation by environment. Significant differentiation in growth traits was observed among provenances and families within provenances. Geographic distance was significantly correlated with the quantitative genetic differentiation (QST) in height (HEIT) and crown breadth. Climate factors were significantly correlated with the QST for each trait. A total of 23 climatic factors were examined. There was a significant effect of temperature on all traits, and minimum relative humidity had a significant effect on the survival rate over four years. By comparing the neutral genetic differentiation (FST) with the QST, the mode of selection acting on survival rate varied, whereas HEIT and the straightness of the main trunk were subject to the same mode of selection. The variation in survival rate was consistent with the variation in genetic differentiation among populations, which was indicative of local adaptation. Overall, our findings provide new insights into the responses of the phenological traits of M. azedarach to changes in the climate conditions of China.
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Kastally C, Niskanen AK, Perry A, Kujala ST, Avia K, Cervantes S, Haapanen M, Kesälahti R, Kumpula TA, Mattila TM, Ojeda DI, Tyrmi JS, Wachowiak W, Cavers S, Kärkkäinen K, Savolainen O, Pyhäjärvi T. Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1337-1350. [PMID: 34897859 PMCID: PMC9303803 DOI: 10.1111/tpj.15628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/05/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
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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Affiliation(s)
- Chedly Kastally
- Department of Ecology and GeneticsUniversity of OuluP.O. Box 300090014OuluFinland
| | - Alina K. Niskanen
- Department of Ecology and GeneticsUniversity of OuluP.O. Box 300090014OuluFinland
| | - Annika Perry
- UK Centre for Ecology & HydrologyBush EstatePenicuikMidlothianEH26 0QBUK
| | - Sonja T. Kujala
- Natural Resources Institute Finland (Luke)Paavo Havaksen tie 390570OuluFinland
| | - Komlan Avia
- Université de StrasbourgINRAESVQV UMR‐A 1131F‐68000ColmarFrance
| | - Sandra Cervantes
- Department of Ecology and GeneticsUniversity of OuluP.O. Box 300090014OuluFinland
| | - Matti Haapanen
- Natural Resources Institute Finland (Luke)Latokartanonkaari 9FI‐00790HelsinkiFinland
| | - Robert Kesälahti
- Department of Ecology and GeneticsUniversity of OuluP.O. Box 300090014OuluFinland
| | - Timo A. Kumpula
- Department of Ecology and GeneticsUniversity of OuluP.O. Box 300090014OuluFinland
| | - Tiina M. Mattila
- Department of Ecology and GeneticsUniversity of OuluP.O. Box 300090014OuluFinland
- Department of Organismal BiologyEBCUppsala UniversityNorbyvägen 18 AUppsala752 36Sweden
| | - Dario I. Ojeda
- Department of Ecology and GeneticsUniversity of OuluP.O. Box 300090014OuluFinland
- Norwegian Institute of Bioeconomy ResearchP.O. Box 115Ås1431Norway
| | - Jaakko S. Tyrmi
- Department of Ecology and GeneticsUniversity of OuluP.O. Box 300090014OuluFinland
| | - Witold Wachowiak
- Institute of Environmental BiologyFaculty of BiologyAdam Mickiewicz University in PoznańUniwersytetu Poznańskiego 661‐614PoznańPoland
| | - Stephen Cavers
- UK Centre for Ecology & HydrologyBush EstatePenicuikMidlothianEH26 0QBUK
| | - Katri Kärkkäinen
- Natural Resources Institute Finland (Luke)Paavo Havaksen tie 390570OuluFinland
| | - Outi Savolainen
- Department of Ecology and GeneticsUniversity of OuluP.O. Box 300090014OuluFinland
| | - Tanja Pyhäjärvi
- Department of Ecology and GeneticsUniversity of OuluP.O. Box 300090014OuluFinland
- Department of Forest SciencesUniversity of HelsinkiP.O. Box 2700014HelsinkiFinland
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Ramírez-Valiente JA, Solé-Medina A, Pyhäjärvi T, Savolainen O, Heer K, Opgenoorth L, Danusevicius D, Robledo-Arnuncio JJ. Adaptive responses to temperature and precipitation variation at the early-life stages of Pinus sylvestris. THE NEW PHYTOLOGIST 2021; 232:1632-1647. [PMID: 34388269 DOI: 10.1111/nph.17678] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 08/07/2021] [Indexed: 06/13/2023]
Abstract
Early-stage fitness variation has been seldom evaluated at broad scales in forest tree species, despite the long tradition of studying climate-driven intraspecific genetic variation. In this study, we evaluated the role of climate in driving patterns of population differentiation at early-life stages in Pinus sylvestris and explored the fitness and growth consequences of seed transfer within the species range. We monitored seedling emergence, survival and growth over a 2-yr period in a multi-site common garden experiment which included 18 European populations and spanned 25° in latitude and 1700 m in elevation. Climate-fitness functions showed that populations exhibited higher seedling survival and growth at temperatures similar to their home environment, which is consistent with local adaptation. Northern populations experienced lower survival and growth at warmer sites, contrary to previous studies on later life stages. Seed mass was higher in populations from warmer areas and was positively associated with survival and growth at more southern sites. Finally, we did not detect a survival-growth trade-off; on the contrary, bigger seedlings exhibited higher survival probabilities under most climatic conditions. In conclusion, our results reveal that contrasting temperature regimes have played an important role in driving the divergent evolution of P. sylvestris populations at early-life stages.
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Affiliation(s)
- José Alberto Ramírez-Valiente
- Department of Forest Ecology & Genetics, Forest Research Centre (INIA, CSIC), Ctra. de la Coruña km 7.5, Madrid, 28040, Spain
- Ecological and Forestry Applications Research Centre, CREAF, Campus de Bellaterra (UAB) Edifici C 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Aida Solé-Medina
- Department of Forest Ecology & Genetics, Forest Research Centre (INIA, CSIC), Ctra. de la Coruña km 7.5, Madrid, 28040, Spain
- Escuela Internacional de Doctorado, Universidad Rey Juan Carlos, C/Tulipán s/n, Móstoles, 28933, Spain
| | - Tanja Pyhäjärvi
- Department of Ecology and Genetics, University of Oulu, Oulu, FI-90014, Finland
- Department of Forest Sciences, University of Helsinki, Helsinki, FI-00014, Finland
| | - Outi Savolainen
- Conservation Biology, Philipps Universität Marburg, Karl-von-Frisch Strasse 8, Marburg, 35043, Germany
| | - Katrin Heer
- Plant Ecology and Geobotany, Philipps Universität Marburg, Karl-von-Frisch Strasse 8, Marburg, 35043, Germany
| | - Lars Opgenoorth
- Plant Ecology and Geobotany, Philipps Universität Marburg, Karl-von-Frisch Strasse 8, Marburg, 35043, Germany
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, Birmensdorf, 8903, Switzerland
| | - Darius Danusevicius
- Faculty of Forest Science and Evology, Vytautas Magnus University, Studentu str. 11, Akademija, Kaunas, LT-53361, Lithuania
| | - Juan José Robledo-Arnuncio
- Department of Forest Ecology & Genetics, Forest Research Centre (INIA, CSIC), Ctra. de la Coruña km 7.5, Madrid, 28040, Spain
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Ramírez-Valiente JA, Solé-Medina A, Pyhäjärvi T, Savolainen O, Cervantes S, Kesälahti R, Kujala ST, Kumpula T, Heer K, Opgenoorth L, Siebertz J, Danusevicius D, Notivol E, Benavides R, Robledo-Arnuncio JJ. Selection patterns on early-life phenotypic traits in Pinus sylvestris are associated with precipitation and temperature along a climatic gradient in Europe. THE NEW PHYTOLOGIST 2021; 229:3009-3025. [PMID: 33098590 DOI: 10.1111/nph.17029] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Understanding the dynamics of selection is key to predicting the response of tree species to new environmental conditions in the current context of climate change. However, selection patterns acting on early recruitment stages and their climatic drivers remain largely unknown in most tree species, despite being a critical period of their life cycle. We measured phenotypic selection on Pinus sylvestris seed mass, emergence time and early growth rate over 2 yr in four common garden experiments established along the latitudinal gradient of the species in Europe. Significant phenotypic plasticity and among-population genetic variation were found for all measured phenotypic traits. Heat and drought negatively affected fitness in the southern sites, but heavy rainfalls also decreased early survival in middle latitudes. Climate-driven directional selection was found for higher seed mass and earlier emergence time, while the form of selection on seedling growth rates differed among sites and populations. Evidence of adaptive and maladaptive phenotypic plasticity was found for emergence time and early growth rate, respectively. Seed mass, emergence time and early growth rate have an adaptive role in the early stages of P. sylvestris and climate strongly influences the patterns of selection on these fitness-related traits.
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Affiliation(s)
| | - Aida Solé-Medina
- Department of Forest Ecology & Genetics, INIA-CIFOR, Ctra. de la Coruña km 7.5, Madrid, 28040, Spain
- Escuela Internacional de Doctorado, Universidad Rey Juan Carlos, C/ Tulipán s/n, Móstoles, 28933, Spain
| | - Tanja Pyhäjärvi
- Department of Ecology and Genetics, University of Oulu, Oulu, FIN-90014, Finland
- Biocenter Oulu, University of Oulu, Oulu, FIN-90014, Finland
| | - Outi Savolainen
- Department of Ecology and Genetics, University of Oulu, Oulu, FIN-90014, Finland
| | - Sandra Cervantes
- Department of Ecology and Genetics, University of Oulu, Oulu, FIN-90014, Finland
- Biocenter Oulu, University of Oulu, Oulu, FIN-90014, Finland
| | - Robert Kesälahti
- Department of Ecology and Genetics, University of Oulu, Oulu, FIN-90014, Finland
| | - Sonja T Kujala
- Department of Ecology and Genetics, University of Oulu, Oulu, FIN-90014, Finland
- Natural Resources Institute Finland (Luke), Jokioinen, 90570, Finland
| | - Timo Kumpula
- Department of Ecology and Genetics, University of Oulu, Oulu, FIN-90014, Finland
| | - Katrin Heer
- Conservation Biology, Philipps Universität Marburg, Karl-von-Frisch Strasse 8, Marburg, 35043, Germany
| | - Lars Opgenoorth
- Plant Ecology and Geobotany, Philipps Universität Marburg, Karl-von-Frisch Strasse 8, Marburg, 35043, Germany
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, Birmensdorf, 8903, Switzerland
| | - Jan Siebertz
- Plant Ecology and Geobotany, Philipps Universität Marburg, Karl-von-Frisch Strasse 8, Marburg, 35043, Germany
| | - Darius Danusevicius
- Faculty of Forest Science and Ecology, Vytautas Magnus University, Studentų str. 11, Akademija, Kaunas, LT-53361, Lithuania
| | - Eduardo Notivol
- Unidad de Recursos Forestales, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda. Montañana 930, Zaragoza, 50059, Spain
| | - Raquel Benavides
- Department of Biogeography and Global Change, LINCGlobal, Museo Nacional de Ciencias Naturales, CSIC, C/ José Gutiérrez Abascal 2, Madrid, 28006, Spain
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Fréchette E, Chang CYY, Ensminger I. Variation in the phenology of photosynthesis among eastern white pine provenances in response to warming. GLOBAL CHANGE BIOLOGY 2020; 26:5217-5234. [PMID: 32396692 DOI: 10.1111/gcb.15150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
In higher-latitude trees, temperature and photoperiod control the beginning and end of the photosynthetically active season. Elevated temperature (ET) has advanced spring warming and delayed autumn cooling while photoperiod remains unchanged. We assessed the effects of warming on the length of the photosynthetically active season of three provenances of Pinus strobus L. seedlings from different latitudes, and evaluated the accuracy of the photochemical reflectance index (PRI) and the chlorophyll/carotenoid index (CCI) for tracking the predicted variation in spring and autumn phenology of photosynthesis among provenances. Seedlings from northern, local and southern P. strobus provenances were planted in a temperature-free-air-controlled enhancement (T-FACE) experiment and exposed to ET (+1.5/3°C; day/night). Over 18 months, we assessed photosynthetic phenology by measuring chlorophyll fluorescence, gas exchange, leaf spectral reflectance and pigment content. During autumn, all seedlings regardless of provenance followed the same sequence of phenological events with the initial downregulation of photosynthesis, followed by the modulation of non-photochemical quenching and associated adjustments of zeaxanthin pool sizes. However, the timing of autumn downregulation differed between provenances, with delayed onset in the southern provenance (SP) and earlier onset in the northern relative to the local provenance, indicating that photoperiod at the provenance origin is a dominant factor controlling autumn phenology. Experimental warming further delayed the downregulation of photosynthesis during autumn in the SP. A provenance effect during spring was also observed but was generally not significant. The vegetation indices PRI and CCI were both effective at tracking the seasonal variations of energy partitioning in needles and the differences of carotenoid pigments indicative of the stress status of needles. These results demonstrate that PRI and CCI can be useful tools for monitoring conifer phenology and for the remote monitoring of the length of the photosynthetically active season of conifers in a changing climate.
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Affiliation(s)
- Emmanuelle Fréchette
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Christine Yao-Yun Chang
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Ingo Ensminger
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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Genomics of Clinal Local Adaptation in Pinus sylvestris Under Continuous Environmental and Spatial Genetic Setting. G3-GENES GENOMES GENETICS 2020; 10:2683-2696. [PMID: 32546502 PMCID: PMC7407466 DOI: 10.1534/g3.120.401285] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding the consequences of local adaptation at the genomic diversity is a central goal in evolutionary genetics of natural populations. In species with large continuous geographical distributions the phenotypic signal of local adaptation is frequently clear, but the genetic basis often remains elusive. We examined the patterns of genetic diversity in Pinus sylvestris, a keystone species in many Eurasian ecosystems with a huge distribution range and decades of forestry research showing that it is locally adapted to the vast range of environmental conditions. Making P. sylvestris an even more attractive subject of local adaptation study, population structure has been shown to be weak previously and in this study. However, little is known about the molecular genetic basis of adaptation, as the massive size of gymnosperm genomes has prevented large scale genomic surveys. We generated a both geographically and genomically extensive dataset using a targeted sequencing approach. By applying divergence-based and landscape genomics methods we identified several loci contributing to local adaptation, but only few with large allele frequency changes across latitude. We also discovered a very large (ca. 300 Mbp) putative inversion potentially under selection, which to our knowledge is the first such discovery in conifers. Our results call for more detailed analysis of structural variation in relation to genomic basis of local adaptation, emphasize the lack of large effect loci contributing to local adaptation in the coding regions and thus point out the need for more attention toward multi-locus analysis of polygenic adaptation.
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Sramkoski LL, McLaughlin WN, Cooley AM, Yuan DC, John A, Wittkopp PJ. Genetic architecture of a body colour cline in Drosophila americana. Mol Ecol 2020; 29:2840-2854. [PMID: 32603541 PMCID: PMC7482988 DOI: 10.1111/mec.15531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 12/11/2022]
Abstract
Phenotypic variation within a species is often structured geographically in clines. In Drosophila americana, a longitudinal cline for body colour exists within North America that appears to be due to local adaptation. The tan and ebony genes have been hypothesized to contribute to this cline, with alleles of both genes that lighten body colour found in D. americana. These alleles are similar in sequence and function to the allele fixed in D. americana's more lightly pigmented sister species, Drosophila novamexicana. Here, we examine the frequency and geographic distribution of these D. novamexicana-like alleles in D. americana. Among alleles from over 100 strains of D. americana isolated from 21 geographic locations, we failed to identify additional alleles of tan or ebony with as much sequence similarity to D. novamexicana as the D. novamexicana-like alleles previously described. However, using genetic analysis of 51 D. americana strains derived from 20 geographic locations, we identified one new allele of ebony and one new allele of tan segregating in D. americana that are functionally equivalent to the D. novamexicana allele. An additional 5 alleles of tan also showed marginal evidence of functional similarity. Given the rarity of these alleles, however, we conclude that they are unlikely to be driving the pigmentation cline. Indeed, phenotypic distributions of the 51 backcross populations analysed indicate a more complex genetic architecture, with diversity in the number and effects of loci altering pigmentation observed both within and among populations of D. americana. This genetic heterogeneity poses a challenge to association studies and genomic scans for clinal variation, but might be common in natural populations.
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Affiliation(s)
| | - Wesley N. McLaughlin
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1048
| | - Arielle M. Cooley
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1048
| | - David C. Yuan
- Department of Molecular, Cellular, and Developmental Biology
| | - Alisha John
- Department of Molecular, Cellular, and Developmental Biology
| | - Patricia J. Wittkopp
- Department of Molecular, Cellular, and Developmental Biology
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1048
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Pyhäjärvi T, Kujala ST, Savolainen O. 275 years of forestry meets genomics in Pinus sylvestris. Evol Appl 2020; 13:11-30. [PMID: 31988655 PMCID: PMC6966708 DOI: 10.1111/eva.12809] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/05/2019] [Accepted: 04/24/2019] [Indexed: 12/12/2022] Open
Abstract
Pinus sylvestris has a long history of basic and applied research that is relevant for both forestry and evolutionary studies. Its patterns of adaptive variation and role in forest economic and ecological systems have been studied extensively for nearly 275 years, detailed demography for a 100 years and mating system more than 50 years. However, its reference genome sequence is not yet available and genomic studies have been lagging compared to, for example, Pinus taeda and Picea abies, two other economically important conifers. Despite the lack of reference genome, many modern genomic methods are applicable for a more detailed look at its biological characteristics. For example, RNA-seq has revealed a complex transcriptional landscape and targeted DNA sequencing displays an excess of rare variants and geographically homogenously distributed molecular genetic diversity. Current DNA and RNA resources can be used as a reference for gene expression studies, SNP discovery, and further targeted sequencing. In the future, specific consequences of the large genome size, such as functional effects of regulatory open chromatin regions and transposable elements, should be investigated more carefully. For forest breeding and long-term management purposes, genomic data can help in assessing the genetic basis of inbreeding depression and the application of genomic tools for genomic prediction and relatedness estimates. Given the challenges of breeding (long generation time, no easy vegetative propagation) and the economic importance, application of genomic tools has a potential to have a considerable impact. Here, we explore how genomic characteristics of P. sylvestris, such as rare alleles and the low extent of linkage disequilibrium, impact the applicability and power of the tools.
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Affiliation(s)
- Tanja Pyhäjärvi
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
- Biocenter OuluUniversity of OuluOuluFinland
| | | | - Outi Savolainen
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
- Biocenter OuluUniversity of OuluOuluFinland
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