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Caré O, Chano V, Erley M, Rogge M, Gailing O. Circadian rhythm and redox homeostasis candidate genes showed association with shallow elevation in Norway spruce. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:508-520. [PMID: 38568928 DOI: 10.1111/plb.13642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/21/2024] [Indexed: 04/05/2024]
Abstract
The analysis of genetic variation underlying local adaptation in natural populations, together with the response to different external stimuli, is currently a hot topic in forest sciences, with the aim of identifying genetic markers controlling key phenotypic traits of interest for their inclusion in restoration and breeding programs. In Europe, one of the main tree species is Norway spruce (Picea abies (L.) H.Karst.). Using the MassARRAY® platform, 568 trees from North Rhine-Westphalia (Germany) were genotyped with 94 single nucleotide polymorphisms (SNPs) related to circadian and growth rhythms, and to stress response. The association analysis of the selected markers with health status and elevation was performed using three different methods, and those identified by at least two of these were considered as high confidence associated SNPs. While just five markers showed a weak association with health condition, 32 SNPs were correlated with elevation, six of which were considered as high confidence associated SNPs, as indicated by at least two different association methods. Among these genes, thioredoxin and pseudo response regulator 1 (PRR1) are involved in redox homeostasis and ROS detoxification, APETALA2-like 3 (AP2L3), a transcription factor, is involved in seasonal apical growth, and a RPS2-like is a disease resistance gene. The function of some of these genes in controlling light-dependent reactions and metabolic processes suggests signatures of adaptation to local photoperiod and the synchronization of the circadian rhythm. This work provides new insights into the genetic basis of local adaptation over a shallow elevation gradient in Norway spruce.
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Affiliation(s)
- O Caré
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, Göttingen, Germany
| | - V Chano
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, Göttingen, Germany
| | - M Erley
- Landesbetrieb Wald und Holz Nordrhein-Westfalen, Arnsberg, Germany
| | - M Rogge
- Landesbetrieb Wald und Holz Nordrhein-Westfalen, Arnsberg, Germany
| | - O Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, Göttingen, Germany
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Hao J, Xu D, Wang C, Cao Q, Zhao Q, Xie M, Zhang H, Zhang L. Phylogeny and expression patterns of ERF genes that are potential reproductive inducers in hybrid larch. BMC Genomics 2024; 25:288. [PMID: 38500084 PMCID: PMC10946173 DOI: 10.1186/s12864-024-10188-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 03/05/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Larch is an important component of northern forests and a major cultivated tree species in restoration of forest cover using improved seed material. In recent years, the continuous low seed production has severely affected the production of improved variety seedlings and natural regeneration. However, research on the reproductive growth of gymnosperms is extremely scarce. RESULTS In this study, based on differential transcriptome analysis of two asexual reproductive phases, namely high-yield and low-yield, we further screened 5 ERF family genes that may affect the reproductive development of larch. We analyzed their genetic relationships and predicted their physicochemical properties. The expression patterns of these genes were analyzed in different tissues, developmental stages, hormone treatments, and environmental conditions in hybrid larch. CONCLUSION The results showed that all 5 genes were induced by low temperature and ABA, and their expression patterns in different tissues suggested a suppressive role in the development of female cones in larch. Among them, LkoERF3-like1 and LkoERF071 may be involved in the flowering age pathway. This study enriches the scarce research on reproductive development in gymnosperms and provides a theoretical basis and research direction for regulating the reproductive development of larch in seed orchards.
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Affiliation(s)
- Junfei Hao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 150040, Harbin, China
| | - Daixi Xu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 150040, Harbin, China
| | - Chen Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 150040, Harbin, China
| | - Qing Cao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 150040, Harbin, China
| | - Qingrong Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 150040, Harbin, China
| | - Miaomiao Xie
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 150040, Harbin, China
| | - Hanguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 150040, Harbin, China.
| | - Lei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 150040, Harbin, China.
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Viejo M, Tengs T, Yakovlev I, Cross H, Krokene P, Olsen JE, Fossdal CG. Epitype-inducing temperatures drive DNA methylation changes during somatic embryogenesis in the long-lived gymnosperm Norway spruce. FRONTIERS IN PLANT SCIENCE 2023; 14:1196806. [PMID: 37546277 PMCID: PMC10399239 DOI: 10.3389/fpls.2023.1196806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023]
Abstract
An epigenetic memory of the temperature sum experienced during embryogenesis is part of the climatic adaptation strategy of the long-lived gymnosperm Norway spruce. This memory has a lasting effect on the timing of bud phenology and frost tolerance in the resulting epitype trees. The epigenetic memory is well characterized phenotypically and at the transcriptome level, but to what extent DNA methylation changes are involved have not previously been determined. To address this, we analyzed somatic epitype embryos of Norway spruce clones produced at contrasting epitype-inducing conditions (18 and 28°C). We screened for differential DNA methylation in 2744 genes related mainly to the epigenetic machinery, circadian clock, and phenology. Of these genes, 68% displayed differential DNA methylation patterns between contrasting epitype embryos in at least one methylation context (CpG, CHG, CHH). Several genes related to the epigenetic machinery (e.g., DNA methyltransferases, ARGONAUTE) and the control of bud phenology (FTL genes) were differentially methylated. This indicates that the epitype-inducing temperature conditions induce an epigenetic memory involving specific DNA methylation changes in Norway spruce.
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Affiliation(s)
- Marcos Viejo
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, Ås, Norway
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
- Department of Functional Biology, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Torstein Tengs
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, Ås, Norway
- Department of Breeding and Genetics, Norwegian Institute of Food, Fisheries and Aquaculture Research (NOFIMA), Ås, Norway
| | - Igor Yakovlev
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Hugh Cross
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, Ås, Norway
- Department of Science, National Ecological Observatory Network, Boulder, CO, United States
| | - Paal Krokene
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Jorunn E. Olsen
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Carl Gunnar Fossdal
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, Ås, Norway
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Ranade SS, García-Gil MR. Clinal variation in PHY (PAS domain) and CRY (CCT domain)-Signs of local adaptation to light quality in Norway spruce. PLANT, CELL & ENVIRONMENT 2023. [PMID: 37291974 DOI: 10.1111/pce.14638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/19/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023]
Abstract
Detection of the genomic basis of local adaptation to environmental conditions is challenging in forest trees. Phytochromes (PHY) and cryptochromes (CRY) perceive the red (R)/far-red (FR) and blue light respectively, thus playing a fundamental role in regulating plant growth and development. PHYO and PHYP from conifers are the equivalents of PHYA/PHYC and PHYB in angiosperms, respectively. Norway spruce shows an adaptive latitudinal cline for shade (low R:FR or FR-enriched light) tolerance and requirement of FR light for its growth. We analyzed the exome capture data that included a uniquely large data set of 1654 Norway spruce trees sampled across many latitudes in Sweden to capture the natural clines for photoperiod and FR light exposure during the growth season. Statistically significant clinal variation was detected in allele and genotype frequencies of missense mutations in coding regions belonging to well-defined functional domains of PHYO (PAS-B), PHYP2 (PAS fold-2), CRY1 (CCT1) and CRY2 (CCT2) that strongly correlates with the latitudinal gradient in response to variable light quality in Norway spruce. The missense SNP in PHYO resulting in Asn835Ser, displayed the steepest cline among all other polymorphisms. We propose that these variations in the photoreceptors represent signs of local adaptation to light quality.
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Affiliation(s)
- Sonali Sachin Ranade
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - María Rosario García-Gil
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
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Ranade SS, García-Gil MR. Molecular signatures of local adaptation to light in Norway spruce. PLANTA 2021; 253:53. [PMID: 33511433 PMCID: PMC7843583 DOI: 10.1007/s00425-020-03517-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 12/02/2020] [Indexed: 05/12/2023]
Abstract
MAIN CONCLUSION Transcriptomic and exome capture analysis reveal an adaptive cline for shade tolerance in Norway spruce. Genes involved in the lignin pathway and immunity seem to play a potential role in contributing towards local adaptation to light. The study of natural variation is an efficient method to elucidate how plants adapt to local climatic conditions, a key process for the evolution of a species. Norway spruce is a shade-tolerant conifer in which the requirement of far-red light for growth increases latitudinally northwards. The objective of the study is to characterize the genetic control of local adaptation to light enriched in far-red in Norway spruce, motivated by a latitudinal gradient for the Red:Far-red (R:FR) ratio to which Norway spruce has been proven to be genetically adapted. We have established the genomic signatures of local adaptation by conducting transcriptomic (total RNA-sequencing) and genomic analyses (exome capture), for the identification of genes differentially regulated along the cline. RNA-sequencing revealed 274 differentially expressed genes in response to SHADE (low R:FR light), between the southern and northern natural populations in Sweden. Exome capture included analysis of a uniquely large data set (1654 trees) that revealed missense variations in coding regions of nine differentially expressed candidate genes, which followed a latitudinal cline in allele and genotype frequencies. These genes included five transcription factors involved in vital processes like bud-set/bud-flush, lignin pathway, and cold acclimation and other genes that take part in cell-wall remodeling, secondary cell-wall thickening, response to starvation, and immunity. Based on these results, we suggest that the northern populations might not only be able to adjust their growing season in response to low R:FR light, but they may also be better adapted towards disease resistance by up-regulation of the lignin pathway that is linked to immunity. This forms a concrete basis for local adaptation to light quality in Norway spruce, one of the most economically important conifer tree species in Sweden.
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Affiliation(s)
- Sonali Sachin Ranade
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
- Department of Plant Physiology, Umeå Plant Science Centre, University of Umeå, 901 87 Umeå, Sweden
| | - María Rosario García-Gil
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
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Mayol M, Riba M, Cavers S, Grivet D, Vincenot L, Cattonaro F, Vendramin GG, González‐Martínez SC. A multiscale approach to detect selection in nonmodel tree species: Widespread adaptation despite population decline in Taxus baccata L. Evol Appl 2020; 13:143-160. [PMID: 31892949 PMCID: PMC6935595 DOI: 10.1111/eva.12838] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/18/2019] [Accepted: 06/24/2019] [Indexed: 01/03/2023] Open
Abstract
Detecting the molecular basis of local adaptation and identifying selective drivers is still challenging in nonmodel species. The use of purely population genetic approaches is limited by some characteristics of genetic systems, such as pleiotropy and polygenic control, and parallel evidence from phenotypic-based experimental comparisons is required. In long-lived organisms, the detection of selective pressures might also be precluded by evolutionary lag times in response to the environment. Here, we used the English yew to showcase an example of a multiscale integrative approach in a nonmodel species with limited plant and genomic resources. We combined information from two independent sources, phenotypes in a common environment and genomic data in natural populations, to investigate the signature of selection. Growth differences among populations in a common environment, and phenological patterns of both shoot elongation and male strobili maturation, were associated with climate clines, providing evidence for local adaptation and guiding us in the selection of populations for genomic analyses. We used information on over 25,000 SNPs from c. 1,200 genes to infer the demographic history and to test for molecular signatures of selection at different levels: SNP, gene, and biological pathway. Our results confirmed an overall demographic history of population decline, but we also found evidence for putative local adaptation at the molecular level. We identified or confirmed several candidate genes for positive and negative selection in forest trees, including the pseudo-response regulator 7 (PRR7), an essential component of the circadian clock in plants. In addition, we successfully tested an approach to detect polygenic adaptation in biological pathways, allowing us to identify the flavonoid biosynthesis pathway as a candidate stress-response pathway that deserves further attention in other plants. Finally, our study contributes to the emerging view that explaining contemporary standing genetic variation requires considering adaptation to past climates, especially for long-lived trees.
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Affiliation(s)
| | - Miquel Riba
- CREAFCerdanyola del VallèsSpain
- Univ. Autònoma BarcelonaCerdanyola del VallèsSpain
| | | | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research CentreINIA‐CIFORMadridSpain
- Sustainable Forest Management Research Institute, INIA‐University of ValladolidMadridSpain
| | | | | | - Giovanni G. Vendramin
- Institute of Biosciences and Bioresources, Division of FlorenceNational Research CouncilSesto FiorentinoItaly
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Alakärppä E, Salo HM, Valledor L, Cañal MJ, Häggman H, Vuosku J. Natural variation of DNA methylation and gene expression may determine local adaptations of Scots pine populations. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:5293-5305. [PMID: 30113688 DOI: 10.1093/jxb/ery292] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 08/01/2018] [Indexed: 05/27/2023]
Abstract
Long-lived conifers are vulnerable to climate change because classical evolutionary processes are slow in developing adaptive responses. Therefore, the capacity of a genotype to adopt different phenotypes is important. Gene expression is the primary mechanism that converts genome-encoded information into phenotypes, and DNA methylation is employed in the epigenetic regulation of gene expression. We investigated variations in global DNA methylation and gene expression between three Scots pine (Pinus sylvestris L.) populations located in northern and southern Finland using mature seeds. Gene expression levels were studied in six DNA methyltransferase (DNMT) genes, which were characterized in this study, and in 19 circadian clock genes regulating adaptive traits. In embryos, expression diversity was found for three DNMT genes, which maintain DNA methylation. The expression of two DNMT genes was strongly correlated with climate variables, which suggests a role for DNA methylation in local adaptation. For adaptation-related genes, expression levels showed between-population variation in 11 genes in megagametophytes and in eight genes in embryos, and many of these genes were linked to climate factors. Altogether, our results suggest that differential DNA methylation and gene expression contribute to local adaptation in Scots pine populations and may enhance the fitness of trees under rapidly changing climatic conditions.
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Affiliation(s)
- Emmi Alakärppä
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Heikki M Salo
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Luis Valledor
- Plant Physiology, Faculty of Biology, University of Oviedo, Oviedo, Spain
| | - Maria Jesús Cañal
- Plant Physiology, Faculty of Biology, University of Oviedo, Oviedo, Spain
| | - Hely Häggman
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Jaana Vuosku
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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Drought Sensitivity of Norway Spruce at the Species' Warmest Fringe: Quantitative and Molecular Analysis Reveals High Genetic Variation Among and Within Provenances. G3-GENES GENOMES GENETICS 2018; 8:1225-1245. [PMID: 29440346 PMCID: PMC5873913 DOI: 10.1534/g3.117.300524] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Norway spruce (Picea abies) is by far the most important timber species in Europe, but its outstanding role in future forests is jeopardized by its high sensitivity to drought. We analyzed drought response of Norway spruce at the warmest fringe of its natural range. Based on a 35-year old provenance experiment we tested for genetic variation among and within seed provenances across consecutively occurring strong drought events using dendroclimatic time series. Moreover, we tested for associations between ≈1,700 variable SNPs and traits related to drought response, wood characteristics and climate-growth relationships. We found significant adaptive genetic variation among provenances originating from the species’ Alpine, Central and Southeastern European range. Genetic variation between individuals varied significantly among provenances explaining up to 44% of the phenotypic variation in drought response. Varying phenotypic correlations between drought response and wood traits confirmed differences in selection intensity among seed provenances. Significant associations were found between 29 SNPs and traits related to drought, climate-growth relationships and wood properties which explained between 11 and 43% of trait variation, though 12 of them were due to single individuals having extreme phenotypes of the respective trait. The majority of these SNPs are located within exons of genes and the most important ones are preferentially expressed in cambium and xylem expansion layers. Phenotype-genotype associations were stronger if only provenances with significant quantitative genetic variation in drought response were considered. The present study confirms the high adaptive variation of Norway spruce in Central and Southeastern Europe and demonstrates how quantitative genetic, dendroclimatic and genomic data can be linked to understand the genetic basis of adaptation to climate extremes in trees.
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Ganthaler A, Stöggl W, Mayr S, Kranner I, Schüler S, Wischnitzki E, Sehr EM, Fluch S, Trujillo-Moya C. Association genetics of phenolic needle compounds in Norway spruce with variable susceptibility to needle bladder rust. PLANT MOLECULAR BIOLOGY 2017; 94:229-251. [PMID: 28190131 PMCID: PMC5443855 DOI: 10.1007/s11103-017-0589-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 01/24/2017] [Indexed: 05/15/2023]
Abstract
KEY MESSAGE Accumulation of phenolic needle metabolites in Norway spruce is regulated by many genes with small and additive effects and is correlated with the susceptibility against fungal attack. Norway spruce accumulates high foliar concentrations of secondary phenolic metabolites, with important functions for pathogen defence responses. However, the molecular genetic basis underlying the quantitative variation of phenolic compounds and their role in enhanced resistance of spruce to infection by needle bladder rust are unknown. To address these questions, a set of 1035 genome-wide single nucleotide polymorphisms (SNPs) was associated to the quantitative variation of four simple phenylpropanoids, eight stilbenes, nine flavonoids, six related arithmetic parameters and the susceptibility to infection by Chrysomyxa rhododendri in an unstructured natural population of Norway spruce. Thirty-one significant genetic associations for the flavonoids gallocatechin, kaempferol 3-glucoside and quercetin 3-glucoside and the stilbenes resveratrol, piceatannol, astringin and isorhapontin were discovered, explaining 22-59% of phenotypic variation, and indicating a regulation of phenolic accumulation by many genes with small and additive effects. The phenolics profile differed between trees with high and low susceptibility to the fungus, underlining the importance of phenolic compounds in the defence mechanisms of Norway spruce to C. rhododendri. Results highlight the utility of association studies in non-model tree species and may enable marker-assisted selection of Norway spruce adapted to severe pathogen attack.
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Affiliation(s)
- Andrea Ganthaler
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, 6020, Innsbruck, Austria.
- alpS - Centre for Climate Change Adaptation, Grabenweg 68, 6020, Innsbruck, Austria.
| | - Wolfgang Stöggl
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, 6020, Innsbruck, Austria
| | - Stefan Mayr
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, 6020, Innsbruck, Austria
| | - Ilse Kranner
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, 6020, Innsbruck, Austria
| | - Silvio Schüler
- Department of Forest Genetics, Federal Research and Training Centre for Forests, Natural Hazards and Landscapes (BFW), Seckendorff-Gudent-Weg 8, 1131, Vienna, Austria
| | - Elisabeth Wischnitzki
- Health and Environment Department, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430, Tulln, Austria
| | - Eva Maria Sehr
- Health and Environment Department, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430, Tulln, Austria
| | - Silvia Fluch
- Health and Environment Department, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430, Tulln, Austria
| | - Carlos Trujillo-Moya
- Department of Forest Genetics, Federal Research and Training Centre for Forests, Natural Hazards and Landscapes (BFW), Seckendorff-Gudent-Weg 8, 1131, Vienna, Austria
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Brousseau L, Postolache D, Lascoux M, Drouzas AD, Källman T, Leonarduzzi C, Liepelt S, Piotti A, Popescu F, Roschanski AM, Zhelev P, Fady B, Vendramin GG. Local Adaptation in European Firs Assessed through Extensive Sampling across Altitudinal Gradients in Southern Europe. PLoS One 2016; 11:e0158216. [PMID: 27392065 PMCID: PMC4938419 DOI: 10.1371/journal.pone.0158216] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 06/13/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Local adaptation is a key driver of phenotypic and genetic divergence at loci responsible for adaptive traits variations in forest tree populations. Its experimental assessment requires rigorous sampling strategies such as those involving population pairs replicated across broad spatial scales. METHODS A hierarchical Bayesian model of selection (HBM) that explicitly considers both the replication of the environmental contrast and the hierarchical genetic structure among replicated study sites is introduced. Its power was assessed through simulations and compared to classical 'within-site' approaches (FDIST, BAYESCAN) and a simplified, within-site, version of the model introduced here (SBM). RESULTS HBM demonstrates that hierarchical approaches are very powerful to detect replicated patterns of adaptive divergence with low false-discovery (FDR) and false-non-discovery (FNR) rates compared to the analysis of different sites separately through within-site approaches. The hypothesis of local adaptation to altitude was further addressed by analyzing replicated Abies alba population pairs (low and high elevations) across the species' southern distribution range, where the effects of climatic selection are expected to be the strongest. For comparison, a single population pair from the closely related species A. cephalonica was also analyzed. The hierarchical model did not detect any pattern of adaptive divergence to altitude replicated in the different study sites. Instead, idiosyncratic patterns of local adaptation among sites were detected by within-site approaches. CONCLUSION Hierarchical approaches may miss idiosyncratic patterns of adaptation among sites, and we strongly recommend the use of both hierarchical (multi-site) and classical (within-site) approaches when addressing the question of adaptation across broad spatial scales.
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Affiliation(s)
- Louise Brousseau
- INRA, UR629 URFM Ecologie des Forêts Méditerranéennes, Domaine Saint Paul, Site Agroparc CS 40509, 84914 Avignon Cedex 9, France
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), Division of Florence, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy
| | - Dragos Postolache
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), Division of Florence, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy
- Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127 Pisa, Italy
- National Institute of Forest Research and Development (INCDS), Research Station Simeria, Str. Biscaria 1, 335900 Simeria, Romania
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Center and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
| | - Andreas D. Drouzas
- School of Biology, Aristotle University of Thessaloniki, GR-54124, Thessaloniki, Greece
| | - Thomas Källman
- Department of Ecology and Genetics, Evolutionary Biology Center and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
| | - Cristina Leonarduzzi
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), Division of Florence, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), Division of Palermo, National 3. Research Council—Corso Calatafimi, 414—I-90129, Palermo (PA), Italy
| | - Sascha Liepelt
- University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Straße 35032 Marburg, Germany
| | - Andrea Piotti
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), Division of Florence, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy
| | - Flaviu Popescu
- National Institute of Forest Research and Development (INCDS), Research Station Simeria, Str. Biscaria 1, 335900 Simeria, Romania
| | - Anna M. Roschanski
- University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Straße 35032 Marburg, Germany
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank Collections North, Inselstrasse 9, D-23999 Malchow/Poel, Germany
| | - Peter Zhelev
- University of Forestry, 10, Kl. Ohridsky Blvd., 1797 Sofia, Bulgaria
| | - Bruno Fady
- INRA, UR629 URFM Ecologie des Forêts Méditerranéennes, Domaine Saint Paul, Site Agroparc CS 40509, 84914 Avignon Cedex 9, France
| | - Giovanni Giuseppe Vendramin
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), Division of Florence, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy
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11
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Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies. G3-GENES GENOMES GENETICS 2016; 6:1979-89. [PMID: 27172202 PMCID: PMC4938651 DOI: 10.1534/g3.116.028753] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The joint inference of selection and past demography remain a costly and demanding task. We used next generation sequencing of two pools of 48 Norway spruce mother trees, one corresponding to the Fennoscandian domain, and the other to the Alpine domain, to assess nucleotide polymorphism at 88 nuclear genes. These genes are candidate genes for phenological traits, and most belong to the photoperiod pathway. Estimates of population genetic summary statistics from the pooled data are similar to previous estimates, suggesting that pooled sequencing is reliable. The nonsynonymous SNPs tended to have both lower frequency differences and lower FST values between the two domains than silent ones. These results suggest the presence of purifying selection. The divergence between the two domains based on synonymous changes was around 5 million yr, a time similar to a recent phylogenetic estimate of 6 million yr, but much larger than earlier estimates based on isozymes. Two approaches, one of them novel and that considers both FST and difference in allele frequencies between the two domains, were used to identify SNPs potentially under diversifying selection. SNPs from around 20 genes were detected, including genes previously identified as main target for selection, such as PaPRR3 and PaGI.
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Detection of SNPs based on transcriptome sequencing in Norway spruce (Picea abies (L.) Karst). CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0520-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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