1
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Capblancq T, Lachmuth S, Fitzpatrick MC, Keller SR. From common gardens to candidate genes: exploring local adaptation to climate in red spruce. THE NEW PHYTOLOGIST 2023; 237:1590-1605. [PMID: 36068997 PMCID: PMC10092705 DOI: 10.1111/nph.18465] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/09/2022] [Indexed: 05/12/2023]
Abstract
Local adaptation to climate is common in plant species and has been studied in a range of contexts, from improving crop yields to predicting population maladaptation to future conditions. The genomic era has brought new tools to study this process, which was historically explored through common garden experiments. In this study, we combine genomic methods and common gardens to investigate local adaptation in red spruce and identify environmental gradients and loci involved in climate adaptation. We first use climate transfer functions to estimate the impact of climate change on seedling performance in three common gardens. We then explore the use of multivariate gene-environment association methods to identify genes underlying climate adaptation, with particular attention to the implications of conducting genome scans with and without correction for neutral population structure. This integrative approach uncovered phenotypic evidence of local adaptation to climate and identified a set of putatively adaptive genes, some of which are involved in three main adaptive pathways found in other temperate and boreal coniferous species: drought tolerance, cold hardiness, and phenology. These putatively adaptive genes segregated into two 'modules' associated with different environmental gradients. This study nicely exemplifies the multivariate dimension of adaptation to climate in trees.
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Affiliation(s)
- Thibaut Capblancq
- Department of Plant BiologyUniversity of VermontBurlingtonVT05405USA
| | - Susanne Lachmuth
- Appalachian LaboratoryUniversity of Maryland Center for Environmental ScienceFrostburgMD21532USA
| | - Matthew C. Fitzpatrick
- Appalachian LaboratoryUniversity of Maryland Center for Environmental ScienceFrostburgMD21532USA
| | - Stephen R. Keller
- Department of Plant BiologyUniversity of VermontBurlingtonVT05405USA
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2
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Abstract
Traditional tree improvement is cumbersome and costly. Our main objective was to assess the extent to which genomic data can currently accelerate and improve decision making in this field. We used diameter at breast height (DBH) and wood density (WD) data for 4430 tree genotypes and single-nucleotide polymorphism (SNP) data for 2446 tree genotypes. Pedigree reconstruction was performed using a combination of maximum likelihood parentage assignment and matching based on identity-by-state (IBS) similarity. In addition, we used best linear unbiased prediction (BLUP) methods to predict phenotypes using SNP markers (GBLUP), recorded pedigree information (ABLUP), and single-step “blended” BLUP (HBLUP) combining SNP and pedigree information. We substantially improved the accuracy of pedigree records, resolving the inconsistent parental information of 506 tree genotypes. This led to substantially increased predictive ability (i.e., by up to 87%) in HBLUP analyses compared to a baseline from ABLUP. Genomic prediction was possible across populations and within previously untested families with moderately large training populations (N = 800–1200 tree genotypes) and using as few as 2000–5000 SNP markers. HBLUP was generally more effective than traditional ABLUP approaches, particularly after dealing appropriately with pedigree uncertainties. Our study provides evidence that genome-wide marker data can significantly enhance tree improvement. The operational implementation of genomic selection has started in radiata pine breeding in New Zealand, but further reductions in DNA extraction and genotyping costs may be required to realise the full potential of this approach.
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3
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Neale DB, Zimin AV, Zaman S, Scott AD, Shrestha B, Workman RE, Puiu D, Allen BJ, Moore ZJ, Sekhwal MK, De La Torre AR, McGuire PE, Burns E, Timp W, Wegrzyn JL, Salzberg SL. Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin. G3 (BETHESDA, MD.) 2022; 12:6460957. [PMID: 35100403 PMCID: PMC8728005 DOI: 10.1093/g3journal/jkab380] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022]
Abstract
Sequencing, assembly, and annotation of the 26.5 Gbp hexaploid genome of coast redwood (Sequoia sempervirens) was completed leading toward discovery of genes related to climate adaptation and investigation of the origin of the hexaploid genome. Deep-coverage short-read Illumina sequencing data from haploid tissue from a single seed were combined with long-read Oxford Nanopore Technologies sequencing data from diploid needle tissue to create an initial assembly, which was then scaffolded using proximity ligation data to produce a highly contiguous final assembly, SESE 2.1, with a scaffold N50 size of 44.9 Mbp. The assembly included several scaffolds that span entire chromosome arms, confirmed by the presence of telomere and centromere sequences on the ends of the scaffolds. The structural annotation produced 118,906 genes with 113 containing introns that exceed 500 Kbp in length and one reaching 2 Mb. Nearly 19 Gbp of the genome represented repetitive content with the vast majority characterized as long terminal repeats, with a 2.9:1 ratio of Copia to Gypsy elements that may aid in gene expression control. Comparison of coast redwood to other conifers revealed species-specific expansions for a plethora of abiotic and biotic stress response genes, including those involved in fungal disease resistance, detoxification, and physical injury/structural remodeling and others supporting flavonoid biosynthesis. Analysis of multiple genes that exist in triplicate in coast redwood but only once in its diploid relative, giant sequoia, supports a previous hypothesis that the hexaploidy is the result of autopolyploidy rather than any hybridizations with separate but closely related conifer species.
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Affiliation(s)
- David B Neale
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
| | - Sumaira Zaman
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.,Department of Computer Science & Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Alison D Scott
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Bikash Shrestha
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Rachael E Workman
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Daniela Puiu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
| | - Brian J Allen
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Zane J Moore
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Manoj K Sekhwal
- School of Forestry, Northern Arizona University, Flagstaff, AZ 86011, USA
| | | | - Patrick E McGuire
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Emily Burns
- Save the Redwoods League, San Francisco, CA 94104, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA.,Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Steven L Salzberg
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA.,Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.,Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
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4
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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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5
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Steele SE, Ryder OA, Maschinski J. RNA-Seq reveals adaptive genetic potential of the rare Torrey pine (Pinus torreyana) in the face of Ips bark beetle outbreaks. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01394-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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6
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Capblancq T, Fitzpatrick MC, Bay RA, Exposito-Alonso M, Keller SR. Genomic Prediction of (Mal)Adaptation Across Current and Future Climatic Landscapes. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-020720-042553] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Signals of local adaptation have been found in many plants and animals, highlighting the heterogeneity in the distribution of adaptive genetic variation throughout species ranges. In the coming decades, global climate change is expected to induce shifts in the selective pressures that shape this adaptive variation. These changes in selective pressures will likely result in varying degrees of local climate maladaptation and spatial reshuffling of the underlying distributions of adaptive alleles. There is a growing interest in using population genomic data to help predict future disruptions to locally adaptive gene-environment associations. One motivation behind such work is to better understand how the effects of changing climate on populations’ short-term fitness could vary spatially across species ranges. Here we review the current use of genomic data to predict the disruption of local adaptation across current and future climates. After assessing goals and motivationsunderlying the approach, we review the main steps and associated statistical methods currently in use and explore our current understanding of the limits and future potential of using genomics to predict climate change (mal)adaptation.
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Affiliation(s)
- Thibaut Capblancq
- Department of Plant Biology, University of Vermont, Burlington, Vermont 05405, USA
| | - Matthew C. Fitzpatrick
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, Maryland 21532, USA
| | - Rachael A. Bay
- Department of Evolution and Ecology, University of California, Davis, California 95616, USA
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Stephen R. Keller
- Department of Plant Biology, University of Vermont, Burlington, Vermont 05405, USA
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7
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Cornwell BH. Gene flow in the anemone
Anthopleura elegantissima
limits signatures of local adaptation across an extensive geographic range. Mol Ecol 2020; 29:2550-2566. [DOI: 10.1111/mec.15506] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 05/22/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023]
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8
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Xiao L, Liu X, Lu W, Chen P, Quan M, Si J, Du Q, Zhang D. Genetic dissection of the gene coexpression network underlying photosynthesis in Populus. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1015-1026. [PMID: 31584236 PMCID: PMC7061883 DOI: 10.1111/pbi.13270] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 09/09/2019] [Accepted: 09/29/2019] [Indexed: 05/06/2023]
Abstract
Photosynthesis is a key reaction that ultimately generates the carbohydrates needed to form woody tissues in trees. However, the genetic regulatory network of protein-encoding genes (PEGs) and regulatory noncoding RNAs (ncRNAs), including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), underlying the photosynthetic pathway is unknown. Here, we integrated data from coexpression analysis, association studies (additive, dominance and epistasis), and expression quantitative trait nucleotide (eQTN) mapping to dissect the causal variants and genetic interaction network underlying photosynthesis in Populus. We initially used 30 PEGs, 6 miRNAs and 12 lncRNAs to construct a coexpression network based on the tissue-specific gene expression profiles of 15 Populus samples. Then, we performed association studies using a natural population of 435 unrelated Populus tomentosa individuals, and identified 72 significant associations (P ≤ 0.001, q ≤ 0.05) with diverse additive and dominance patterns underlying photosynthesis-related traits. Analysis of epistasis and eQTNs revealed that the complex genetic interactions in the coexpression network contribute to phenotypes at various levels. Finally, we demonstrated that heterologously expressing the most highly linked gene (PtoPsbX1) in this network significantly improved photosynthesis in Arabidopsis thaliana, pointing to the functional role of PtoPsbX1 in the photosynthetic pathway. This study provides an integrated strategy for dissecting a complex genetic interaction network, which should accelerate marker-assisted breeding efforts to genetically improve woody plants.
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Affiliation(s)
- Liang Xiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Xin Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Wenjie Lu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Panfei Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Mingyang Quan
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Jingna Si
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Qingzhang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Deqiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
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9
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Köbölkuti ZA, Cseke K, Benke A, Báder M, Borovics A, Németh R. Allelic variation in candidate genes associated with wood properties of cultivated poplars (Populus). Biol Futur 2019; 70:286-294. [PMID: 34554544 DOI: 10.1556/019.70.2019.32] [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: 03/13/2019] [Accepted: 10/26/2019] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Since Populus has veritable value as timber, plywood, pulp, and paper, genomic research should create the sound basis for further breeding toward desirable wood quality attributes. MATERIALS AND METHODS In this study, we addressed the need for a research methodology that initially identifies and then characterize candidate genes encoding enzymes with wood property phenotypic traits, toward the aim of developing a genomics-based breeding technology. RESULTS On 23 different poplar species/hybrid samples, we successfully amplified 55 primers designed on Populus trichocarpa L. Considering the number of polymorphic sites, out of 73,206 bp, 51 SNPs and 31 indel events were found. Non-synonymous single base mutations could be detected in number of 30, 21 out of 164 sequences were the number of minimum recombination events and 41 significant pairwise comparisons between loci could be detected. DISCUSSION AND CONCLUSION Our results provide a roadmap for a future association genetic study between nucleotide diversity and precise evaluation of phenotype.
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Affiliation(s)
- Zoltán Attila Köbölkuti
- Department of Tree Breeding, National Agricultural Research and Innovation Centre, Forest Research Institute, Várkerulet 30/A, Sárvár, 9600, Hungary.
| | - Klára Cseke
- Department of Tree Breeding, National Agricultural Research and Innovation Centre, Forest Research Institute, Várkerulet 30/A, Sárvár, 9600, Hungary
| | - Attila Benke
- Department of Tree Breeding, National Agricultural Research and Innovation Centre, Forest Research Institute, Várkerulet 30/A, Sárvár, 9600, Hungary
| | - Mátyás Báder
- Simonyi Karoly Faculty of Engineering, Wood Sciences and Applied Arts, University of Sopron, Bajcsy Zs. u. 4, 9400, Sopron, Hungary
| | - Attila Borovics
- Department of Tree Breeding, National Agricultural Research and Innovation Centre, Forest Research Institute, Várkerulet 30/A, Sárvár, 9600, Hungary
| | - Róbert Németh
- Simonyi Karoly Faculty of Engineering, Wood Sciences and Applied Arts, University of Sopron, Bajcsy Zs. u. 4, 9400, Sopron, Hungary
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10
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A comprehensive genomic scan reveals gene dosage balance impacts on quantitative traits in Populus trees. Proc Natl Acad Sci U S A 2019; 116:13690-13699. [PMID: 31213538 DOI: 10.1073/pnas.1903229116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Gene dosage variation and the associated changes in gene expression influence a wide variety of traits, ranging from cancer in humans to yield in plants. It is also expected to affect important traits of ecological and agronomic importance in forest trees, but this variation has not been systematically characterized or exploited. Here we performed a comprehensive scan of the Populus genome for dosage-sensitive loci affecting quantitative trait variation for spring and fall phenology and biomass production. The study population was a large collection of clonally propagated F1 hybrid lines of Populus that saturate the genome 10-fold with deletions and insertions (indels) of known sizes and positions. As a group, the phenotypic means of the indel lines consistently differed from control nonindel lines, with an overall negative effect of both insertions and deletions on all biomass-related traits but more diverse effects and an overall wider phenotypic distribution of the indel lines for the phenology-related traits. We also investigated the correlation between gene dosage at specific chromosomal locations and phenotype, to identify dosage quantitative trait loci (dQTL). Such dQTL were detected for most phenotypes examined, but stronger effect dQTL were identified for the phenology-related traits than for the biomass traits. Our genome-wide screen for dosage sensitivity in a higher eukaryote demonstrates the importance of global genomic balance and the impact of dosage on life history traits.
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11
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Thongkumkoon P, Chomdej S, Kampuansai J, Pradit W, Waikham P, Elliott S, Chairuangsri S, Shannon DP, Wangpakapattanawong P, Liu A. Genetic assessment of three Fagaceae species in forest restoration trials. PeerJ 2019; 7:e6958. [PMID: 31179177 PMCID: PMC6544010 DOI: 10.7717/peerj.6958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/14/2019] [Indexed: 11/20/2022] Open
Abstract
Restoring isolated patches of forest ecosystems in degraded landscapes could potentially lead to genetic loss and inbreeding. Therefore, this study determined the occurrence of genetic diversity among the tree species Castanopsis tribuloides, C. calathiformis, and Lithocarpus polystachyus all of which were proven previously to be effective native tree species in the restoration of upland evergreen forests in northern Thailand when using the seed sample collection method. We tested our hypothesis as to whether the genetic diversity of a plant population that had been planted from the seeds of 4–6 adult trees would be lower and whether incidences of fixation index (Fis) would be higher among the second generation seedlings of these three Fagaceae species in isolated forest restoration trial plots. Microsatellite primers were selected from the entire genome sequence of C. tribuloides and the genetic sequences of C. tribuloides, L. polystachyus, and C. calathiformis were analyzed. Our results indicated a high degree of genetic diversity (He) in C. tribuloides (0.736) and C. calathiformis (0.481); however, a low level of genetic diversity was observed in L. polystachyus (0.281) within the restored forest. The fixation index for the second generation of L. polystachyus and C. calathiformis in the restored forest showed evidence of inbreeding. These results imply the efficiency of the seed sample collection method and verify that it does not reduce the level of genetic diversity in C. tribuloides and C. calathiformis. However, it may result in incidences of an inbreeding phenomena, suggesting the need to increase the number of adult trees used at the seed collection stage.
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Affiliation(s)
- Patcharawadee Thongkumkoon
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Siriwadee Chomdej
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Jatupol Kampuansai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Waranee Pradit
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Pimubon Waikham
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Stephen Elliott
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Forest Restoration Research Unit, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Sutthathorn Chairuangsri
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Forest Restoration Research Unit, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Dia Panitnard Shannon
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Forest Restoration Research Unit, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Prasit Wangpakapattanawong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Aizhong Liu
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China (Ministry of Education), Southwest Forestry University, Kunming, China
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12
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Warschefsky EJ, von Wettberg EJB. Population genomic analysis of mango (Mangifera indica) suggests a complex history of domestication. THE NEW PHYTOLOGIST 2019; 222:2023-2037. [PMID: 30730057 DOI: 10.1111/nph.15731] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 01/21/2019] [Indexed: 05/22/2023]
Abstract
Humans have domesticated diverse species from across the plant kingdom, yet much of our foundational knowledge of domestication has come from studies investigating relatively few of the most important annual food crops. Here, we examine the impacts of domestication on genetic diversity in a tropical perennial fruit species, mango (Mangifera indica). We used restriction site associated DNA sequencing to generate genomic single nucleotide polymorphism (SNP) data from 106 mango cultivars from seven geographical regions along with 52 samples of closely related species and unidentified cultivars to identify centers of mango genetic diversity and examine how post-domestication dispersal shaped the geographical distribution of diversity. We identify two gene pools of cultivated mango, representing Indian and Southeast Asian germplasm. We found no significant genetic bottleneck associated with the introduction of mango into new regions of the world. By contrast, we show that mango populations in introduced regions have elevated levels of diversity. Our results suggest that mango has a more complex history of domestication than previously supposed, perhaps including multiple domestication events, hybridization and regional selection. Our work has direct implications for mango breeding and genebank management, and also builds on recent efforts to understand how woody perennial crops respond to domestication.
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Affiliation(s)
- Emily J Warschefsky
- Biological Sciences, Florida International University, 11200 SW 8th St., Miami, FL, 33199, USA
| | - Eric J B von Wettberg
- Biological Sciences, Florida International University, 11200 SW 8th St., Miami, FL, 33199, USA
- Plant and Soil Science, The University of Vermont, 63 Carrigan Drive, Burlington, VT, USA
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13
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Suarez-Gonzalez A, Hefer CA, Lexer C, Douglas CJ, Cronk QCB. Introgression from Populus balsamifera underlies adaptively significant variation and range boundaries in P. trichocarpa. THE NEW PHYTOLOGIST 2018; 217:416-427. [PMID: 29124769 DOI: 10.1111/nph.14779] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 08/03/2017] [Indexed: 06/07/2023]
Abstract
Introgression can be an important source of adaptive phenotypes, although conversely it can have deleterious effects. Evidence for adaptive introgression is accumulating but information on the genetic architecture of introgressed traits lags behind. Here we determine trait architecture in Populus trichocarpa under introgression from P. balsamifera using admixture mapping and phenotypic analyses. Our results reveal that admixture is a key driver of clinal adaptation and suggest that the northern range extension of P. trichocarpa depends, at least in part, on introgression from P. balsamifera. However, admixture with P. balsamifera can lead to potentially maladaptive early phenology, and a reduction in growth and disease resistance in P. trichocarpa. Strikingly, an introgressed chromosome 9 haplotype block from P. balsamifera restores the late phenology and high growth parental phenotype in admixed P. trichocarpa. This epistatic restorer block may be strongly advantageous in maximizing carbon assimilation and disease resistance in the southernmost populations where admixture has been detected. We also confirm a previously demonstrated case of adaptive introgression in chromosome 15 and show that introgression generates a transgressive chlorophyll-content phenotype. We provide strong support that introgression provides a reservoir of genetic variation associated with adaptive characters that allows improved survival in new environments.
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Affiliation(s)
| | - Charles A Hefer
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
- Biotechnology Platform, Agricultural Research Council, Private Bag X05, Onderstepoort, 0110, South Africa
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, 1030, Austria
| | - Carl J Douglas
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Quentin C B Cronk
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
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14
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Genetic Diversity and Its Spatial Distribution in Self-Regenerating Norway Spruce and Scots Pine Stands. FORESTS 2017. [DOI: 10.3390/f8120470] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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De La Torre AR, Li Z, Van de Peer Y, Ingvarsson PK. Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants. Mol Biol Evol 2017; 34:1363-1377. [PMID: 28333233 PMCID: PMC5435085 DOI: 10.1093/molbev/msx069] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The majority of variation in rates of molecular evolution among seed plants remains both unexplored and unexplained. Although some attention has been given to flowering plants, reports of molecular evolutionary rates for their sister plant clade (gymnosperms) are scarce, and to our knowledge differences in molecular evolution among seed plant clades have never been tested in a phylogenetic framework. Angiosperms and gymnosperms differ in a number of features, of which contrasting reproductive biology, life spans, and population sizes are the most prominent. The highly conserved morphology of gymnosperms evidenced by similarity of extant species to fossil records and the high levels of macrosynteny at the genomic level have led scientists to believe that gymnosperms are slow-evolving plants, although some studies have offered contradictory results. Here, we used 31,968 nucleotide sites obtained from orthologous genes across a wide taxonomic sampling that includes representatives of most conifers, cycads, ginkgo, and many angiosperms with a sequenced genome. Our results suggest that angiosperms and gymnosperms differ considerably in their rates of molecular evolution per unit time, with gymnosperm rates being, on average, seven times lower than angiosperm species. Longer generation times and larger genome sizes are some of the factors explaining the slow rates of molecular evolution found in gymnosperms. In contrast to their slow rates of molecular evolution, gymnosperms possess higher substitution rate ratios than angiosperm taxa. Finally, our study suggests stronger and more efficient purifying and diversifying selection in gymnosperm than in angiosperm species, probably in relation to larger effective population sizes.
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Affiliation(s)
- Amanda R De La Torre
- Department of Plant Sciences, University of California-Davis, Davis, CA.,Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - Zhen Li
- Department of Plant Systems Biology, VIB, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, South Africa
| | - Pär K Ingvarsson
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden.,Department of Plant Biology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
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16
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Lind BM, Friedline CJ, Wegrzyn JL, Maloney PE, Vogler DR, Neale DB, Eckert AJ. Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin, USA. Mol Ecol 2017; 26:3168-3185. [PMID: 28316116 DOI: 10.1111/mec.14106] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 03/03/2017] [Accepted: 03/06/2017] [Indexed: 12/18/2022]
Abstract
Patterns of local adaptation at fine spatial scales are central to understanding how evolution proceeds, and are essential to the effective management of economically and ecologically important forest tree species. Here, we employ single and multilocus analyses of genetic data (n = 116 231 SNPs) to describe signatures of fine-scale adaptation within eight whitebark pine (Pinus albicaulis Engelm.) populations across the local extent of the environmentally heterogeneous Lake Tahoe Basin, USA. We show that despite highly shared genetic variation (FST = 0.0069), there is strong evidence for adaptation to the rain shadow experienced across the eastern Sierra Nevada. Specifically, we build upon evidence from a common garden study and find that allele frequencies of loci associated with four phenotypes (mean = 236 SNPs), 18 environmental variables (mean = 99 SNPs), and those detected through genetic differentiation (n = 110 SNPs) exhibit significantly higher signals of selection (covariance of allele frequencies) than could be expected to arise, given the data. We also provide evidence that this covariance tracks environmental measures related to soil water availability through subtle allele frequency shifts across populations. Our results replicate empirical support for theoretical expectations of local adaptation for populations exhibiting strong gene flow and high selective pressures and suggest that ongoing adaptation of many P. albicaulis populations within the Lake Tahoe Basin will not be constrained by the lack of genetic variation. Even so, some populations exhibit low levels of heritability for the traits presumed to be related to fitness. These instances could be used to prioritize management to maintain adaptive potential. Overall, we suggest that established practices regarding whitebark pine conservation be maintained, with the additional context of fine-scale adaptation.
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Affiliation(s)
- Brandon M Lind
- Integrative Life Sciences Program, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | | | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Patricia E Maloney
- Department of Plant Pathology and Tahoe Environmental Research Center, University of California, Davis, CA, 95616, USA
| | - Detlev R Vogler
- USDA, Forest Service, Pacific Southwest Research Station, Institute of Forest Genetics, 2480 Carson Road, Placerville, CA, 95667, USA
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
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Ingvarsson PK, Hvidsten TR, Street NR. Towards integration of population and comparative genomics in forest trees. THE NEW PHYTOLOGIST 2016; 212:338-44. [PMID: 27575589 DOI: 10.1111/nph.14153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/27/2016] [Indexed: 05/08/2023]
Abstract
Contents 338 I. 338 II. 339 III. 340 IV. 342 343 References 343 SUMMARY: The past decade saw the initiation of an ongoing revolution in sequencing technologies that is transforming all fields of biology. This has been driven by the advent and widespread availability of high-throughput, massively parallel short-read sequencing (MPS) platforms. These technologies have enabled previously unimaginable studies, including draft assemblies of the massive genomes of coniferous species and population-scale resequencing. Transcriptomics studies have likewise been transformed, with RNA-sequencing enabling studies in nonmodel organisms, the discovery of previously unannotated genes (novel transcripts), entirely new classes of RNAs and previously unknown regulatory mechanisms. Here we touch upon current developments in the areas of genome assembly, comparative regulomics and population genetics as they relate to studies of forest tree species.
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Affiliation(s)
- Pär K Ingvarsson
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, 901 87, Umeå, Sweden
| | - Torgeir R Hvidsten
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87, Umeå, Sweden
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87, Umeå, Sweden.
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18
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Akagi T, Hanada T, Yaegaki H, Gradziel TM, Tao R. Genome-wide view of genetic diversity reveals paths of selection and cultivar differentiation in peach domestication. DNA Res 2016; 23:271-82. [PMID: 27085183 PMCID: PMC4909313 DOI: 10.1093/dnares/dsw014] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/02/2016] [Indexed: 01/19/2023] Open
Abstract
Domestication and cultivar differentiation are requisite processes for establishing cultivated crops. These processes inherently involve substantial changes in population structure, including those from artificial selection of key genes. In this study, accessions of peach (Prunus persica) and its wild relatives were analysed genome-wide to identify changes in genetic structures and gene selections associated with their differentiation. Analysis of genome-wide informative single-nucleotide polymorphism loci revealed distinct changes in genetic structures and delineations among domesticated peach and its wild relatives and among peach landraces and modern fruit (F) and modern ornamental (O-A) cultivars. Indications of distinct changes in linkage disequilibrium extension/decay and of strong population bottlenecks or inbreeding were identified. Site frequency spectrum- and extended haplotype homozygosity-based evaluation of genome-wide genetic diversities supported selective sweeps distinguishing the domesticated peach from its wild relatives and each F/O-A cluster from the landrace clusters. The regions with strong selective sweeps harboured promising candidates for genes subjected to selection. Further sequence-based evaluation further defined the candidates and revealed their characteristics. All results suggest opportunities for identifying critical genes associated with each differentiation by analysing genome-wide genetic diversity in currently established populations. This approach obviates the special development of genetic populations, which is particularly difficult for long-lived tree crops.
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Affiliation(s)
- Takashi Akagi
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kita-shirakawa, Oiwake-cho, Kyoto 606-8502, Japan
| | - Toshio Hanada
- Apple Research Division, NARO Institute of Fruit Tree Science, Morioka 020-0123, Japan
| | - Hideaki Yaegaki
- Breeding and Pest Management Division, NARO Institute, Tsukuba, Ibaragi 305-8605, Japan
| | - Thomas M Gradziel
- Department of Plant Sciences, University of California Davis, CA 95616, USA
| | - Ryutaro Tao
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kita-shirakawa, Oiwake-cho, Kyoto 606-8502, Japan
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19
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Brunet J, Zalapa J, Guries R. Conservation of genetic diversity in slippery elm (Ulmus rubra) in Wisconsin despite the devastating impact of Dutch elm disease. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0838-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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20
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Breeding Systems, Mating Systems, and Genomics of Gender Determination in Angiosperm Trees. COMPARATIVE AND EVOLUTIONARY GENOMICS OF ANGIOSPERM TREES 2016. [DOI: 10.1007/7397_2016_21] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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21
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Mariette S, Wong Jun Tai F, Roch G, Barre A, Chague A, Decroocq S, Groppi A, Laizet Y, Lambert P, Tricon D, Nikolski M, Audergon JM, Abbott AG, Decroocq V. Genome-wide association links candidate genes to resistance to Plum Pox Virus in apricot (Prunus armeniaca). THE NEW PHYTOLOGIST 2016; 209:773-84. [PMID: 26356603 DOI: 10.1111/nph.13627] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 07/26/2015] [Indexed: 05/06/2023]
Abstract
In fruit tree species, many important traits have been characterized genetically by using single-family descent mapping in progenies segregating for the traits. However, most mapped loci have not been sufficiently resolved to the individual genes due to insufficient progeny sizes for high resolution mapping and the previous lack of whole-genome sequence resources of the study species. To address this problem for Plum Pox Virus (PPV) candidate resistance gene identification in Prunus species, we implemented a genome-wide association (GWA) approach in apricot. This study exploited the broad genetic diversity of the apricot (Prunus armeniaca) germplasm containing resistance to PPV, next-generation sequence-based genotyping, and the high-quality peach (Prunus persica) genome reference sequence for single nucleotide polymorphism (SNP) identification. The results of this GWA study validated previously reported PPV resistance quantitative trait loci (QTL) intervals, highlighted other potential resistance loci, and resolved each to a limited set of candidate genes for further study. This work substantiates the association genetics approach for resolution of QTL to candidate genes in apricot and suggests that this approach could simplify identification of other candidate genes for other marked trait intervals in this germplasm.
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Affiliation(s)
- Stéphanie Mariette
- UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Université de Bordeaux, CS20032, F-33882, Villenave d'Ornon, France
- UMR 1202 BIOGECO, INRA, F-33610, Cestas, France
- UMR 1202 BIOGECO, Université de Bordeaux, F-33400, Talence, France
| | - Fabienne Wong Jun Tai
- UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Université de Bordeaux, CS20032, F-33882, Villenave d'Ornon, France
- Bordeaux Bioinformatics Center CBiB, Université de Bordeaux, 351 cours de la Libération, F-33405, Talence, France
| | - Guillaume Roch
- UR1052 GAFL, Domaine Saint Maurice, INRA, CS60094, F-84143, Montfavet, France
- CEP INNOVATION, INRA, 23 rue Jean Baldassini, F-69364, LYON Cedex 7, France
| | - Aurélien Barre
- Bordeaux Bioinformatics Center CBiB, Université de Bordeaux, 351 cours de la Libération, F-33405, Talence, France
| | - Aurélie Chague
- UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Université de Bordeaux, CS20032, F-33882, Villenave d'Ornon, France
| | - Stéphane Decroocq
- UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Université de Bordeaux, CS20032, F-33882, Villenave d'Ornon, France
| | - Alexis Groppi
- Bordeaux Bioinformatics Center CBiB, Université de Bordeaux, 351 cours de la Libération, F-33405, Talence, France
| | - Yec'han Laizet
- UMR 1202 BIOGECO, INRA, F-33610, Cestas, France
- UMR 1202 BIOGECO, Université de Bordeaux, F-33400, Talence, France
| | - Patrick Lambert
- UR1052 GAFL, Domaine Saint Maurice, INRA, CS60094, F-84143, Montfavet, France
| | - David Tricon
- UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Université de Bordeaux, CS20032, F-33882, Villenave d'Ornon, France
| | - Macha Nikolski
- Bordeaux Bioinformatics Center CBiB, Université de Bordeaux, 351 cours de la Libération, F-33405, Talence, France
| | - Jean-Marc Audergon
- UR1052 GAFL, Domaine Saint Maurice, INRA, CS60094, F-84143, Montfavet, France
| | - Albert G Abbott
- UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Université de Bordeaux, CS20032, F-33882, Villenave d'Ornon, France
- University of Kentucky, 106 T. P. Cooper Hall, Lexington, KY, 40546-0073, USA
| | - Véronique Decroocq
- UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Université de Bordeaux, CS20032, F-33882, Villenave d'Ornon, France
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22
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Du S, Wang Z, Ingvarsson PK, Wang D, Wang J, Wu Z, Tembrock LR, Zhang J. Multilocus analysis of nucleotide variation and speciation in three closely relatedPopulus(Salicaceae) species. Mol Ecol 2015; 24:4994-5005. [DOI: 10.1111/mec.13368] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 08/31/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Shuhui Du
- State Key Laboratory of Tree Genetics and Breeding; Key Laboratory of Silviculture of the State Forestry Administration; Research Institute of Forestry; Chinese Academy of Forestry; Beijing 100091 China
- College of Forestry; Shandong Agriculture University; Taian Shandong Province 271000 China
| | - Zhaoshan Wang
- State Key Laboratory of Tree Genetics and Breeding; Key Laboratory of Silviculture of the State Forestry Administration; Research Institute of Forestry; Chinese Academy of Forestry; Beijing 100091 China
- Collaborative Innovation Center of Sustainable Forestry in Southern China; Nanjing Forestry University; Nanjing Jiangsu Province 210000 China
| | - Pär K. Ingvarsson
- Department of Ecology and Environmental Science; Umeå Plant Science Centre; Umeå University; Umeå 90187 Sweden
| | - Dongsheng Wang
- State Key Laboratory of Tree Genetics and Breeding; Key Laboratory of Silviculture of the State Forestry Administration; Research Institute of Forestry; Chinese Academy of Forestry; Beijing 100091 China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding; Key Laboratory of Silviculture of the State Forestry Administration; Research Institute of Forestry; Chinese Academy of Forestry; Beijing 100091 China
| | - Zhiqiang Wu
- Department of Biology; Colorado State University; Fort Collins CO 80523 USA
| | - Luke R. Tembrock
- Department of Biology; Colorado State University; Fort Collins CO 80523 USA
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding; Key Laboratory of Silviculture of the State Forestry Administration; Research Institute of Forestry; Chinese Academy of Forestry; Beijing 100091 China
- Collaborative Innovation Center of Sustainable Forestry in Southern China; Nanjing Forestry University; Nanjing Jiangsu Province 210000 China
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DeWoody J, Trewin H, Taylor G. Genetic and morphological differentiation in Populus nigra L.: isolation by colonization or isolation by adaptation? Mol Ecol 2015; 24:2641-55. [PMID: 25857321 PMCID: PMC4692097 DOI: 10.1111/mec.13192] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 03/26/2015] [Accepted: 04/02/2015] [Indexed: 01/19/2023]
Abstract
Identifying processes underlying the genetic and morphological differences among populations is a central question of evolutionary biology. Forest trees typically contain high levels of neutral genetic variation, and genetic differences are often correlated with geographic distance between populations [isolation by distance (IBD)] or are due to historic vicariance events [isolation by colonization (IBC)]. In contrast, morphological differences are largely due to local adaptation. Here, we examined genetic (microsatellite) and morphological (from a common garden experiment) variation in Populus nigra L., European black poplar, collected from 13 sites across western Europe and grown in a common garden in Belgium. Significant genetic differentiation was observed, with populations from France displaying greater admixture than the distinct Spanish and central European gene pools, consistent with previously described glacial refugia (IBC). Many quantitative traits displayed a bimodal distribution, approximately corresponding to small-leaf and large-leaf ecotypes. Examination of nine climatic variables revealed the sampling locations to have diverse climates, and although the correlation between morphological and climatic differences was significant, the pattern was not consistent with strict local adaptation. Partial Mantel tests based on multivariate summary statistics identified significant residual correlation in comparisons of small-leaf to large-leaf ecotypes, and within the small-leaf samples, but not within large-leaf ecotypes, indicating that variation within the small-leaf morphotype in particular may be adaptive. Some small-leaf populations experience climates very similar to those in large-leaf sites. We conclude that adaptive differentiation and persistent IBC acted in combination to produce the genetic and morphological patterns observed in P. nigra.
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Affiliation(s)
- Jennifer DeWoody
- Centre for Life Sciences, Unviersity of Southampton, Building 85, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Harriet Trewin
- Centre for Life Sciences, Unviersity of Southampton, Building 85, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Gail Taylor
- Centre for Life Sciences, Unviersity of Southampton, Building 85, Highfield Campus, Southampton, SO17 1BJ, UK
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Mimura M, Mishima M, Lascoux M, Yahara T. Range shift and introgression of the rear and leading populations in two ecologically distinct Rubus species. BMC Evol Biol 2014; 2014:209. [PMID: 25344198 PMCID: PMC4221717 DOI: 10.1186/s12862-014-0209-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 09/23/2014] [Indexed: 11/15/2022] Open
Abstract
Background The margins of a species’ range might be located at the margins of a species’ niche, and in such cases, can be highly vulnerable to climate changes. They, however, may also undergo significant evolutionary changes due to drastic population dynamics in response to climate changes, which may increase the chances of isolation and contact among species. Such species interactions induced by climate changes could then regulate or facilitate further responses to climatic changes. We hypothesized that climate changes lead to species contacts and subsequent genetic exchanges due to differences in population dynamics at the species boundaries. We sampled two closely related Rubus species, one temperate (Rubus palmatus) and the other subtropical (R. grayanus) near their joint species boundaries in southern Japan. Coalescent analysis, based on molecular data and ecological niche modelling during the Last Glacial Maximum (LGM), were used to infer past population dynamics. At the contact zones on Yakushima (Yaku Island), where the two species are parapatrically distributed, we tested hybridization along altitudinal gradients. Results Coalescent analysis suggested that the southernmost populations of R. palmatus predated the LGM (~20,000 ya). Conversely, populations at the current northern limit of R. grayanus diverged relatively recently and likely represent young outposts of a northbound range shift. These population dynamics were partly supported by the ensemble forecasting of six different species distribution models. Both past and ongoing hybridizations were detected near and on Yakushima. Backcrosses and advanced-generation hybrids likely generated the clinal hybrid zones along altitudinal gradients on the island where the two species are currently parapatrically distributed. Conclusions Climate oscillations during the Quaternary Period and the response of a species in range shifts likely led to repeated contacts with the gene pools of ecologically distinct relatives. Such species interactions, induced by climate changes, may bring new genetic material to the marginal populations where species tend to experience more extreme climatic conditions at the margins of the species distribution. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0209-9) contains supplementary material, which is available to authorized users.
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25
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Karam MJ, Lefèvre F, Dagher-Kharrat MB, Pinosio S, Vendramin G. Genomic exploration and molecular marker development in a large and complex conifer genome using RADseq and mRNAseq. Mol Ecol Resour 2014; 15:601-12. [DOI: 10.1111/1755-0998.12329] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 08/30/2014] [Accepted: 09/05/2014] [Indexed: 01/05/2023]
Affiliation(s)
- M.-J. Karam
- INRA; UR 629 Ecologie des Forêts Méditerranéennes; URFM; Avignon France
| | - F. Lefèvre
- INRA; UR 629 Ecologie des Forêts Méditerranéennes; URFM; Avignon France
| | - M. Bou Dagher-Kharrat
- Laboratoire Caractérisation Génomique des Plantes; Département Sciences de la Vie et de la Terre; Faculté des Sciences; Campus Sciences et Technologies; Université Saint-Joseph; Mar Roukos Mkalles Lebanon
| | - S. Pinosio
- Istituto di Genomica Applicata (IGA); Udine Italy
- Institute of Biosciences and Bioresources; National Research Council; Florence Italy
| | - G.G. Vendramin
- Institute of Biosciences and Bioresources; National Research Council; Florence Italy
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Csilléry K, Lalagüe H, Vendramin GG, González-Martínez SC, Fady B, Oddou-Muratorio S. Detecting short spatial scale local adaptation and epistatic selection in climate-related candidate genes in European beech (Fagus sylvatica) populations. Mol Ecol 2014; 23:4696-708. [PMID: 25156570 DOI: 10.1111/mec.12902] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 08/20/2014] [Accepted: 08/22/2014] [Indexed: 01/17/2023]
Abstract
Detecting signatures of selection in tree populations threatened by climate change is currently a major research priority. Here, we investigated the signature of local adaptation over a short spatial scale using 96 European beech (Fagus sylvatica L.) individuals originating from two pairs of populations on the northern and southern slopes of Mont Ventoux (south-eastern France). We performed both single and multilocus analysis of selection based on 53 climate-related candidate genes containing 546 SNPs. FST outlier methods at the SNP level revealed a weak signal of selection, with three marginally significant outliers in the northern populations. At the gene level, considering haplotypes as alleles, two additional marginally significant outliers were detected, one on each slope. To account for the uncertainty of haplotype inference, we averaged the Bayes factors over many possible phase reconstructions. Epistatic selection offers a realistic multilocus model of selection in natural populations. Here, we used a test suggested by Ohta based on the decomposition of the variance of linkage disequilibrium. Overall populations, 0.23% of the SNP pairs (haplotypes) showed evidence of epistatic selection, with nearly 80% of them being within genes. One of the between gene epistatic selection signals arose between an FST outlier and a nonsynonymous mutation in a drought response gene. Additionally, we identified haplotypes containing selectively advantageous allele combinations which were unique to high or low elevations and northern or southern populations. Several haplotypes contained nonsynonymous mutations situated in genes with known functional importance for adaptation to climatic factors.
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Affiliation(s)
- Katalin Csilléry
- UR629, Écologie Forestière Méditerranéenne, INRA, Domaine Saint Paul, Avignon, F-84914, France
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27
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Evolution and biogeography of gymnosperms. Mol Phylogenet Evol 2014; 75:24-40. [DOI: 10.1016/j.ympev.2014.02.005] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 02/06/2014] [Accepted: 02/10/2014] [Indexed: 11/20/2022]
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DeGiorgio M, Syring J, Eckert AJ, Liston A, Cronn R, Neale DB, Rosenberg NA. An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines. BMC Evol Biol 2014; 14:67. [PMID: 24678701 PMCID: PMC4021425 DOI: 10.1186/1471-2148-14-67] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 02/10/2014] [Indexed: 12/26/2022] Open
Abstract
Background As it becomes increasingly possible to obtain DNA sequences of orthologous genes from diverse sets of taxa, species trees are frequently being inferred from multilocus data. However, the behavior of many methods for performing this inference has remained largely unexplored. Some methods have been proven to be consistent given certain evolutionary models, whereas others rely on criteria that, although appropriate for many parameter values, have peculiar zones of the parameter space in which they fail to converge on the correct estimate as data sets increase in size. Results Here, using North American pines, we empirically evaluate the behavior of 24 strategies for species tree inference using three alternative outgroups (72 strategies total). The data consist of 120 individuals sampled in eight ingroup species from subsection Strobus and three outgroup species from subsection Gerardianae, spanning ∼47 kilobases of sequence at 121 loci. Each “strategy” for inferring species trees consists of three features: a species tree construction method, a gene tree inference method, and a choice of outgroup. We use multivariate analysis techniques such as principal components analysis and hierarchical clustering to identify tree characteristics that are robustly observed across strategies, as well as to identify groups of strategies that produce trees with similar features. We find that strategies that construct species trees using only topological information cluster together and that strategies that use additional non-topological information (e.g., branch lengths) also cluster together. Strategies that utilize more than one individual within a species to infer gene trees tend to produce estimates of species trees that contain clades present in trees estimated by other strategies. Strategies that use the minimize-deep-coalescences criterion to construct species trees tend to produce species tree estimates that contain clades that are not present in trees estimated by the Concatenation, RTC, SMRT, STAR, and STEAC methods, and that in general are more balanced than those inferred by these other strategies. Conclusions When constructing a species tree from a multilocus set of sequences, our observations provide a basis for interpreting differences in species tree estimates obtained via different approaches that have a two-stage structure in common, one step for gene tree estimation and a second step for species tree estimation. The methods explored here employ a number of distinct features of the data, and our analysis suggests that recovery of the same results from multiple methods that tend to differ in their patterns of inference can be a valuable tool for obtaining reliable estimates.
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Affiliation(s)
- Michael DeGiorgio
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
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Bradbury D, Smithson A, Krauss SL. Signatures of diversifying selection at EST-SSR loci and association with climate in natural Eucalyptus populations. Mol Ecol 2014; 22:5112-29. [PMID: 24118117 DOI: 10.1111/mec.12463] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 07/03/2013] [Accepted: 07/12/2013] [Indexed: 01/17/2023]
Abstract
Understanding the environmental parameters that drive adaptation among populations is important in predicting how species may respond to global climatic changes and how gene pools might be managed to conserve adaptive genetic diversity. Here, we used Bayesian FST outlier tests and allele-climate association analyses to reveal two Eucalyptus EST-SSR loci as strong candidates for diversifying selection in natural populations of a southwestern Australian forest tree, Eucalyptus gomphocephala (Myrtaceae). The Eucalyptus homolog of a CONSTANS-like gene was an FST outlier, and allelic variation showed significant latitudinal clinal associations with annual and winter solar radiation, potential evaporation, summer precipitation and aridity. A second FST outlier locus, homologous to quinone oxidoreductase, was significantly associated with measures of temperature range, high summer temperature and summer solar radiation, with important implications for predicting the effect of temperature on natural populations in the context of climate change. We complemented these data with investigations into neutral population genetic structure and diversity throughout the species range. This study provides an investigation into selection signatures at gene-homologous EST-SSRs in natural Eucalyptus populations, and contributes to our understanding of the relationship between climate and adaptive genetic variation, informing the conservation of both putatively neutral and adaptive components of genetic diversity.
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Affiliation(s)
- Donna Bradbury
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6005, Australia; Botanic Gardens and Parks Authority, Kings Park and Botanic Garden, Fraser Avenue, West Perth, WA 6009, Australia
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Uchiyama K, Iwata H, Moriguchi Y, Ujino-Ihara T, Ueno S, Taguchi Y, Tsubomura M, Mishima K, Iki T, Watanabe A, Futamura N, Shinohara K, Tsumura Y. Demonstration of genome-wide association studies for identifying markers for wood property and male strobili traits in Cryptomeria japonica. PLoS One 2013; 8:e79866. [PMID: 24260312 PMCID: PMC3833940 DOI: 10.1371/journal.pone.0079866] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 09/26/2013] [Indexed: 12/02/2022] Open
Abstract
Genome-wide association studies (GWAS) are an alternative to bi-parental QTL mapping in long-lived perennials. In the present study, we examined the potential of GWAS in conifers using 367 unrelated plus trees of Cryptomeria japonica D. Don, which is the most widely planted and commercially important tree species in Japan, and tried to detect significant associations between wood property traits and quantity of male strobili on the one hand, and 1,032 single nucleotide polymorphisms (SNPs) assigned to 1,032 genes on the other. Association analysis was performed with the mixed linear model taking into account kinship relationships and subpopulation structure. In total, 6 SNPs were found to have significant associations with the variations in phenotype. These SNPs were not associated with the positions of known genes and QTLs that have been reported to date, thus they may identify novel QTLs. These 6 SNPs were all found in sequences showing similarities with known genes, although further analysis is required to dissect the ways in which they affect wood property traits and abundance of male strobili. These presumptive QTL loci provide opportunities for improvement of C. japonica, based on a marker approach. The results suggest that GWAS has potential for use in future breeding programs in C. japonica.
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Affiliation(s)
- Kentaro Uchiyama
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Hiroyoshi Iwata
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Yoshinari Moriguchi
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Tokuko Ujino-Ihara
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Saneyoshi Ueno
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Yuriko Taguchi
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Miyoko Tsubomura
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Hitachi, Ibaraki, Japan
| | - Kentaro Mishima
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Hitachi, Ibaraki, Japan
| | - Taiichi Iki
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Hitachi, Ibaraki, Japan
| | - Atsushi Watanabe
- Faculty of Agriculture, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Norihiro Futamura
- Department of Molecular and Cell Biology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Kenji Shinohara
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Yoshihiko Tsumura
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
- * E-mail:
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Eckert AJ, Bower AD, Jermstad KD, Wegrzyn JL, Knaus BJ, Syring JV, Neale DB. Multilocus analyses reveal little evidence for lineage-wide adaptive evolution within major clades of soft pines (Pinus subgenus Strobus). Mol Ecol 2013; 22:5635-50. [PMID: 24134614 DOI: 10.1111/mec.12514] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 08/27/2013] [Accepted: 08/29/2013] [Indexed: 12/26/2022]
Abstract
Estimates from molecular data for the fraction of new nonsynonymous mutations that are adaptive vary strongly across plant species. Much of this variation is due to differences in life history strategies as they influence the effective population size (Ne ). Ample variation for these estimates, however, remains even when comparisons are made across species with similar values of Ne . An open question thus remains as to why the large disparity for estimates of adaptive evolution exists among plant species. Here, we have estimated the distribution of deleterious fitness effects (DFE) and the fraction of adaptive nonsynonymous substitutions (α) for 11 species of soft pines (subgenus Strobus) using DNA sequence data from 167 orthologous nuclear gene fragments. Most newly arising nonsynonymous mutations were inferred to be so strongly deleterious that they would rarely become fixed. Little evidence for long-term adaptive evolution was detected, as all 11 estimates for α were not significantly different from zero. Nucleotide diversity at synonymous sites, moreover, was strongly correlated with attributes of the DFE across species, thus illustrating a strong consistency with the expectations from the Nearly Neutral Theory of molecular evolution. Application of these patterns to genome-wide expectations for these species, however, was difficult as the loci chosen for the analysis were a biased set of conserved loci, which greatly influenced the estimates of the DFE and α. This implies that genome-wide parameter estimates will need truly genome-wide data, so that many of the existing patterns documented previously for forest trees (e.g. little evidence for signature of selection) may need revision.
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Affiliation(s)
- Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
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The evolutionary genetics of the genes underlying phenotypic associations for loblolly pine (Pinus taeda, Pinaceae). Genetics 2013; 195:1353-72. [PMID: 24121773 DOI: 10.1534/genetics.113.157198] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
A primary goal of evolutionary genetics is to discover and explain the genetic basis of fitness-related traits and how this genetic basis evolves within natural populations. Unprecedented technological advances have fueled the discovery of genetic variants associated with ecologically relevant phenotypes in many different life forms, as well as the ability to scan genomes for deviations from selectively neutral models of evolution. Theoretically, the degree of overlap between lists of genomic regions identified using each approach is related to the genetic architecture of fitness-related traits and the strength and type of natural selection molding variation at these traits within natural populations. Here we address for the first time in a plant the degree of overlap between these lists, using patterns of nucleotide diversity and divergence for >7000 unique amplicons described from the extensive expressed sequence tag libraries generated for loblolly pine (Pinus taeda L.) in combination with the >1000 published genetic associations. We show that loci associated with phenotypic traits are distinct with regard to neutral expectations. Phenotypes measured at the whole plant level (e.g., disease resistance) exhibit an approximately twofold increase in the proportion of adaptive nonsynonymous substitutions over the genome-wide average. As expected for polygenic traits, these signals were apparent only when loci were considered at the level of functional sets. The ramifications of this result are discussed in light of the continued efforts to dissect the genetic basis of quantitative traits.
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Palle SR, Seeve CM, Eckert AJ, Wegrzyn JL, Neale DB, Loopstra CA. Association of loblolly pine xylem development gene expression with single-nucleotide polymorphisms. TREE PHYSIOLOGY 2013; 33:763-74. [PMID: 23933831 DOI: 10.1093/treephys/tpt054] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Variation in the expression of genes with putative roles in wood development was associated with single-nucleotide polymorphisms (SNPs) using a population of loblolly pine (Pinus taeda L.) that included individuals from much of the native range. Association studies were performed using 3938 SNPs and expression data obtained using quantitative real-time polymerase chain reaction (PCR) (qRT-PCR) for 106 xylem development genes in 400 clonally replicated loblolly pine individuals. A general linear model (GLM) approach, which takes the underlying population structure into consideration, was used to discover significant associations. After adjustment for multiple testing using a false discovery rate correction, 88 statistically significant associations (Q<0.05) were observed for 80 SNPs with the expression data of 33 xylem development genes. Thirty SNPs caused nonsynonymous mutations, 18 resulted in synonymous mutations, 11 were in 3' untranslated regions (UTRs), 1 was in a 5' UTR and 20 were in introns. Using AraNet, we found that Arabidopsis genes with high similarity to the loblolly pine genes involved in 21 of the 88 statistically significant associations are connected in functional gene networks. Comparisons of gene expression values revealed that in most cases the average expression in plants homozygous for the rare SNP allele was lower than that of plants that were heterozygous or homozygous for the abundant allele. Although there are association studies of SNPs and expression profiles for humans, Arabidopsis and white spruce, to the best of our knowledge, this is the first example of such an association genetic study in pines. Functional validation of these associations will lead to a deeper understanding of the molecular basis of phenotypic differences in wood development among individuals in conifer populations.
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Affiliation(s)
- Sreenath R Palle
- Department of Ecosystem Science and Management, Molecular and Environmental Plant Sciences, Texas A&M University, TAMU 2138, College Station, TX 77843, USA
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Alberto FJ, Aitken SN, Alía R, González-Martínez SC, Hänninen H, Kremer A, Lefèvre F, Lenormand T, Yeaman S, Whetten R, Savolainen O. Potential for evolutionary responses to climate change - evidence from tree populations. GLOBAL CHANGE BIOLOGY 2013; 19:1645-61. [PMID: 23505261 PMCID: PMC3664019 DOI: 10.1111/gcb.12181] [Citation(s) in RCA: 373] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 02/01/2013] [Accepted: 02/03/2013] [Indexed: 05/18/2023]
Abstract
Evolutionary responses are required for tree populations to be able to track climate change. Results of 250 years of common garden experiments show that most forest trees have evolved local adaptation, as evidenced by the adaptive differentiation of populations in quantitative traits, reflecting environmental conditions of population origins. On the basis of the patterns of quantitative variation for 19 adaptation-related traits studied in 59 tree species (mostly temperate and boreal species from the Northern hemisphere), we found that genetic differentiation between populations and clinal variation along environmental gradients were very common (respectively, 90% and 78% of cases). Thus, responding to climate change will likely require that the quantitative traits of populations again match their environments. We examine what kind of information is needed for evaluating the potential to respond, and what information is already available. We review the genetic models related to selection responses, and what is known currently about the genetic basis of the traits. We address special problems to be found at the range margins, and highlight the need for more modeling to understand specific issues at southern and northern margins. We need new common garden experiments for less known species. For extensively studied species, new experiments are needed outside the current ranges. Improving genomic information will allow better prediction of responses. Competitive and other interactions within species and interactions between species deserve more consideration. Despite the long generation times, the strong background in quantitative genetics and growing genomic resources make forest trees useful species for climate change research. The greatest adaptive response is expected when populations are large, have high genetic variability, selection is strong, and there is ecological opportunity for establishment of better adapted genotypes.
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Affiliation(s)
- Florian J Alberto
- Department of Biology and Biocenter Oulu, University of OuluFIN-90014, Oulu, Finland
- UMR1202 Biodiversité Gènes et Communautés, INRAF-33610, Cestas, France
- UMR1202 Biodiversité Gènes et Communautés, Université de BordeauxF-33410, Talence, France
| | - Sally N Aitken
- Department of Forest and Conservation Sciences and Centre for Forest Conservation Genetics, University of British ColumbiaVancouver, BC V6T 1Z4, Canada
| | - Ricardo Alía
- Department of Forest Ecology and Genetics, INIA - Forest Research CentreE-28040, Madrid, Spain
| | | | - Heikki Hänninen
- Department of Biosciences, University of HelsinkiFIN-00014, Helsinki, Finland
| | - Antoine Kremer
- UMR1202 Biodiversité Gènes et Communautés, INRAF-33610, Cestas, France
- UMR1202 Biodiversité Gènes et Communautés, Université de BordeauxF-33410, Talence, France
| | - François Lefèvre
- URFM, UR629 Ecologie des Forêts Méditerranéennes, INRAF-84914, Avignon, France
| | - Thomas Lenormand
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de MontpellierUMR 5175, F-34293, Montpellier, France
| | - Sam Yeaman
- Department of Forest and Conservation Sciences and Centre for Forest Conservation Genetics, University of British ColumbiaVancouver, BC V6T 1Z4, Canada
- Institute of Biology, Université de NeuchâtelCH-2000, Neuchâtel, Switzerland
| | - Ross Whetten
- Department of Forestry & Environmental Resources, NC State UniversityRaleigh, NC, 27695-8008, USA
| | - Outi Savolainen
- Department of Biology and Biocenter Oulu, University of OuluFIN-90014, Oulu, Finland
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Cornille A, Giraud T, Bellard C, Tellier A, Le Cam B, Smulders MJM, Kleinschmit J, Roldan-Ruiz I, Gladieux P. Postglacial recolonization history of the European crabapple (Malus sylvestrisMill.), a wild contributor to the domesticated apple. Mol Ecol 2013; 22:2249-63. [DOI: 10.1111/mec.12231] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 12/11/2012] [Accepted: 12/13/2012] [Indexed: 11/27/2022]
Affiliation(s)
- A. Cornille
- CNRS; Laboratoire Ecologie Systématique et Evolution; UMR8079; Bâtiment 360 91405 Orsay France
- University of Paris Sud; 91405 Orsay France
- AgroParisTech; 91405 Orsay France
| | - T. Giraud
- CNRS; Laboratoire Ecologie Systématique et Evolution; UMR8079; Bâtiment 360 91405 Orsay France
- University of Paris Sud; 91405 Orsay France
- AgroParisTech; 91405 Orsay France
| | - C. Bellard
- CNRS; Laboratoire Ecologie Systématique et Evolution; UMR8079; Bâtiment 360 91405 Orsay France
- University of Paris Sud; 91405 Orsay France
- AgroParisTech; 91405 Orsay France
| | - A. Tellier
- Section of Population Genetics; Center of Life and Food Sciences Weihenstephan; Technische Universität München; 85354 Freising Deutschland
| | - B. Le Cam
- INRA; IRHS; PRES UNAM; SFR QUASAV; Rue G. Morel F-49071 Beaucouzé France
| | - M. J. M. Smulders
- Plant Research International; Wageningen UR Plant Breeding; PO Box 16 6700 AA Wageningen The Netherlands
| | - J. Kleinschmit
- Department of Forest Genetic Resources; Northwest German Forest Research Institute; Professor-Oelkers Str. 6, 34346 Hann. Münden Germany
| | - I. Roldan-Ruiz
- ILVO; Plant-Growth and Development; Caritasstraat 21 9090 Melle Belgium
| | - P. Gladieux
- CNRS; Laboratoire Ecologie Systématique et Evolution; UMR8079; Bâtiment 360 91405 Orsay France
- University of Paris Sud; 91405 Orsay France
- AgroParisTech; 91405 Orsay France
- Department of Plant and Microbial Biology; University of California; Berkeley CA 94720-3102 USA
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Mosca E, Eckert AJ, Liechty JD, Wegrzyn JL, La Porta N, Vendramin GG, Neale DB. Contrasting patterns of nucleotide diversity for four conifers of Alpine European forests. Evol Appl 2012; 5:762-75. [PMID: 23144662 PMCID: PMC3492901 DOI: 10.1111/j.1752-4571.2012.00256.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 02/11/2012] [Indexed: 11/29/2022] Open
Abstract
A candidate gene approach was used to identify levels of nucleotide diversity and to identify genes departing from neutral expectations in coniferous species of the Alpine European forest. Twelve samples were collected from four species that dominate montane and subalpine forests throughout Europe: Abies alba Mill, Larix decidua Mill, Pinus cembra L., and Pinus mugo Turra. A total of 800 genes, originally resequenced in Pinus taeda L., were resequenced across 12 independent trees for each of the four species. Genes were assigned to two categories, candidate and control, defined through homology-based searches to Arabidopsis. Estimates of nucleotide diversity per site varied greatly between polymorphic candidate genes (range: 0.0004–0.1295) and among species (range: 0.0024–0.0082), but were within the previously established ranges for conifers. Tests of neutrality using stringent significance thresholds, performed under the standard neutral model, revealed one to seven outlier loci for each species. Some of these outliers encode proteins that are involved with plant stress responses and form the basis for further evolutionary enquiries.
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Affiliation(s)
- Elena Mosca
- Department of Plant Sciences, University of California at Davis Davis, CA, USA ; IASMA Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige Italy
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Slavov GT, DiFazio SP, Martin J, Schackwitz W, Muchero W, Rodgers-Melnick E, Lipphardt MF, Pennacchio CP, Hellsten U, Pennacchio LA, Gunter LE, Ranjan P, Vining K, Pomraning KR, Wilhelm LJ, Pellegrini M, Mockler TC, Freitag M, Geraldes A, El-Kassaby YA, Mansfield SD, Cronk QCB, Douglas CJ, Strauss SH, Rokhsar D, Tuskan GA. Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. THE NEW PHYTOLOGIST 2012; 196:713-725. [PMID: 22861491 DOI: 10.1111/j.1469-8137.2012.04258.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
• Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. For example, the detection of reliable phenotype-genotype associations and molecular signatures of selection requires a detailed knowledge about genome-wide patterns of allele frequency variation, linkage disequilibrium and recombination. • We resequenced 16 genomes of the model tree Populus trichocarpa and genotyped 120 trees from 10 subpopulations using 29,213 single-nucleotide polymorphisms. • Significant geographic differentiation was present at multiple spatial scales, and range-wide latitudinal allele frequency gradients were strikingly common across the genome. The decay of linkage disequilibrium with physical distance was slower than expected from previous studies in Populus, with r(2) dropping below 0.2 within 3-6 kb. Consistent with this, estimates of recent effective population size from linkage disequilibrium (N(e) ≈ 4000-6000) were remarkably low relative to the large census sizes of P. trichocarpa stands. Fine-scale rates of recombination varied widely across the genome, but were largely predictable on the basis of DNA sequence and methylation features. • Our results suggest that genetic drift has played a significant role in the recent evolutionary history of P. trichocarpa. Most importantly, the extensive linkage disequilibrium detected suggests that genome-wide association studies and genomic selection in undomesticated populations may be more feasible in Populus than previously assumed.
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Affiliation(s)
- Gancho T Slavov
- Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA
| | - Joel Martin
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Wendy Schackwitz
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Wellington Muchero
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Eli Rodgers-Melnick
- Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA
| | - Mindie F Lipphardt
- Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA
| | | | - Uffe Hellsten
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Len A Pennacchio
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Lee E Gunter
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Priya Ranjan
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Kelly Vining
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331-5752, USA
| | - Kyle R Pomraning
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331-7305, USA
| | | | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095-1606, USA
| | - Todd C Mockler
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331-7305, USA
| | - Armando Geraldes
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Yousry A El-Kassaby
- Department of Forest Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Shawn D Mansfield
- Department of Wood Science, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Quentin C B Cronk
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Carl J Douglas
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331-5752, USA
| | - Dan Rokhsar
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Gerald A Tuskan
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Tsumura Y, Uchiyama K, Moriguchi Y, Ueno S, Ihara-Ujino T. Genome scanning for detecting adaptive genes along environmental gradients in the Japanese conifer, Cryptomeria japonica. Heredity (Edinb) 2012; 109:349-60. [PMID: 22929151 DOI: 10.1038/hdy.2012.50] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Local adaptation is important in evolutionary processes and speciation. We used multiple tests to identify several candidate genes that may be involved in local adaptation from 1026 loci in 14 natural populations of Cryptomeria japonica, the most economically important forestry tree in Japan. We also studied the relationships between genotypes and environmental variables to obtain information on the selective pressures acting on individual populations. Outlier loci were mapped onto a linkage map, and the positions of loci associated with specific environmental variables are considered. The outlier loci were not randomly distributed on the linkage map; linkage group 11 was identified as a genomic island of divergence. Three loci in this region were also associated with environmental variables such as mean annual temperature, daily maximum temperature, maximum snow depth, and so on. Outlier loci identified with high significance levels will be essential for conservation purposes and for future work on molecular breeding.
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Affiliation(s)
- Y Tsumura
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
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Khan MA, Korban SS. Association mapping in forest trees and fruit crops. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:4045-60. [PMID: 22511806 DOI: 10.1093/jxb/ers105] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Association mapping (AM), also known as linkage disequilibrium (LD) mapping, is a viable approach to overcome limitations of pedigree-based quantitative trait loci (QTL) mapping. In AM, genotypic and phenotypic correlations are investigated in unrelated individuals. Unlike QTL mapping, AM takes advantage of both LD and historical recombination present within the gene pool of an organism, thus utilizing a broader reference population. In plants, AM has been used in model species with available genomic resources. Pursuing AM in tree species requires both genotyping and phenotyping of large populations with unique architectures. Recently, genome sequences and genomic resources for forest and fruit crops have become available. Due to abundance of single nucleotide polymorphisms (SNPs) within a genome, along with availability of high-throughput resequencing methods, SNPs can be effectively used for genotyping trees. In addition to DNA polymorphisms, copy number variations (CNVs) in the form of deletions, duplications, and insertions also play major roles in control of expression of phenotypic traits. Thus, CNVs could provide yet another valuable resource, beyond those of microsatellite and SNP variations, for pursuing genomic studies. As genome-wide SNP data are generated from high-throughput sequencing efforts, these could be readily reanalysed to identify CNVs, and subsequently used for AM studies. However, forest and fruit crops possess unique architectural and biological features that ought to be taken into consideration when collecting genotyping and phenotyping data, as these will also dictate which AM strategies should be pursued. These unique features as well as their impact on undertaking AM studies are outlined and discussed.
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Affiliation(s)
- M Awais Khan
- Department of Natural Resources & Environmental Sciences, University of Illinois, Urbana, IL 61801 USA.
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Cornille A, Gladieux P, Smulders MJM, Roldán-Ruiz I, Laurens F, Le Cam B, Nersesyan A, Clavel J, Olonova M, Feugey L, Gabrielyan I, Zhang XG, Tenaillon MI, Giraud T. New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties. PLoS Genet 2012; 8:e1002703. [PMID: 22589740 PMCID: PMC3349737 DOI: 10.1371/journal.pgen.1002703] [Citation(s) in RCA: 162] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 03/26/2012] [Indexed: 11/23/2022] Open
Abstract
The apple is the most common and culturally important fruit crop of temperate areas. The elucidation of its origin and domestication history is therefore of great interest. The wild Central Asian species Malus sieversii has previously been identified as the main contributor to the genome of the cultivated apple (Malus domestica), on the basis of morphological, molecular, and historical evidence. The possible contribution of other wild species present along the Silk Route running from Asia to Western Europe remains a matter of debate, particularly with respect to the contribution of the European wild apple. We used microsatellite markers and an unprecedented large sampling of five Malus species throughout Eurasia (839 accessions from China to Spain) to show that multiple species have contributed to the genetic makeup of domesticated apples. The wild European crabapple M. sylvestris, in particular, was a major secondary contributor. Bidirectional gene flow between the domesticated apple and the European crabapple resulted in the current M. domestica being genetically more closely related to this species than to its Central Asian progenitor, M. sieversii. We found no evidence of a domestication bottleneck or clonal population structure in apples, despite the use of vegetative propagation by grafting. We show that the evolution of domesticated apples occurred over a long time period and involved more than one wild species. Our results support the view that self-incompatibility, a long lifespan, and cultural practices such as selection from open-pollinated seeds have facilitated introgression from wild relatives and the maintenance of genetic variation during domestication. This combination of processes may account for the diversification of several long-lived perennial crops, yielding domestication patterns different from those observed for annual species.
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Affiliation(s)
- Amandine Cornille
- CNRS, Laboratoire Ecologie Systématique et Evolution - UMR8079, Orsay, France.
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Holliday JA, Suren H, Aitken SN. Divergent selection and heterogeneous migration rates across the range of Sitka spruce (Picea sitchensis). Proc Biol Sci 2012; 279:1675-83. [PMID: 22113032 PMCID: PMC3297444 DOI: 10.1098/rspb.2011.1805] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 10/31/2011] [Indexed: 11/12/2022] Open
Abstract
Gene flow and effective population size (N(e)) should depend on a population's position within its range: those near the edges are expected to have smaller N(e) and lower relative emigration rates, whereas those nearer the centre should have larger N(e) and higher relative emigration rates. In species with continuous ranges, this phenomenon may limit the ability of peripheral populations to respond to divergent selection. Here, we employ Sitka spruce as a model to test these predictions. We previously genotyped 339 single nucleotide polymorphisms (SNPs) in 410 individuals from 13 populations, and used these data to identify putative targets of divergent selection, as well as to explore the extent to which central-peripheral structure may impede adaptation. Fourteen SNPs had outlier F(ST) estimates suggestive of divergent selection, of which nine were previously associated with phenotypic variation in adaptive traits (timing of autumn budset and cold hardiness). Using coalescent simulations, we show that populations from near the centre of the range have higher effective populations sizes than those from the edges, and that central populations contribute more migrants to marginal populations than the reverse. Our results suggest that while divergent selection appears to have shaped allele frequencies among populations, asymmetrical movement of alleles from the centre to the edges of the species range may affect the adaptive capacity of peripheral populations. In southern peripheral populations, the movement of cold-adapted alleles from the north represents a significant impediment to adaptation under climate change, while in the north, movement of warm-adapted alleles from the south may enhance adaptation.
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Affiliation(s)
- Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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Buschiazzo E, Ritland C, Bohlmann J, Ritland K. Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms. BMC Evol Biol 2012; 12:8. [PMID: 22264329 PMCID: PMC3328258 DOI: 10.1186/1471-2148-12-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 01/20/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Comparative genomics can inform us about the processes of mutation and selection across diverse taxa. Among seed plants, gymnosperms have been lacking in genomic comparisons. Recent EST and full-length cDNA collections for two conifers, Sitka spruce (Picea sitchensis) and loblolly pine (Pinus taeda), together with full genome sequences for two angiosperms, Arabidopsis thaliana and poplar (Populus trichocarpa), offer an opportunity to infer the evolutionary processes underlying thousands of orthologous protein-coding genes in gymnosperms compared with an angiosperm orthologue set. RESULTS Based upon pairwise comparisons of 3,723 spruce and pine orthologues, we found an average synonymous genetic distance (dS) of 0.191, and an average dN/dS ratio of 0.314. Using a fossil-established divergence time of 140 million years between spruce and pine, we extrapolated a nucleotide substitution rate of 0.68 × 10(-9) synonymous substitutions per site per year. When compared to angiosperms, this indicates a dramatically slower rate of nucleotide substitution rates in conifers: on average 15-fold. Coincidentally, we found a three-fold higher dN/dS for the spruce-pine lineage compared to the poplar-Arabidopsis lineage. This joint occurrence of a slower evolutionary rate in conifers with higher dN/dS, and possibly positive selection, showcases the uniqueness of conifer genome evolution. CONCLUSIONS Our results are in line with documented reduced nucleotide diversity, conservative genome evolution and low rates of diversification in conifers on the one hand and numerous examples of local adaptation in conifers on the other hand. We propose that reduced levels of nucleotide mutation in large and long-lived conifer trees, coupled with large effective population size, were the main factors leading to slow substitution rates but retention of beneficial mutations.
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Affiliation(s)
- Emmanuel Buschiazzo
- Department of Forest Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada.
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Miller AJ, Gross BL. From forest to field: perennial fruit crop domestication. AMERICAN JOURNAL OF BOTANY 2011; 98:1389-414. [PMID: 21865506 DOI: 10.3732/ajb.1000522] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
PREMISE OF THE STUDY Archaeological and genetic analyses of seed-propagated annual crops have greatly advanced our understanding of plant domestication and evolution. Comparatively little is known about perennial plant domestication, a relevant topic for understanding how genes and genomes evolve in long-lived species, and how perennials respond to selection pressures operating on a relatively short time scale. Here, we focus on long-lived perennial crops (mainly trees and other woody plants) grown for their fruits. KEY RESULTS We reviewed (1) the basic biology of long-lived perennials, setting the stage for perennial domestication by considering how these species evolve in nature; (2) the suite of morphological features associated with perennial fruit crops undergoing domestication; (3) the origins and evolution of domesticated perennials grown for their fruits; and (4) the genetic basis of domestication in perennial fruit crops. CONCLUSIONS Long-lived perennials have lengthy juvenile phases, extensive outcrossing, widespread hybridization, and limited population structure. Under domestication, these features, combined with clonal propagation, multiple origins, and ongoing crop-wild gene flow, contribute to mild domestication bottlenecks in perennial fruit crops. Morphological changes under domestication have many parallels to annual crops, but with key differences for mating system evolution and mode of reproduction. Quantitative trait loci associated with domestication traits in perennials are mainly of minor effect and may not be stable across years. Future studies that take advantage of genomic approaches and consider demographic history will elucidate the genetics of agriculturally and ecologically important traits in perennial fruit crops and their wild relatives.
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Affiliation(s)
- Allison J Miller
- Department of Biology, Saint Louis University, 3507 Laclede Avenue, Saint Louis, Missouri 63103 USA.
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Liu JJ, Sniezko RA, Ekramoddoullah AKM. Association of a novel Pinus monticola chitinase gene (PmCh4B) with quantitative resistance to Cronartium ribicola. PHYTOPATHOLOGY 2011; 101:904-11. [PMID: 21469933 DOI: 10.1094/phyto-10-10-0282] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Multiple families of pathogenesis-related (PR) proteins are believed to contribute to plant quantitative resistance to various pathogens. Along with other host PR proteins, PR3 chitinase is one protein component participating in genetic resistance of western white pine (Pinus monticola) to the white pine blister rust (WPBR) pathogen (Cronartium ribicola). In the present study, we characterized a novel P. monticola class IV chitinase gene (PmCh4B) and further analyzed its nucleotide variations in the open-pollinated seed families of diverse geographical distribution and variable levels of quantitative resistance to C. ribicola infection. PmCh4B showed high haplotype diversity (Hd=0.94) and nucleotide diversity (π=0.00965), similar to those of other conifer genes related to environmental stresses. A low level of intragenic linkage disequilibrium (LD) (but most of the levels with statistical significance) was found within a distance of ≈800 bp. Based on PmCh4B haplotype frequency, moderate to high levels of population structure were observed among P. monticola seed families currently used in breeding programs for WPBR resistance (average FST=0.163, P<0.001). Association analysis revealed that allelic variants and multiple single-nucleotide polymorphisms of PmCh4B were significantly associated with quantitative levels of P. monticola resistance against C. ribicola. This work represents the first association study for quantitative resistance in western white pine pathosystem and provides a potential for marker-assisted selection in white pine breeding.
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Affiliation(s)
- Jun-Jun Liu
- Pacific Forestry Centre, Canadian Forestry Service, Natural Resources Canada, Victoria, BC, Canada.
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Geraldes A, Pang J, Thiessen N, Cezard T, Moore R, Zhao Y, Tam A, Wang S, Friedmann M, Birol I, Jones SJM, Cronk QCB, Douglas CJ. SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing. Mol Ecol Resour 2011; 11 Suppl 1:81-92. [PMID: 21429165 DOI: 10.1111/j.1755-0998.2010.02960.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The western black cottonwood (Populus trichocarpa) was the first tree to have its genome fully sequenced and has emerged as the model species for the study of secondary growth and wood formation. It is also a good candidate species for the production of lignocellulosic biofuels. Here, we present and make available to the research community the results of the sequencing of the transcriptome of developing xylem in 20 accessions with high-throughput next generation sequencing technology. We found over 0.5 million putative single nucleotide polymorphisms (SNPs) in 26,595 genes that are expressed in developing secondary xylem. More than two-thirds of all SNPs were found in annotated exons, with 18% and 14% in regions of the genome annotated as introns and intergenic, respectively, where only 3% and 4% of sequence reads mapped. This suggests that the current annotation of the poplar genome is remarkably incomplete and that there are many transcripts and novel genes waiting to be annotated. We hope that this resource will stimulate further research in expression profiling, detection of alternative splicing and adaptive evolution in poplar.
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Affiliation(s)
- Armando Geraldes
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.
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Kuchma O, Finkeldey R. Evidence for selection in response to radiation exposure: Pinus sylvestris in the Chernobyl exclusion zone. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2011; 159:1606-1612. [PMID: 21429640 DOI: 10.1016/j.envpol.2011.02.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 02/17/2011] [Accepted: 02/26/2011] [Indexed: 05/30/2023]
Abstract
Changes of genetic structures due to viability selection are likely to occur in populations exposed to rapidly and extremely changing environmental conditions after catastrophic events. However, very little is known about the extent of selective responses and in particular the proportion of the genome involved in putatively adaptive reactions for non-model plants. We used amplified fragment length polymorphisms (AFLPs) in order to investigate genetic differences between pine (Pinus sylvestris) trees which were partially exposed to extreme environmental conditions. Genetic variation patterns of pines exposed to high radiation in the Chernobyl exclusion zone with or without phenotypic stress symptoms were compared to control trees with a similar origin. Six percent of the investigated loci (15 of 222 loci) were identified as candidates for selective responses. Moderate differentiation was observed between groups of trees showing either weak or strong phenotypic responses to high radiation levels.
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Affiliation(s)
- Oleksandra Kuchma
- Forest Genetics and Forest Tree Breeding, Büsgen Institute, Georg-August University Göttingen, Büsgenweg 2, Göttingen 37077, Germany
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Wachowiak W, Salmela MJ, Ennos RA, Iason G, Cavers S. High genetic diversity at the extreme range edge: nucleotide variation at nuclear loci in Scots pine (Pinus sylvestris L.) in Scotland. Heredity (Edinb) 2011; 106:775-87. [PMID: 20823905 PMCID: PMC3186241 DOI: 10.1038/hdy.2010.118] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 07/02/2010] [Accepted: 07/30/2010] [Indexed: 02/01/2023] Open
Abstract
Nucleotide polymorphism at 12 nuclear loci was studied in Scots pine populations across an environmental gradient in Scotland, to evaluate the impacts of demographic history and selection on genetic diversity. At eight loci, diversity patterns were compared between Scottish and continental European populations. At these loci, a similar level of diversity (θ(sil)= ~0.01) was found in Scottish vs mainland European populations, contrary to expectations for recent colonization, however, less rapid decay of linkage disequilibrium was observed in the former (ρ=0.0086±0.0009, ρ=0.0245±0.0022, respectively). Scottish populations also showed a deficit of rare nucleotide variants (multi-locus Tajima's D=0.316 vs D=-0.379) and differed significantly from mainland populations in allelic frequency and/or haplotype structure at several loci. Within Scotland, western populations showed slightly reduced nucleotide diversity (π(tot)=0.0068) compared with those from the south and east (0.0079 and 0.0083, respectively) and about three times higher recombination to diversity ratio (ρ/θ=0.71 vs 0.15 and 0.18, respectively). By comparison with results from coalescent simulations, the observed allelic frequency spectrum in the western populations was compatible with a relatively recent bottleneck (0.00175 × 4N(e) generations) that reduced the population to about 2% of the present size. However, heterogeneity in the allelic frequency distribution among geographical regions in Scotland suggests that subsequent admixture of populations with different demographic histories may also have played a role.
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Affiliation(s)
- W Wachowiak
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, UK
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
| | - M J Salmela
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, UK
- Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | - R A Ennos
- Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | - G Iason
- Macaulay Land Use Research Institute, Craigiebuckler, Aberdeen, UK
| | - S Cavers
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, UK
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Parchman TL, Benkman CW, Jenkins B, Buerkle CA. Low levels of population genetic structure in Pinus contorta (Pinaceae) across a geographic mosaic of co-evolution. AMERICAN JOURNAL OF BOTANY 2011; 98:669-679. [PMID: 21613166 DOI: 10.3732/ajb.1000378] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
PREMISE OF THE STUDY Population genetic analyses provide information on the population context in which evolutionary processes operate and are important for understanding the evolution of geographically variable traits. Earlier studies showed that cone structure of lodgepole pine in the Rocky Mountains diverged among populations because of geographic variation in coevolutionary interactions involving mammalian and avian seed predators. Analyses of population genetic variation are needed to determine whether this divergence has arisen despite extensive gene flow and whether populations to the east and west of the Rocky Mountains have evolved convergent phenotypes independently. METHODS We investigated genetic structuring across 22 stands of lodgepole pine in the central Rocky Mountains and in isolated peripheral populations that experience different seed predators and exhibit parallel divergence in cone traits using a set of nine simple sequence repeats and 235 AFLP loci. KEY RESULTS Our analyses reveal high levels of genetic diversity within and low genetic differentiation among populations. Nonetheless, geographic and genetic distances were correlated, and isolated populations to the east and west of the Rocky Mountains had higher levels of differentiation than did populations in the central part of the range. CONCLUSIONS These data indicate not only that adaptive divergence of cone traits across a geographic mosaic of coevolution has occurred despite minimal genetic differentiation, but also that isolated populations to the east and west of the Rocky Mountains have evolved distinctive cones independently and in parallel. The population structure quantified here will inform future research aimed at detecting genetic variants associated with divergent adaptive traits.
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Affiliation(s)
- Thomas L Parchman
- Department of Botany, Dept. 3165, 1000 E. University Ave., University of Wyoming, Laramie, Wyoming 82071, USA.
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Nucleotide Diversities and Genetic Relationship in the Three Japanese Pine Species; Pinus thunbergii, Pinus densiflora, and Pinus luchuensis. DIVERSITY-BASEL 2011. [DOI: 10.3390/d3010121] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
Over the past two decades, research in forest tree genomics has lagged behind that of model and agricultural systems. However, genomic research in forest trees is poised to enter into an important and productive phase owing to the advent of next-generation sequencing technologies, the enormous genetic diversity in forest trees and the need to mitigate the effects of climate change. Research on long-lived woody perennials is extending our molecular knowledge of complex life histories and adaptations to the environment - enriching a field that has traditionally drawn biological inference from a few short-lived herbaceous species.
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Affiliation(s)
- David B Neale
- Department of Plant Sciences, University of California, Davis, California 95616, USA.
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