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Modica A, Lalagüe H, Muratorio S, Scotti I. Rolling down that mountain: microgeographical adaptive divergence during a fast population expansion along a steep environmental gradient in European beech. Heredity (Edinb) 2024; 133:99-112. [PMID: 38890557 PMCID: PMC11286953 DOI: 10.1038/s41437-024-00696-z] [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: 02/07/2024] [Revised: 05/23/2024] [Accepted: 05/23/2024] [Indexed: 06/20/2024] Open
Abstract
Forest tree populations harbour high genetic diversity thanks to large effective population sizes and strong gene flow, allowing them to diversify through adaptation to local environmental pressures within dispersal distance. Many tree populations also experienced historical demographic fluctuations, including spatial population contraction or expansions at various temporal scales, which may constrain their ability to adapt to environmental variations. Our aim is to investigate how recent contraction and expansion events interfere with local adaptation, by studying patterns of adaptive divergence between closely related stands undergoing environmentally contrasted conditions, and having or not recently expanded. To investigate genome-wide signatures of local adaptation while accounting for demography, we analysed divergence in a European beech population by testing pairwise differentiation among four tree stands at ~35k Single Nucleotide Polymorphisms from ~9k genomic regions. We applied three divergence outlier search methods resting on different assumptions and targeting either single SNPs or contiguous genomic regions, while accounting for the effect of population size variations on genetic divergence. We found 27 signals of selective signatures in 19 target regions. Putatively adaptive divergence involved all stand pairs. We retrieved signals both when comparing old-growth stands and recently colonised areas and when comparing stands within the old-growth area. Therefore, adaptive divergence processes have taken place both over short time spans, under strong environmental contrasts, and over short ecological gradients, in populations that have been stable in the long term. This suggests that standing genetic variation supports local, microgeographic divergence processes, which can maintain genetic diversity at the landscape level.
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Affiliation(s)
- Andrea Modica
- INRAE, URFM, 228, Route de l'Aérodrome, 84914, Avignon, France
| | - Hadrien Lalagüe
- INRAE, EcoFoG, Campus agronomique, 97310, Kourou, French Guiana
| | - Sylvie Muratorio
- INRAE, EcoBioP, 173, Route de Saint-Jean-de-Luz RD 918, 64310, Saint-Pée-sur-Nivelle, France
| | - Ivan Scotti
- INRAE, URFM, 228, Route de l'Aérodrome, 84914, Avignon, France.
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2
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Müller M, Leuschner C, Weithmann G, Weigel R, Banzragch BE, Steiner W, Gailing O. A genome-wide genetic association study reveals SNPs significantly associated with environmental variables and specific leaf area in European beech. PHYSIOLOGIA PLANTARUM 2024; 176:e14334. [PMID: 38705836 DOI: 10.1111/ppl.14334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/19/2024] [Accepted: 04/25/2024] [Indexed: 05/07/2024]
Abstract
European beech is negatively affected by climate change and a further growth decline is predicted for large parts of its distribution range. Despite the importance of this species, little is known about its genetic adaptation and especially the genetic basis of its physiological traits. Here, we used genotyping by sequencing to identify SNPs in 43 German European beech populations growing under different environmental conditions. In total, 28 of these populations were located along a precipitation and temperature gradient in northern Germany, and single tree-based hydraulic and morphological traits were available. We obtained a set of 13,493 high-quality SNPs that were used for environmental and SNP-trait association analysis. In total, 22 SNPs were identified that were significantly associated with environmental variables or specific leaf area (SLA). Several SNPs were located in genes related to stress response. The majority of the significant SNPs were located in non-coding (intergenic and intronic) regions. These may be in linkage disequilibrium with the causative coding or regulatory regions. Our study gives insights into the genetic basis of abiotic adaptation in European beech, and provides genetic resources that can be used in future studies on this species. Besides clear patterns of local adaptation to environmental conditions of the investigated populations, the analyzed morphological and hydraulic traits explained most of the explainable genetic variation. Thus, they could successfully be altered in tree breeding programs, which may help to increase the adaptation of European beech to changing environmental conditions in the future.
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Affiliation(s)
- Markus Müller
- University of Göttingen, Forest Genetics and Forest Tree Breeding, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
| | - Christoph Leuschner
- Department Plant Ecology and Ecosystems Research, University of Göttingen, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, Göttingen, Germany
| | - Greta Weithmann
- Department Plant Ecology and Ecosystems Research, University of Göttingen, Göttingen, Germany
| | - Robert Weigel
- Department Plant Ecology and Ecosystems Research, University of Göttingen, Göttingen, Germany
- Ecological-Botanical Garden, University of Bayreuth, Bayreuth, Germany
| | - Bat-Enerel Banzragch
- Department Plant Ecology and Ecosystems Research, University of Göttingen, Göttingen, Germany
- Applied Vegetation Ecology, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
| | - Wilfried Steiner
- Department Forest Genetic Resources, Northwest German Forest Research Institute, Hann. Münden, Germany
| | - Oliver Gailing
- University of Göttingen, Forest Genetics and Forest Tree Breeding, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, Göttingen, Germany
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3
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Zhang X, Chen J, Luo H, Chen X, Zhong J, Ji X. Climate-driven mitochondrial selection in lacertid lizards. Ecol Evol 2024; 14:e11176. [PMID: 38529027 PMCID: PMC10961475 DOI: 10.1002/ece3.11176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 02/04/2024] [Accepted: 03/05/2024] [Indexed: 03/27/2024] Open
Abstract
The mitochondrion, which is an intracellular organelle responsible for most of the energy-producing pathways, can have its genome targeted for climate-driven selection. However, climate-driven mitochondrial selection remains a sparsely studied area in reptiles. Here, we reported the complete mitochondrial genome sequence of a lacertid lizard (Takydromus intermedius) and used mitogenomes from 54 species of lacertid lizards to study their phylogenetic relationships and to identify the mitochondrial genes under positive selection by climate. The length of the complete mitochondrial genome sequence of T. intermedius was 17,713 bp, which was within the range of lengths (17,224-18,943) ever reported for Takydromus species. The arrangement of mitochondrial genes in T. intermedius was the same as in other congeneric species. The 54 lacertid species could be divided into three geographically and climatically different clades. We identified three mitochondrial genes (ATP6, ATP8, and ND3) under positive selection by climate, and found that isothermality, temperature seasonality, precipitation of wettest month, and precipitation seasonality were the most important climatic variables contributing to the gene selection.
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Affiliation(s)
- Xiang Zhang
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
| | - Jian Chen
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
| | - Hong‐Yu Luo
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
| | - Xin Chen
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
| | - Jun Zhong
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
| | - Xiang Ji
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
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Marchesini A, Silverj A, Torre S, Rota-Stabelli O, Girardi M, Passeri I, Fracasso I, Sebastiani F, Vernesi C. First genome-wide data from Italian European beech (Fagus sylvatica L.): Strong and ancient differentiation between Alps and Apennines. PLoS One 2023; 18:e0288986. [PMID: 37471380 PMCID: PMC10358878 DOI: 10.1371/journal.pone.0288986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 07/10/2023] [Indexed: 07/22/2023] Open
Abstract
The European beech (Fagus sylvatica L.) is one of the most widespread forest trees in Europe whose distribution and intraspecific diversity has been largely shaped by repeated glacial cycles. Previous studies, mainly based on palaeobotanical evidence and a limited set of chloroplast and nuclear genetic markers, highlighted a complex phylogeographic scenario, with southern and western Europe characterized by a rather heterogeneous genetic structure, as a result of recolonization from different glacial refugia. Despite its ecological and economic importance, the genome of this broad-leaved tree has only recently been assembled, and its intra-species genomic diversity is still largely unexplored. Here, we performed whole-genome resequencing of nine Italian beech individuals sampled from two stands located in the Alpine and Apennine mountain ranges. We investigated patterns of genetic diversity at chloroplast, mitochondrial and nuclear genomes and we used chloroplast genomes to reconstruct a temporally-resolved phylogeny. Results allowed us to test European beech differentiation on a whole-genome level and to accurately date their divergence time. Our results showed comparable, relatively high levels of genomic diversity in the two populations and highlighted a clear differentiation at chloroplast, mitochondrial and nuclear genomes. The molecular clock analysis indicated an ancient split between the Alpine and Apennine populations, occurred between the Günz and the Riss glaciations (approximately 660 kyrs ago), suggesting a long history of separation for the two gene pools. This information has important conservation implications in the context of adaptation to ongoing climate changes.
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Affiliation(s)
- Alexis Marchesini
- Institute for Sustainable Plant Protection (IPSP), The National Research Council of Italy (CNR), Sesto Fiorentino (Florence), Italy
- Research Institute on Terrestrial Ecosystems (IRET), The National Research Council of Italy (CNR), Porano (Terni), Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Andrea Silverj
- Centre Agriculture Food Environment, University of Trento, San Michele all’Adige, Italy
- Department CIBIO, University of Trento, Trento, Italy
| | - Sara Torre
- Institute for Sustainable Plant Protection (IPSP), The National Research Council of Italy (CNR), Sesto Fiorentino (Florence), Italy
| | - Omar Rota-Stabelli
- Centre Agriculture Food Environment, University of Trento, San Michele all’Adige, Italy
- Department CIBIO, University of Trento, Trento, Italy
- Plant Protection Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all’Adige (Trento), Italy
| | - Matteo Girardi
- Conservation Genomics Unit, Research and Innovation Centre- Fondazione Edmund Mach, S. Michele all’Adige (Trento), Italy
| | - Iacopo Passeri
- Institute for Sustainable Plant Protection (IPSP), The National Research Council of Italy (CNR), Sesto Fiorentino (Florence), Italy
| | - Ilaria Fracasso
- Forest Ecology Unit, Research and Innovation Centre- Fondazione Edmund Mach, S. Michele all’Adige (Trento), Italy
- Faculty of Science and Technology, Free University of Bolzano-Bozen, Bolzano, Italy
| | - Federico Sebastiani
- Institute for Sustainable Plant Protection (IPSP), The National Research Council of Italy (CNR), Sesto Fiorentino (Florence), Italy
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre- Fondazione Edmund Mach, S. Michele all’Adige (Trento), Italy
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Wu ZY, Milne RI, Liu J, Nathan R, Corlett RT, Li DZ. The establishment of plants following long-distance dispersal. Trends Ecol Evol 2023; 38:289-300. [PMID: 36456382 DOI: 10.1016/j.tree.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/30/2022]
Abstract
Long-distance dispersal (LDD) beyond the range of a species is an important driver of ecological and evolutionary patterns, but insufficient attention has been given to postdispersal establishment. In this review, we summarize current knowledge of the post-LDD establishment phase in plant colonization, identify six key determinants of establishment success, develop a general quantitative framework for post-LDD establishment, and address the major challenges and opportunities in future research. These include improving detection and understanding of LDD using novel approaches, investigating mechanisms determining post-LDD establishment success using mechanistic modeling and inference, and comparison of establishment between past and present. By addressing current knowledge gaps, we aim to further our understanding of how LDD affects plant distributions, and the long-term consequences of LDD events.
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Affiliation(s)
- Zeng-Yuan Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Richard I Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, UK
| | - Jie Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ran Nathan
- Movement Ecology Laboratory, Department of Ecology, Evolution and Behavior, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Richard T Corlett
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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Feng S, Wan W, Li Y, Wang D, Ren G, Ma T, Ru D. Transcriptome-based analyses of adaptive divergence between two closely related spruce species on the Qinghai-Tibet plateau and adjacent regions. Mol Ecol 2023; 32:476-491. [PMID: 36320185 DOI: 10.1111/mec.16758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 10/07/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022]
Abstract
Speciation among populations connected by gene flow is driven by adaptation to different environments, but underlying gene-environment associations remain largely unknown. Here, 162 individuals from 32 populations were sampled to obtain 191,648 independent single nucleotide polymorphisms (SNPs) across the genomes of two closely related spruce species, Picea asperata and Picea crassifolia, which occur on the Qinghai-Tibet Plateau and in surrounding regions. Using the SNP data set, genotype-environment associations and demographic modelling were used to examine local adaptation and genetic divergence between these two species. While morphologically similar, the two Picea species were genetically differentiated in multiple analyses. These species diverged despite continuous gene flow, and their initial divergence was dated back to the late Quaternary. The effective population sizes of both species have expanded since their divergence, as confirmed by niche distribution simulations. A total of 6365 genes were associated with the tested environmental variables; of these, 41 were positively selected in P. asperata and were mainly associated with temperature, while 83 were positively selected in P. crassifolia and were primarily associated with precipitation. These results deepen our understanding of the adaptive divergence and demographic histories of these two spruce species and highlight the importance of genomic data in deciphering the environmental selection underlying Quaternary interspecific divergence.
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Affiliation(s)
- Shuo Feng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Wei Wan
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Yang Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - DongLei Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Guangpeng Ren
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Tao Ma
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Dafu Ru
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
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Stefanini C, Csilléry K, Ulaszewski B, Burczyk J, Schaepman ME, Schuman MC. A novel synthesis of two decades of microsatellite studies on European beech reveals decreasing genetic diversity from glacial refugia. TREE GENETICS & GENOMES 2022; 19:3. [PMID: 36532711 PMCID: PMC9744708 DOI: 10.1007/s11295-022-01577-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/26/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Genetic diversity influences the evolutionary potential of forest trees under changing environmental conditions, thus indirectly the ecosystem services that forests provide. European beech (Fagus sylvatica L.) is a dominant European forest tree species that increasingly suffers from climate change-related die-back. Here, we conducted a systematic literature review of neutral genetic diversity in European beech and created a meta-data set of expected heterozygosity (He) from all past studies providing nuclear microsatellite data. We propose a novel approach, based on population genetic theory and a min-max scaling to make past studies comparable. Using a new microsatellite data set with unprecedented geographic coverage and various re-sampling schemes to mimic common sampling biases, we show the potential and limitations of the scaling approach. The scaled meta-dataset reveals the expected trend of decreasing genetic diversity from glacial refugia across the species range and also supports the hypothesis that different lineages met and admixed north of the European mountain ranges. As a result, we present a map of genetic diversity across the range of European beech which could help to identify seed source populations harboring greater diversity and guide sampling strategies for future genome-wide and functional investigations of genetic variation. Our approach illustrates how to combine information from several nuclear microsatellite data sets to describe patterns of genetic diversity extending beyond the geographic scale or mean number of loci used in each individual study, and thus is a proof-of-concept for synthesizing knowledge from existing studies also in other species. Supplementary Information The online version contains supplementary material available at 10.1007/s11295-022-01577-4.
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Affiliation(s)
- Camilla Stefanini
- Biodiversity and Conservation Biology Unit, Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Dietikon, Switzerland
| | - Katalin Csilléry
- Biodiversity and Conservation Biology Unit, Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Dietikon, Switzerland
| | - Bartosz Ulaszewski
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064 Bydgoszcz, Poland
| | - Jarosław Burczyk
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064 Bydgoszcz, Poland
| | - Michael E Schaepman
- Remote Sensing Laboratories, Department of Geography, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Meredith C Schuman
- Remote Sensing Laboratories, Department of Geography, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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Li M, Zhou J, Lang X, Han D, Hu Y, Ding Y, Wang G, Guo J, Shi L. Integrating transcriptomic and metabolomic analysis in roots of wild soybean seedlings in response to low-phosphorus stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1006806. [PMID: 36466240 PMCID: PMC9713585 DOI: 10.3389/fpls.2022.1006806] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Plants undergo divergent adaptations to form different ecotypes when exposed to different habitats. Ecotypes with ecological adaptation advantages are excellent germplasm resources for crop improvement. METHODS his study comprehensively compared the differences in morphology and physiological mechanisms in the roots of two different ecotypes of wild soybean (Glycine soja) seedlings under artificially simulated low-phosphorus (LP) stress. RESULT The seedlings of barren-tolerant wild soybean (GS2) suffered less damage than common wild soybean (GS1). GS2 absorbed more phosphorus (P) by increasing root length. In-depth integrated analyses of transcriptomics and metabolomics revealed the formation process of the ecological adaptability of the two different ecotypes wild soybean from the perspective of gene expression and metabolic changes. This study revealed the adaptation process of GS2 from the perspective of the adaptation of structural and molecular metabolism, mainly including: (1) Enhancing the metabolism of phenolic compounds, lignin, and organic acid metabolism could activate unavailable soil P; (2) Up-regulating genes encoding pectinesterase and phospholipase C (PLC) specifically could promote the reuse of structural P; (3) Some factors could reduce the oxidative damage to the membranes caused by LP stress, such as accumulating the metabolites putrescine and ascorbate significantly, up-regulating the genes encoding SQD2 (the key enzyme of sulfolipid substitution of phospholipids) substantially and enhancing the synthesis of secondary antioxidant metabolite anthocyanins and the AsA-GSH cycle; (4) enhancing the uptake of soil P by upregulating inorganic phosphate transporter, acid phosphatase ACP1, and purple acid phosphatase genes; (5) HSFA6b and MYB61 are the key TFs to resist LP stress. DISCUSSION In general, GS2 could resist LP stress by activating unavailable soil P, reusing plant structural P, rebuilding membrane lipids, and enhancing the antioxidant membrane protection system. Our study provides a new perspective for the study of divergent adaptation of plants.
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Affiliation(s)
- Mingxia Li
- School of Life Sciences, Changchun Normal University, Changchun, China
| | - Ji Zhou
- Land Consolidation and Rehabilitation Centre, The Ministry of Land and Resources, Beijing, China
| | - Xianyu Lang
- School of Life Sciences, Changchun Normal University, Changchun, China
| | - Defu Han
- School of Life Sciences, Changchun Normal University, Changchun, China
| | - Yongjun Hu
- School of Life Sciences, Changchun Normal University, Changchun, China
| | - Yinan Ding
- School of Life Sciences, Changchun Normal University, Changchun, China
| | - Guangye Wang
- School of Life Sciences, Changchun Normal University, Changchun, China
| | - Jixun Guo
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China
| | - Lianxuan Shi
- Institute of Grassland Science, Northeast Normal University, Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China
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A set of nuclear SNP loci derived from single sample double digest RAD and from pool sequencing for large-scale genetic studies in the European beech Fagus sylvatica. CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01256-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractThe large-scale spatial genetic structure of European beech, Fagus sylvatica, has been until now poorly studied. We conducted double digest RAD sequencing (ddRADseq) on 54 beech individuals stemming from 36 provenances to discover spatially informative nuclear SNP loci. In addition, two pools derived from 14 early and 14 late flushing individuals each were sequenced with Illumina HiSeq. From an initial amount of 5,464 loci detected by ddRADseq, we selected 559 informative loci. Further 27 additional loci showing significant allelic differences among early and late flushing individuals could be identified after a genotyping on 95 test individuals. The final selection of 578 loci was submitted to probe design for targeted genotyping by sequencing, which yielded 543 loci. The new set of SNP loci should be, after validation on a larger sample size, useful for large-scale genetic studies in this economically-important species.
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