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Alakärppä E, Salo HM, Suokas M, Jokipii-Lukkari S, Vuosku J, Häggman H. Targeted bisulfite sequencing of Scots pine adaptation-related genes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112173. [PMID: 38944158 DOI: 10.1016/j.plantsci.2024.112173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/01/2024]
Abstract
During environmental changes, epigenetic processes can enable adaptive responses faster than natural selection. In plants, very little is known about the role of DNA methylation during long-term adaptation. Scots pine is a widely distributed coniferous species which must adapt to different environmental conditions throughout its long lifespan. Thus, epigenetic modifications may contribute towards this direction. We provide bisulfite next-generation sequencing data from the putative promoters and exons of eight adaptation-related genes (A3IP2, CCA1, COL1, COL2, FTL2, MFT1, PHYO, and ZTL) in three Scots pine populations located in northern and southern parts of Finland. DNA methylation levels were studied in the two seed tissues: the maternal megagametophyte which contributes to embryo viability, and the biparental embryo which represents the next generation. In most genes, differentially methylated cytosines (DMCs) were in line with our previously demonstrated gene expression differences found in the same Scots pine populations. In addition, we found a strong correlation of total methylation levels between the embryo and megagametophyte tissues of a given individual tree, which indicates that DNA methylation can be inherited from the maternal parent. In conclusion, our results imply that DNA methylation differences may contribute to the adaptation of Scots pine populations in different climatic conditions.
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Affiliation(s)
- Emmi Alakärppä
- Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, FI-90014 Oulu, Finland.
| | - Heikki M Salo
- Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, FI-90014 Oulu, Finland
| | - Marko Suokas
- Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, FI-90014 Oulu, Finland
| | - Soile Jokipii-Lukkari
- Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, FI-90014 Oulu, Finland
| | - Jaana Vuosku
- Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, FI-90014 Oulu, Finland
| | - Hely Häggman
- Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, FI-90014 Oulu, Finland
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2
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Caré O, Chano V, Erley M, Rogge M, Gailing O. Circadian rhythm and redox homeostasis candidate genes showed association with shallow elevation in Norway spruce. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:508-520. [PMID: 38568928 DOI: 10.1111/plb.13642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/21/2024] [Indexed: 04/05/2024]
Abstract
The analysis of genetic variation underlying local adaptation in natural populations, together with the response to different external stimuli, is currently a hot topic in forest sciences, with the aim of identifying genetic markers controlling key phenotypic traits of interest for their inclusion in restoration and breeding programs. In Europe, one of the main tree species is Norway spruce (Picea abies (L.) H.Karst.). Using the MassARRAY® platform, 568 trees from North Rhine-Westphalia (Germany) were genotyped with 94 single nucleotide polymorphisms (SNPs) related to circadian and growth rhythms, and to stress response. The association analysis of the selected markers with health status and elevation was performed using three different methods, and those identified by at least two of these were considered as high confidence associated SNPs. While just five markers showed a weak association with health condition, 32 SNPs were correlated with elevation, six of which were considered as high confidence associated SNPs, as indicated by at least two different association methods. Among these genes, thioredoxin and pseudo response regulator 1 (PRR1) are involved in redox homeostasis and ROS detoxification, APETALA2-like 3 (AP2L3), a transcription factor, is involved in seasonal apical growth, and a RPS2-like is a disease resistance gene. The function of some of these genes in controlling light-dependent reactions and metabolic processes suggests signatures of adaptation to local photoperiod and the synchronization of the circadian rhythm. This work provides new insights into the genetic basis of local adaptation over a shallow elevation gradient in Norway spruce.
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Affiliation(s)
- O Caré
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, Göttingen, Germany
| | - V Chano
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, Göttingen, Germany
| | - M Erley
- Landesbetrieb Wald und Holz Nordrhein-Westfalen, Arnsberg, Germany
| | - M Rogge
- Landesbetrieb Wald und Holz Nordrhein-Westfalen, Arnsberg, Germany
| | - O Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, Göttingen, Germany
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3
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Zlobin IE. Tree post-drought recovery: scenarios, regulatory mechanisms and ways to improve. Biol Rev Camb Philos Soc 2024. [PMID: 38581143 DOI: 10.1111/brv.13083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/08/2024]
Abstract
Efficient post-drought recovery of growth and assimilation enables a plant to return to its undisturbed state and functioning. Unlike annual plants, trees suffer not only from the current drought, but also from cumulative impacts of consecutive water stresses which cause adverse legacy effects on survival and performance. This review provides an integrated assessment of ecological, physiological and molecular evidence on the recovery of growth and photosynthesis in trees, with a view to informing the breeding of trees with a better ability to recover from water stress. Suppression of recovery processes can result not only from stress damage but also from a controlled downshift of recovery as part of tree acclimation to water-limited conditions. In the latter case, recovery processes could potentially be activated by turning off the controlling mechanisms, but several obstacles make this unlikely. Tree phenology, and specifically photoperiodic constraints, can limit post-drought recovery of growth and photosynthesis, and targeting these constraints may represent a promising way to breed trees with an enhanced ability to recover post-drought. The mechanisms of photoperiod-dependent regulation of shoot, secondary and root growth and of assimilation processes are reviewed. Finally, the limitations and trade-offs of altering the photoperiodic regulation of growth and assimilation processes are discussed.
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Affiliation(s)
- Ilya E Zlobin
- K.A. Timiryazev Institute of Plant Physiology, RAS, 35 Botanicheskaya St, Moscow, 127276, Russia
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4
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Meger J, Ulaszewski B, Chmura DJ, Burczyk J. Signatures of local adaptation to current and future climate in phenology-related genes in natural populations of Quercus robur. BMC Genomics 2024; 25:78. [PMID: 38243199 PMCID: PMC10797717 DOI: 10.1186/s12864-023-09897-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 12/12/2023] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND Local adaptation is a key evolutionary process that enhances the growth of plants in their native habitat compared to non-native habitats, resulting in patterns of adaptive genetic variation across the entire geographic range of the species. The study of population adaptation to local environments and predicting their response to future climate change is important because of climate change. RESULTS Here, we explored the genetic diversity of candidate genes associated with bud burst in pedunculate oak individuals sampled from 6 populations in Poland. Single nucleotide polymorphism (SNP) diversity was assessed in 720 candidate genes using the sequence capture technique, yielding 18,799 SNPs. Using landscape genomic approaches, we identified 8 FST outliers and 781 unique SNPs in 389 genes associated with geography, climate, and phenotypic variables (individual/family spring and autumn phenology, family diameter at breast height (DBH), height, and survival) that are potentially involved in local adaptation. Then, using a nonlinear multivariate model, Gradient Forests, we identified vulnerable areas of the pedunculate oak distribution in Poland that are at risk from climate change. CONCLUSIONS The model revealed that pedunculate oak populations in the eastern part of the analyzed geographical region are the most sensitive to climate change. Our results might offer an initial evaluation of a potential management strategy for preserving the genetic diversity of pedunculate oak.
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Affiliation(s)
- Joanna Meger
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland
| | - Bartosz Ulaszewski
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland
| | - Daniel J Chmura
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035, Kórnik, Poland
| | - Jarosław Burczyk
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland.
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5
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Li L, Milesi P, Tiret M, Chen J, Sendrowski J, Baison J, Chen Z, Zhou L, Karlsson B, Berlin M, Westin J, Garcia‐Gil MR, Wu HX, Lascoux M. Teasing apart the joint effect of demography and natural selection in the birth of a contact zone. THE NEW PHYTOLOGIST 2022; 236:1976-1987. [PMID: 36093739 PMCID: PMC9828440 DOI: 10.1111/nph.18480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/23/2022] [Indexed: 05/26/2023]
Abstract
Vast population movements induced by recurrent climatic cycles have shaped the genetic structure of plant species. During glacial periods species were confined to low-latitude refugia from which they recolonized higher latitudes as the climate improved. This multipronged recolonization led to many lineages that later met and formed large contact zones. We utilize genomic data from 5000 Picea abies trees to test for the presence of natural selection during recolonization and establishment of a contact zone in Scandinavia. Scandinavian P. abies is today made up of a southern genetic cluster originating from the Baltics, and a northern one originating from Northern Russia. The contact zone delineating them closely matches the limit between two major climatic regions. We show that natural selection contributed to its establishment and maintenance. First, an isolation-with-migration model with genome-wide linked selection fits the data better than a purely neutral one. Second, many loci show signatures of selection or are associated with environmental variables. These loci, regrouped in clusters on chromosomes, are often related to phenology. Altogether, our results illustrate how climatic cycles, recolonization and selection can establish strong local adaptation along contact zones and affect the genetic architecture of adaptive traits.
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Affiliation(s)
- Lili Li
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
| | - Pascal Milesi
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
| | - Mathieu Tiret
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
| | - Jun Chen
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
- College of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Janek Sendrowski
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
| | - John Baison
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
| | - Zhi‐qiang Chen
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
| | - Linghua Zhou
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
| | | | - Mats Berlin
- SkogforskUppsala Science Park751 83UppsalaSweden
| | - Johan Westin
- Unit for Field‐Based Forest ResearchSwedish University of Agricultural SciencesSE‐922 91VindelnSweden
| | - Maria Rosario Garcia‐Gil
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
| | - Harry X. Wu
- Department Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSE‐90183Sweden
- CSIRO National Collection Research AustraliaBlack Mountain LaboratoryCanberraACT2601Australia
| | - Martin Lascoux
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, EBC and SciLife LabUppsala University75236UppsalaSweden
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6
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Meger J, Ulaszewski B, Burczyk J. Genomic signatures of natural selection at phenology-related genes in a widely distributed tree species Fagus sylvatica L. BMC Genomics 2021; 22:583. [PMID: 34332553 PMCID: PMC8325806 DOI: 10.1186/s12864-021-07907-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/20/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Diversity among phenology-related genes is predicted to be a contributing factor in local adaptations seen in widely distributed plant species that grow in climatically variable geographic areas, such as forest trees. European beech (Fagus sylvatica L.) is widespread, and is one of the most important broadleaved tree species in Europe; however, its potential for adaptation to climate change is a matter of uncertainty, and little is known about the molecular basis of climate change-relevant traits like bud burst. RESULTS We explored single nucleotide polymorphisms (SNP) at candidate genes related to bud burst in beech individuals sampled across 47 populations from Europe. SNP diversity was monitored for 380 candidate genes using a sequence capture approach, providing 2909 unlinked SNP loci. We used two complementary analytical methods to find loci significantly associated with geographic variables, climatic variables (expressed as principal components), or phenotypic variables (spring and autumn phenology, height, survival). Redundancy analysis (RDA) was used to detect candidate markers across two spatial scales (entire study area and within subregions). We revealed 201 candidate SNPs at the broadest scale, 53.2% of which were associated with phenotypic variables. Additive polygenic scores, which provide a measure of the cumulative signal across significant candidate SNPs, were correlated with a climate variable (first principal component, PC1) related to temperature and precipitation availability, and spring phenology. However, different genotype-environment associations were identified within Southeastern Europe as compared to the entire geographic range of European beech. CONCLUSIONS Environmental conditions play important roles as drivers of genetic diversity of phenology-related genes that could influence local adaptation in European beech. Selection in beech favors genotypes with earlier bud burst under warmer and wetter habitats within its range; however, selection pressures may differ across spatial scales.
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Affiliation(s)
- Joanna Meger
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland
| | - Bartosz Ulaszewski
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland
| | - Jaroslaw Burczyk
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland.
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7
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Colicchio JM, Hamm LN, Verdonk HE, Kooyers NJ, Blackman BK. Adaptive and nonadaptive causes of heterogeneity in genetic differentiation across the Mimulus guttatus genome. Mol Ecol 2021; 30:6486-6507. [PMID: 34289200 DOI: 10.1111/mec.16087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 11/29/2022]
Abstract
Genetic diversity becomes structured among populations over time due to genetic drift and divergent selection. Although population structure is often treated as a uniform underlying factor, recent resequencing studies of wild populations have demonstrated that diversity in many regions of the genome may be structured quite dissimilar to the genome-wide pattern. Here, we explored the adaptive and nonadaptive causes of such genomic heterogeneity using population-level, whole genome resequencing data obtained from annual Mimulus guttatus individuals collected across a rugged environment landscape. We found substantial variation in how genetic differentiation is structured both within and between chromosomes, although, in contrast to other studies, known inversion polymorphisms appear to serve only minor roles in this heterogeneity. In addition, much of the genome can be clustered into eight among-population genetic differentiation patterns, but only two of these clusters are particularly consistent with patterns of isolation by distance. By performing genotype-environment association analysis, we also identified genomic intervals where local adaptation to specific climate factors has accentuated genetic differentiation among populations, and candidate genes in these windows indicate climate adaptation may proceed through changes affecting specialized metabolism, drought resistance, and development. Finally, by integrating our findings with previous studies, we show that multiple aspects of plant reproductive biology may be common targets of balancing selection and that variants historically involved in climate adaptation among populations have probably also fuelled rapid adaptation to microgeographic environmental variation within sites.
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Affiliation(s)
- Jack M Colicchio
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Lauren N Hamm
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Hannah E Verdonk
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Nicholas J Kooyers
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.,Department of Biology, University of Virginia, Charlottesville, Virginia, USA.,Department of Biology, University of Louisiana, Lafayette, Lafayette, Louisiana, USA
| | - Benjamin K Blackman
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.,Department of Biology, University of Virginia, Charlottesville, Virginia, USA
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8
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Opgenoorth L, Dauphin B, Benavides R, Heer K, Alizoti P, Martínez-Sancho E, Alía R, Ambrosio O, Audrey A, Auñón F, Avanzi C, Avramidou E, Bagnoli F, Barbas E, Bastias CC, Bastien C, Ballesteros E, Beffa G, Bernier F, Bignalet H, Bodineau G, Bouic D, Brodbeck S, Brunetto W, Buchovska J, Buy M, Cabanillas-Saldaña AM, Carvalho B, Cheval N, Climent JM, Correard M, Cremer E, Danusevičius D, Del Caño F, Denou JL, di Gerardi N, Dokhelar B, Ducousso A, Eskild Nilsen A, Farsakoglou AM, Fonti P, Ganopoulos I, García Del Barrio JM, Gilg O, González-Martínez SC, Graf R, Gray A, Grivet D, Gugerli F, Hartleitner C, Hollenbach E, Hurel A, Issehut B, Jean F, Jorge V, Jouineau A, Kappner JP, Kärkkäinen K, Kesälahti R, Knutzen F, Kujala ST, Kumpula TA, Labriola M, Lalanne C, Lambertz J, Lascoux M, Lejeune V, Le-Provost G, Levillain J, Liesebach M, López-Quiroga D, Meier B, Malliarou E, Marchon J, Mariotte N, Mas A, Matesanz S, Meischner H, Michotey C, Milesi P, Morganti S, Nievergelt D, Notivol E, Ostreng G, Pakull B, Perry A, Piotti A, Plomion C, Poinot N, Pringarbe M, Puzos L, Pyhäjärvi T, Raffin A, Ramírez-Valiente JA, Rellstab C, Remi D, Richter S, Robledo-Arnuncio JJ, San Segundo S, Savolainen O, Schueler S, Schneck V, Scotti I, Semerikov V, Slámová L, Sønstebø JH, Spanu I, Thevenet J, Tollefsrud MM, Turion N, Vendramin GG, Villar M, von Arx G, Westin J, Fady B, Myking T, Valladares F, Aravanopoulos FA, Cavers S. The GenTree Platform: growth traits and tree-level environmental data in 12 European forest tree species. Gigascience 2021; 10:6177710. [PMID: 33734368 PMCID: PMC7970660 DOI: 10.1093/gigascience/giab010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 12/07/2020] [Accepted: 02/03/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Progress in the field of evolutionary forest ecology has been hampered by the huge challenge of phenotyping trees across their ranges in their natural environments, and the limitation in high-resolution environmental information. FINDINGS The GenTree Platform contains phenotypic and environmental data from 4,959 trees from 12 ecologically and economically important European forest tree species: Abies alba Mill. (silver fir), Betula pendula Roth. (silver birch), Fagus sylvatica L. (European beech), Picea abies (L.) H. Karst (Norway spruce), Pinus cembra L. (Swiss stone pine), Pinus halepensis Mill. (Aleppo pine), Pinus nigra Arnold (European black pine), Pinus pinaster Aiton (maritime pine), Pinus sylvestris L. (Scots pine), Populus nigra L. (European black poplar), Taxus baccata L. (English yew), and Quercus petraea (Matt.) Liebl. (sessile oak). Phenotypic (height, diameter at breast height, crown size, bark thickness, biomass, straightness, forking, branch angle, fructification), regeneration, environmental in situ measurements (soil depth, vegetation cover, competition indices), and environmental modeling data extracted by using bilinear interpolation accounting for surrounding conditions of each tree (precipitation, temperature, insolation, drought indices) were obtained from trees in 194 sites covering the species' geographic ranges and reflecting local environmental gradients. CONCLUSION The GenTree Platform is a new resource for investigating ecological and evolutionary processes in forest trees. The coherent phenotyping and environmental characterization across 12 species in their European ranges allow for a wide range of analyses from forest ecologists, conservationists, and macro-ecologists. Also, the data here presented can be linked to the GenTree Dendroecological collection, the GenTree Leaf Trait collection, and the GenTree Genomic collection presented elsewhere, which together build the largest evolutionary forest ecology data collection available.
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Affiliation(s)
- Lars Opgenoorth
- Philipps University Marburg, Faculty of Biology, Plant Ecology and Geobotany, Karl-von-Frisch Strasse 8, 35043, Marburg, Germany.,Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Benjamin Dauphin
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Raquel Benavides
- LINCGlobal, Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales, CSIC, Serrano 115 dpdo, 28006, Madrid, Spain
| | - Katrin Heer
- Philipps University Marburg, Faculty of Biology, Plant Ecology and Geobotany, Karl-von-Frisch Strasse 8, 35043, Marburg, Germany
| | - Paraskevi Alizoti
- Aristotle University of Thessaloniki, School of Forestry and Natural Environment, Laboratory of Forest Genetics and Tree Improvement, 54124, Thessaloniki, Greece
| | | | - Ricardo Alía
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Olivier Ambrosio
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Albet Audrey
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - Francisco Auñón
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Camilla Avanzi
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto, Fiorentino, Italy
| | - Evangelia Avramidou
- Aristotle University of Thessaloniki, School of Forestry and Natural Environment, Laboratory of Forest Genetics and Tree Improvement, 54124, Thessaloniki, Greece
| | - Francesca Bagnoli
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto, Fiorentino, Italy
| | - Evangelos Barbas
- Aristotle University of Thessaloniki, School of Forestry and Natural Environment, Laboratory of Forest Genetics and Tree Improvement, 54124, Thessaloniki, Greece
| | - Cristina C Bastias
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), CNRS, UMR 5175, 34090, Montpellier, France
| | - Catherine Bastien
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Dept ECOFA, 45075, Orléans, France
| | - Eduardo Ballesteros
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Giorgia Beffa
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Frédéric Bernier
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - Henri Bignalet
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - Guillaume Bodineau
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), GBFOR, 45075, Orléans, France
| | - Damien Bouic
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - Sabine Brodbeck
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - William Brunetto
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Jurata Buchovska
- Vytautas Magnus University, Studentu Street 11, 53361, Akademija, Lithuania
| | - Melanie Buy
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Ana M Cabanillas-Saldaña
- Departamento de Agricultura, Ganadería y Medio Ambiente, Gobierno de Aragón, P. Mª Agustín 36, 50071, Zaragoza, Spain
| | - Bárbara Carvalho
- LINCGlobal, Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales, CSIC, Serrano 115 dpdo, 28006, Madrid, Spain
| | - Nicolas Cheval
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - José M Climent
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Marianne Correard
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Eva Cremer
- Bavarian Institute for Forest Genetics, Forstamtsplatz 1, 83317, Teisendorf, Germany
| | | | - Fernando Del Caño
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Jean-Luc Denou
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - Nicolas di Gerardi
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Bernard Dokhelar
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | | | - Anne Eskild Nilsen
- Division of Forestry and Forest Resources, Norwegian Institute of Bioeconomy Research (NIBIO), P.O. Box 115, 1431, Ås, Norway
| | - Anna-Maria Farsakoglou
- Aristotle University of Thessaloniki, School of Forestry and Natural Environment, Laboratory of Forest Genetics and Tree Improvement, 54124, Thessaloniki, Greece
| | - Patrick Fonti
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), 57001, Thermi, Greece
| | - José M García Del Barrio
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Olivier Gilg
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | | | - René Graf
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Alan Gray
- UK Centre for Ecology and Hydrology, Bush Estate Penicuik, EH26 0QB, Edinburgh, UK
| | - Delphine Grivet
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Felix Gugerli
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | | | - Enja Hollenbach
- Philipps University Marburg, Faculty of Biology, Plant Ecology and Geobotany, Karl-von-Frisch Strasse 8, 35043, Marburg, Germany
| | - Agathe Hurel
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - Bernard Issehut
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - Florence Jean
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Veronique Jorge
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), ONF, BIOFORA, 45075, Orléans, France
| | - Arnaud Jouineau
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Jan-Philipp Kappner
- Philipps University Marburg, Faculty of Biology, Plant Ecology and Geobotany, Karl-von-Frisch Strasse 8, 35043, Marburg, Germany
| | - Katri Kärkkäinen
- Natural Resources Institute Finland, Paavo Havaksentie 3, 90014, University of Oulu, Finland
| | - Robert Kesälahti
- University of Oulu, Pentti Kaiteran katu 1, 90014, University of Oulu, Finland
| | - Florian Knutzen
- Bavarian Institute for Forest Genetics, Forstamtsplatz 1, 83317, Teisendorf, Germany
| | - Sonja T Kujala
- Natural Resources Institute Finland, Paavo Havaksentie 3, 90014, University of Oulu, Finland
| | - Timo A Kumpula
- University of Oulu, Pentti Kaiteran katu 1, 90014, University of Oulu, Finland
| | - Mariaceleste Labriola
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto, Fiorentino, Italy
| | - Celine Lalanne
- INRAE, Univsité de Bordeaux, BIOGECO, 33770, Cestas, France
| | - Johannes Lambertz
- Philipps University Marburg, Faculty of Biology, Plant Ecology and Geobotany, Karl-von-Frisch Strasse 8, 35043, Marburg, Germany
| | - Martin Lascoux
- Department of Ecology & Genetics, EBC, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Vincent Lejeune
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), GBFOR, 45075, Orléans, France
| | | | - Joseph Levillain
- Université de Lorraine, AgroParisTech, INRAE, SILVA, 54000, Nancy, France
| | - Mirko Liesebach
- Thünen Institute of Forest Genetics, Sieker Landstr. 2, 22927, Grosshansdorf, Germany
| | - David López-Quiroga
- LINCGlobal, Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales, CSIC, Serrano 115 dpdo, 28006, Madrid, Spain
| | - Benjamin Meier
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Ermioni Malliarou
- Aristotle University of Thessaloniki, School of Forestry and Natural Environment, Laboratory of Forest Genetics and Tree Improvement, 54124, Thessaloniki, Greece
| | - Jérémy Marchon
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Nicolas Mariotte
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Antonio Mas
- LINCGlobal, Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales, CSIC, Serrano 115 dpdo, 28006, Madrid, Spain
| | - Silvia Matesanz
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Calle Tulipán s/n, 28933, Móstoles, Spain
| | - Helge Meischner
- Philipps University Marburg, Faculty of Biology, Plant Ecology and Geobotany, Karl-von-Frisch Strasse 8, 35043, Marburg, Germany
| | - Célia Michotey
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), URGI, Versailles, France
| | - Pascal Milesi
- Department of Ecology & Genetics, EBC, Science for Life Laboratory, Uppsala University, 75236, Uppsala, Sweden
| | - Sandro Morganti
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Daniel Nievergelt
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Eduardo Notivol
- Centro de Investigación y Tecnología Agroalimentaria de Aragón - Unidad de Recursos Forestales (CITA), Avda. Montañana 930, 50059, Zaragoza, Spain
| | - Geir Ostreng
- Division of Forestry and Forest Resources, Norwegian Institute of Bioeconomy Research (NIBIO), P.O. Box 115, 1431, Ås, Norway
| | - Birte Pakull
- Thünen Institute of Forest Genetics, Sieker Landstr. 2, 22927, Grosshansdorf, Germany
| | - Annika Perry
- UK Centre for Ecology and Hydrology, Bush Estate Penicuik, EH26 0QB, Edinburgh, UK
| | - Andrea Piotti
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto, Fiorentino, Italy
| | | | - Nicolas Poinot
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - Mehdi Pringarbe
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Luc Puzos
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - Tanja Pyhäjärvi
- University of Oulu, Pentti Kaiteran katu 1, 90014, University of Oulu, Finland
| | - Annie Raffin
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - José A Ramírez-Valiente
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Christian Rellstab
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Dourthe Remi
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - Sebastian Richter
- Philipps University Marburg, Faculty of Biology, Plant Ecology and Geobotany, Karl-von-Frisch Strasse 8, 35043, Marburg, Germany
| | - Juan J Robledo-Arnuncio
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Sergio San Segundo
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Outi Savolainen
- University of Oulu, Pentti Kaiteran katu 1, 90014, University of Oulu, Finland
| | - Silvio Schueler
- Austrian Research Centre for Forests (BFW), Seckendorff-Gudent-Weg 8, 1131, Wien, Austria
| | - Volker Schneck
- Thünen Institute of Forest Genetics, Eberswalder Chaussee 3a, 15377, Waldsieversdorf, Germany
| | - Ivan Scotti
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Vladimir Semerikov
- Institute of Plant and Animal Ecology, Ural branch of RAS, 8 Marta St. 202, 620144, Ekaterinburg, Russia
| | - Lenka Slámová
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Jørn Henrik Sønstebø
- Division of Forestry and Forest Resources, Norwegian Institute of Bioeconomy Research (NIBIO), P.O. Box 115, 1431, Ås, Norway
| | - Ilaria Spanu
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto, Fiorentino, Italy
| | - Jean Thevenet
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Mari Mette Tollefsrud
- Division of Forestry and Forest Resources, Norwegian Institute of Bioeconomy Research (NIBIO), P.O. Box 115, 1431, Ås, Norway
| | - Norbert Turion
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Giovanni Giuseppe Vendramin
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto, Fiorentino, Italy
| | - Marc Villar
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), ONF, BIOFORA, 45075, Orléans, France
| | - Georg von Arx
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | | | - Bruno Fady
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Tor Myking
- Division of Forestry and Forest Resources, Norwegian Institute of Bioeconomy Research (NIBIO), P.O. Box 115, 1431, Ås, Norway
| | - Fernando Valladares
- LINCGlobal, Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales, CSIC, Serrano 115 dpdo, 28006, Madrid, Spain
| | - Filippos A Aravanopoulos
- Aristotle University of Thessaloniki, School of Forestry and Natural Environment, Laboratory of Forest Genetics and Tree Improvement, 54124, Thessaloniki, Greece
| | - Stephen Cavers
- UK Centre for Ecology and Hydrology, Bush Estate Penicuik, EH26 0QB, Edinburgh, UK
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Wos G, Bohutínská M, Nosková J, Mandáková T, Kolář F. Parallelism in gene expression between foothill and alpine ecotypes in Arabidopsis arenosa. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1211-1224. [PMID: 33258160 DOI: 10.1111/tpj.15105] [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: 06/15/2020] [Revised: 11/13/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Abstract
Parallel adaptation results from the independent evolution of similar traits between closely related lineages and allows us to test to what extent evolution is repeatable. Similar gene expression changes are often detected but the identity of genes shaped by parallel selection and the causes of expression parallelism remain largely unknown. By comparing genomes and transcriptomes of four distinct foothill-alpine population pairs across four treatments, we addressed the genetic underpinnings, plasticity and functional consequences of gene expression parallelism in alpine adaptation. Seeds of eight populations of Arabidopsis arenosa were raised under four treatments that differed in temperature and irradiance, factors varying strongly with elevation. Parallelism in differential gene expression between the foothill and alpine ecotypes was quantified by RNA-seq in leaves of young plants. By manipulating temperature and irradiance, we also tested for parallelism in plasticity (i.e., gene-environment interaction, GEI). In spite of global non-parallel patterns transcriptome wide, we found significant parallelism in gene expression at the level of individual loci with an over-representation of genes involved in biotic stress response. In addition, we demonstrated significant parallelism in GEI, indicating a shared differential response of the originally foothill versus alpine populations to environmental variation across mountain regions. A fraction of genes showing expression parallelism also encompassed parallel outliers for genomic differentiation, with greater enrichment of such variants in cis-regulatory elements in some mountain regions. In summary, our results suggest frequent evolutionary repeatability in gene expression changes associated with the colonization of a challenging environment that combines constitutive expression differences and plastic interaction with the surrounding environment.
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Affiliation(s)
- Guillaume Wos
- Department of Botany, Charles University, Prague, 128 01, Czech Republic
| | - Magdalena Bohutínská
- Department of Botany, Charles University, Prague, 128 01, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Průhonice, 252 43, Czech Republic
| | - Jana Nosková
- Department of Botany, Charles University, Prague, 128 01, Czech Republic
| | - Terezie Mandáková
- Central European Institute of Technology and Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
| | - Filip Kolář
- Department of Botany, Charles University, Prague, 128 01, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Průhonice, 252 43, Czech Republic
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10
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Ranade SS, García-Gil MR. Molecular signatures of local adaptation to light in Norway spruce. PLANTA 2021; 253:53. [PMID: 33511433 PMCID: PMC7843583 DOI: 10.1007/s00425-020-03517-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 12/02/2020] [Indexed: 05/12/2023]
Abstract
MAIN CONCLUSION Transcriptomic and exome capture analysis reveal an adaptive cline for shade tolerance in Norway spruce. Genes involved in the lignin pathway and immunity seem to play a potential role in contributing towards local adaptation to light. The study of natural variation is an efficient method to elucidate how plants adapt to local climatic conditions, a key process for the evolution of a species. Norway spruce is a shade-tolerant conifer in which the requirement of far-red light for growth increases latitudinally northwards. The objective of the study is to characterize the genetic control of local adaptation to light enriched in far-red in Norway spruce, motivated by a latitudinal gradient for the Red:Far-red (R:FR) ratio to which Norway spruce has been proven to be genetically adapted. We have established the genomic signatures of local adaptation by conducting transcriptomic (total RNA-sequencing) and genomic analyses (exome capture), for the identification of genes differentially regulated along the cline. RNA-sequencing revealed 274 differentially expressed genes in response to SHADE (low R:FR light), between the southern and northern natural populations in Sweden. Exome capture included analysis of a uniquely large data set (1654 trees) that revealed missense variations in coding regions of nine differentially expressed candidate genes, which followed a latitudinal cline in allele and genotype frequencies. These genes included five transcription factors involved in vital processes like bud-set/bud-flush, lignin pathway, and cold acclimation and other genes that take part in cell-wall remodeling, secondary cell-wall thickening, response to starvation, and immunity. Based on these results, we suggest that the northern populations might not only be able to adjust their growing season in response to low R:FR light, but they may also be better adapted towards disease resistance by up-regulation of the lignin pathway that is linked to immunity. This forms a concrete basis for local adaptation to light quality in Norway spruce, one of the most economically important conifer tree species in Sweden.
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Affiliation(s)
- Sonali Sachin Ranade
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
- Department of Plant Physiology, Umeå Plant Science Centre, University of Umeå, 901 87 Umeå, Sweden
| | - María Rosario García-Gil
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
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11
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Osnato M, Cota I, Nebhnani P, Cereijo U, Pelaz S. Photoperiod Control of Plant Growth: Flowering Time Genes Beyond Flowering. FRONTIERS IN PLANT SCIENCE 2021; 12:805635. [PMID: 35222453 PMCID: PMC8864088 DOI: 10.3389/fpls.2021.805635] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/23/2021] [Indexed: 05/02/2023]
Abstract
Fluctuations in environmental conditions greatly influence life on earth. Plants, as sessile organisms, have developed molecular mechanisms to adapt their development to changes in daylength, or photoperiod. One of the first plant features that comes to mind as affected by the duration of the day is flowering time; we all bring up a clear image of spring blossom. However, for many plants flowering happens at other times of the year, and many other developmental aspects are also affected by changes in daylength, which range from hypocotyl elongation in Arabidopsis thaliana to tuberization in potato or autumn growth cessation in trees. Strikingly, many of the processes affected by photoperiod employ similar gene networks to respond to changes in the length of light/dark cycles. In this review, we have focused on developmental processes affected by photoperiod that share similar genes and gene regulatory networks.
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Affiliation(s)
- Michela Osnato
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institute of Environmental Science and Technology of the Universitat Autònoma de Barcelona, Barcelona, Spain
- *Correspondence: Michela Osnato,
| | - Ignacio Cota
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Poonam Nebhnani
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Unai Cereijo
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Soraya Pelaz
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Soraya Pelaz,
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12
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Milesi P, Berlin M, Chen J, Orsucci M, Li L, Jansson G, Karlsson B, Lascoux M. Assessing the potential for assisted gene flow using past introduction of Norway spruce in southern Sweden: Local adaptation and genetic basis of quantitative traits in trees. Evol Appl 2019; 12:1946-1959. [PMID: 31700537 PMCID: PMC6824079 DOI: 10.1111/eva.12855] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/05/2019] [Accepted: 07/11/2019] [Indexed: 12/20/2022] Open
Abstract
Norway spruce (Picea abies) is a dominant conifer species of major economic importance in northern Europe. Extensive breeding programs were established to improve phenotypic traits of economic interest. In southern Sweden, seeds used to create progeny tests were collected on about 3,000 trees of outstanding phenotype ('plus' trees) across the region. In a companion paper, we showed that some were of local origin but many were recent introductions from the rest of the natural range. The mixed origin of the trees together with partial sequencing of the exome of >1,500 of these trees and phenotypic data retrieved from the Swedish breeding program offered a unique opportunity to dissect the genetic basis of local adaptation of three quantitative traits (height, diameter and bud-burst) and assess the potential of assisted gene flow. Through a combination of multivariate analyses and genome-wide association studies, we showed that there was a very strong effect of geographical origin on growth (height and diameter) and phenology (bud-burst) with trees from southern origins outperforming local provenances. Association studies revealed that growth traits were highly polygenic and bud-burst somewhat less. Hence, our results suggest that assisted gene flow and genomic selection approaches could help to alleviate the effect of climate change on P. abies breeding programs in Sweden.
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Affiliation(s)
- Pascal Milesi
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Mats Berlin
- The Forestry Research Institute of Sweden (Skogforsk)UppsalaSweden
| | - Jun Chen
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Marion Orsucci
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Lili Li
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Gunnar Jansson
- The Forestry Research Institute of Sweden (Skogforsk)UppsalaSweden
| | - Bo Karlsson
- The Forestry Research Institute of Sweden (Skogforsk)EkeboSweden
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
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Chen J, Li L, Milesi P, Jansson G, Berlin M, Karlsson B, Aleksic J, Vendramin GG, Lascoux M. Genomic data provide new insights on the demographic history and the extent of recent material transfers in Norway spruce. Evol Appl 2019; 12:1539-1551. [PMID: 31462913 PMCID: PMC6708423 DOI: 10.1111/eva.12801] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/28/2019] [Accepted: 04/02/2019] [Indexed: 12/23/2022] Open
Abstract
Primeval forests are today exceedingly rare in Europe, and transfer of forest reproductive material for afforestation and improvement has been very common, especially over the last two centuries. This can be a serious impediment when inferring past population movements in response to past climate changes such as the last glacial maximum (LGM), some 18,000 years ago. In the present study, we genotyped 1,672 individuals from three Picea species (P. abies, P. obovata, and P. omorika) at 400K SNPs using exome capture to infer the past demographic history of Norway spruce (P. abies) and estimate the amount of recent introduction used to establish the Norway spruce breeding program in southern Sweden. Most of these trees belong to P. abies and originate from the base populations of the Swedish breeding program. Others originate from populations across the natural ranges of the three species. Of the 1,499 individuals stemming from the breeding program, a large proportion corresponds to recent introductions from mainland Europe. The split of P. omorika occurred 23 million years ago (mya), while the divergence between P. obovata and P. abies began 17.6 mya. Demographic inferences retrieved the same main clusters within P. abies than previous studies, that is, a vast northern domain ranging from Norway to central Russia, where the species is progressively replaced by Siberian spruce (P. obovata) and two smaller domains, an Alpine domain and a Carpathian one, but also revealed further subdivision and gene flow among clusters. The three main domains divergence was ancient (15 mya), and all three went through a bottleneck corresponding to the LGM. Approximately 17% of P. abies Nordic domain migrated from P. obovata ~103K years ago, when both species had much larger effective population sizes. Our analysis of genomewide polymorphism data thus revealed the complex demographic history of Picea genus in Western Europe and highlighted the importance of material transfer in Swedish breeding program.
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Affiliation(s)
- Jun Chen
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Lili Li
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Pascal Milesi
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Gunnar Jansson
- Forestry Research Institute of Sweden (Skogforsk)UppsalaSweden
| | - Mats Berlin
- Forestry Research Institute of Sweden (Skogforsk)UppsalaSweden
| | - Bo Karlsson
- Forestry Research Institute of Sweden (Skogforsk)EkeboSweden
| | - Jelena Aleksic
- Institute of Molecular Genetics and Genetic EngineeringUniversity of BelgradeBelgradeSerbia
| | - Giovanni G. Vendramin
- Division of Florence, Institute of Biosciences and BioResourcesNational Research Council (IBBR‐CNR)Sesto FiorentinoItaly
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
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14
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Salmela MJ, Weinig C. The fitness benefits of genetic variation in circadian clock regulation. CURRENT OPINION IN PLANT BIOLOGY 2019; 49:86-93. [PMID: 31302588 DOI: 10.1016/j.pbi.2019.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 05/31/2019] [Accepted: 06/04/2019] [Indexed: 06/10/2023]
Abstract
Functional circadian clocks are essential for fitness in diverse ecosystems, facilitating detection of predictable light-dark and temperature cycles. The molecular basis of endogenous clocks is variable across the tree of life, but it has one omnipresent attribute: natural genetic diversity that manifests as variation for instance in circadian period length around the hypothesised optimum of 24 hours. Latitudinal variation in photoperiod alone is unlikely to account for the vast diversity documented in varied organisms, but we have yet to achieve a solid understanding of the interplay between clock variability and natural selection. Recent circadian studies sampling populations have drawn attention to the hierarchical structure of genetic diversity in the wild, unveiling pronounced genetic variation even on a scale of metres.
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Affiliation(s)
- Matti J Salmela
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790 Helsinki, Finland
| | - Cynthia Weinig
- Department of Botany, 3165, University of Wyoming, 1000 E. University Ave., Laramie, WY 82071, USA; Program in Ecology, University of Wyoming, Laramie, WY 82071, USA; Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA.
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15
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Alakärppä E, Salo HM, Valledor L, Cañal MJ, Häggman H, Vuosku J. Natural variation of DNA methylation and gene expression may determine local adaptations of Scots pine populations. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:5293-5305. [PMID: 30113688 DOI: 10.1093/jxb/ery292] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 08/01/2018] [Indexed: 05/27/2023]
Abstract
Long-lived conifers are vulnerable to climate change because classical evolutionary processes are slow in developing adaptive responses. Therefore, the capacity of a genotype to adopt different phenotypes is important. Gene expression is the primary mechanism that converts genome-encoded information into phenotypes, and DNA methylation is employed in the epigenetic regulation of gene expression. We investigated variations in global DNA methylation and gene expression between three Scots pine (Pinus sylvestris L.) populations located in northern and southern Finland using mature seeds. Gene expression levels were studied in six DNA methyltransferase (DNMT) genes, which were characterized in this study, and in 19 circadian clock genes regulating adaptive traits. In embryos, expression diversity was found for three DNMT genes, which maintain DNA methylation. The expression of two DNMT genes was strongly correlated with climate variables, which suggests a role for DNA methylation in local adaptation. For adaptation-related genes, expression levels showed between-population variation in 11 genes in megagametophytes and in eight genes in embryos, and many of these genes were linked to climate factors. Altogether, our results suggest that differential DNA methylation and gene expression contribute to local adaptation in Scots pine populations and may enhance the fitness of trees under rapidly changing climatic conditions.
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Affiliation(s)
- Emmi Alakärppä
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Heikki M Salo
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Luis Valledor
- Plant Physiology, Faculty of Biology, University of Oviedo, Oviedo, Spain
| | - Maria Jesús Cañal
- Plant Physiology, Faculty of Biology, University of Oviedo, Oviedo, Spain
| | - Hely Häggman
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Jaana Vuosku
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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16
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Ding J, Böhlenius H, Rühl MG, Chen P, Sane S, Zambrano JA, Zheng B, Eriksson ME, Nilsson O. GIGANTEA-like genes control seasonal growth cessation in Populus. THE NEW PHYTOLOGIST 2018. [PMID: 29532940 DOI: 10.1111/nph.15087] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Survival of trees growing in temperate zones requires cycling between active growth and dormancy. This involves growth cessation in the autumn triggered by a photoperiod shorter than the critical day length. Variations in GIGANTEA (GI)-like genes have been associated with phenology in a range of different tree species, but characterization of the functions of these genes in the process is still lacking. We describe the identification of the Populus orthologs of GI and their critical role in short-day-induced growth cessation. Using ectopic expression and silencing, gene expression analysis, protein interaction and chromatin immunoprecipitation experiments, we show that PttGIs are likely to act in a complex with PttFKF1s (FLAVIN-BINDING, KELCH REPEAT, F-BOX 1) and PttCDFs (CYCLING DOF FACTOR) to control the expression of PttFT2, the key gene regulating short-day-induced growth cessation in Populus. In contrast to Arabidopsis, in which the GI-CONSTANS (CO)-FLOWERING LOCUS T (FT) regulon is a crucial day-length sensor for flowering time, our study suggests that, in Populus, PttCO-independent regulation of PttFT2 by PttGI is more important in the photoperiodic control of growth cessation and bud set.
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Affiliation(s)
- Jihua Ding
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Henrik Böhlenius
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, 230 53, Alnarp, Sweden
| | - Mark Georg Rühl
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Peng Chen
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Shashank Sane
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Jose A Zambrano
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Bo Zheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry, Huazhong Agricultural University, 430070, Wuhan, China
| | - Maria E Eriksson
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87, Umeå, Sweden
| | - Ove Nilsson
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
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17
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Marcer A, Vidigal DS, James PMA, Fortin MJ, Méndez-Vigo B, Hilhorst HWM, Bentsink L, Alonso-Blanco C, Picó FX. Temperature fine-tunes Mediterranean Arabidopsis thaliana life-cycle phenology geographically. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20 Suppl 1:148-156. [PMID: 28241389 DOI: 10.1111/plb.12558] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/22/2017] [Indexed: 06/06/2023]
Abstract
To understand how adaptive evolution in life-cycle phenology operates in plants, we need to unravel the effects of geographic variation in putative agents of natural selection on life-cycle phenology by considering all key developmental transitions and their co-variation patterns. We address this goal by quantifying the temperature-driven and geographically varying relationship between seed dormancy and flowering time in the annual Arabidopsis thaliana across the Iberian Peninsula. We used data on genetic variation in two major life-cycle traits, seed dormancy (DSDS50) and flowering time (FT), in a collection of 300 A. thaliana accessions from the Iberian Peninsula. The geographically varying relationship between life-cycle traits and minimum temperature, a major driver of variation in DSDS50 and FT, was explored with geographically weighted regressions (GWR). The environmentally varying correlation between DSDS50 and FT was analysed by means of sliding window analysis across a minimum temperature gradient. Maximum local adjustments between minimum temperature and life-cycle traits were obtained in the southwest Iberian Peninsula, an area with the highest minimum temperatures. In contrast, in off-southwest locations, the effects of minimum temperature on DSDS50 were rather constant across the region, whereas those of minimum temperature on FT were more variable, with peaks of strong local adjustments of GWR models in central and northwest Spain. Sliding window analysis identified a minimum temperature turning point in the relationship between DSDS50 and FT around a minimum temperature of 7.2 °C. Above this minimum temperature turning point, the variation in the FT/DSDS50 ratio became rapidly constrained and the negative correlation between FT and DSDS50 did not increase any further with increasing minimum temperatures. The southwest Iberian Peninsula emerges as an area where variation in life-cycle phenology appears to be restricted by the duration and severity of the hot summer drought. The temperature-driven varying relationship between DSDS50 and FT detected environmental boundaries for the co-evolution between FT and DSDS50 in A. thaliana. In the context of global warming, we conclude that A. thaliana phenology from the southwest Iberian Peninsula, determined by early flowering and deep seed dormancy, might become the most common life-cycle phenotype for this annual plant in the region.
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Affiliation(s)
- A Marcer
- CREAF, Cerdanyola del Vallès, Spain
- Univ. Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - D S Vidigal
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
| | - P M A James
- Département de Sciences Biologiques, Université de Montréal, Montréal, Canada
| | - M-J Fortin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - B Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - H W M Hilhorst
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
| | - L Bentsink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
| | - C Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - F X Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
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18
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Taulavuori K, Taulavuori E, Saravesi K, Jylänki T, Kainulainen A, Pajala J, Markkola A, Suominen O, Saikkonen K. Competitive success of southern populations of Betula pendula and Sorbus aucuparia under simulated southern climate experiment in the subarctic. Ecol Evol 2017. [PMID: 28649360 PMCID: PMC5478116 DOI: 10.1002/ece3.3026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Global warming has been commonly accepted to facilitate species' range shifts across latitudes. Cross-latitudinal transplantations support this; many tree species can well adapt to new geographical areas. However, these studies fail to capture species' adaptations to new light environment because the experiments were not designed to explicitly separate species' responses to light and temperature. Here we tested reaction norms of tree seedlings in reciprocal transplantations 1,000 km apart from each other at two latitudes (60°N and 69°N). In contrast to past studies, we exposed our experimental plants to same temperature in both sites (temperature of 60°N growing site is recorded to adjust temperature of 69°N site in real time via Internet connection) while light environment (photoperiod, light quality) remained ambient. Shoot elongation and autumn coloration were studied in seedlings of two deciduous trees (Betula pendula and Sorbus aucuparia), which were expected to respond differently to day length. Sorbus as a member of Rosaceae family was assumed to be indifferent to photoperiod, while Betula responds strongly to day length. We hypothesized that (1) southern and northern populations of both species perform differently; (2) southern populations perform better in both sites; (3) autumn phenology of southern populations may delay in the northern site; (4) and Sorbus aucuparia is less dependent on light environment. According to the hypotheses, shoot elongation of northern population was inherently low in both species. An evolutionary consequence of this may be a competitive success of southern populations under warming climate. Southern population of B. pendula was delayed in autumn coloration, but not in growth cessation. Sorbus aucuparia was less responsive to light environment. The results suggest that light provides selection pressure in range shifts, but the response is species dependent.
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Affiliation(s)
- Kari Taulavuori
- Department of Ecology and Genetics University of Oulu Oulu Finland
| | - Erja Taulavuori
- Department of Ecology and Genetics University of Oulu Oulu Finland
| | - Karita Saravesi
- Department of Ecology and Genetics University of Oulu Oulu Finland
| | - Tanja Jylänki
- Department of Ecology and Genetics University of Oulu Oulu Finland
| | - Aila Kainulainen
- Department of Ecology and Genetics University of Oulu Oulu Finland
| | - Jonna Pajala
- Department of Ecology and Genetics University of Oulu Oulu Finland
| | | | - Otso Suominen
- Centre for Environmental Research Kevo Subarctic Research Institute University of Turku Turku Finland
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19
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Nadeau S, Meirmans PG, Aitken SN, Ritland K, Isabel N. The challenge of separating signatures of local adaptation from those of isolation by distance and colonization history: The case of two white pines. Ecol Evol 2016; 6:8649-8664. [PMID: 28035257 PMCID: PMC5192886 DOI: 10.1002/ece3.2550] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/25/2016] [Accepted: 09/06/2016] [Indexed: 01/13/2023] Open
Abstract
Accurately detecting signatures of local adaptation using genetic‐environment associations (GEAs) requires controlling for neutral patterns of population structure to reduce the risk of false positives. However, a high degree of collinearity between climatic gradients and neutral population structure can greatly reduce power, and the performance of GEA methods in such case is rarely evaluated in empirical studies. In this study, we attempted to disentangle the effects of local adaptation and isolation by environment (IBE) from those of isolation by distance (IBD) and isolation by colonization from glacial refugia (IBC) using range‐wide samples in two white pine species. For this, SNPs from 168 genes, including 52 candidate genes for growth and phenology, were genotyped in 133 and 61 populations of Pinus strobus and P. monticola, respectively. For P. strobus and using all 153 SNPs, climate (IBE) did not significantly explained among‐population variation when controlling for IBD and IBC in redundancy analyses (RDAs). However, 26 SNPs were significantly associated with climate in single‐locus GEA analyses (Bayenv2 and LFMM), suggesting that local adaptation took place in the presence of high gene flow. For P. monticola, we found no evidence of IBE using RDAs and weaker signatures of local adaptation using GEA and FST outlier tests, consistent with adaptation via phenotypic plasticity. In both species, the majority of the explained among‐population variation (69 to 96%) could not be partitioned between the effects of IBE, IBD, and IBC. GEA methods can account differently for this confounded variation, and this could explain the small overlap of SNPs detected between Bayenv2 and LFMM. Our study illustrates the inherent difficulty of taking into account neutral structure in natural populations and the importance of sampling designs that maximize climatic variation, while minimizing collinearity between climatic gradients and neutral structure.
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Affiliation(s)
- Simon Nadeau
- Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre Québec QC Canada; Department of Forest and Conservation Sciences The University of British Columbia Vancouver BC Canada
| | - Patrick G Meirmans
- Institute for Biodiversity and Ecosystem Dynamics University of Amsterdam Amsterdam The Netherlands
| | - Sally N Aitken
- Department of Forest and Conservation Sciences The University of British Columbia Vancouver BC Canada
| | - Kermit Ritland
- Department of Forest and Conservation Sciences The University of British Columbia Vancouver BC Canada
| | - Nathalie Isabel
- Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre Québec QC Canada
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20
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Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies. G3-GENES GENOMES GENETICS 2016; 6:1979-89. [PMID: 27172202 PMCID: PMC4938651 DOI: 10.1534/g3.116.028753] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The joint inference of selection and past demography remain a costly and demanding task. We used next generation sequencing of two pools of 48 Norway spruce mother trees, one corresponding to the Fennoscandian domain, and the other to the Alpine domain, to assess nucleotide polymorphism at 88 nuclear genes. These genes are candidate genes for phenological traits, and most belong to the photoperiod pathway. Estimates of population genetic summary statistics from the pooled data are similar to previous estimates, suggesting that pooled sequencing is reliable. The nonsynonymous SNPs tended to have both lower frequency differences and lower FST values between the two domains than silent ones. These results suggest the presence of purifying selection. The divergence between the two domains based on synonymous changes was around 5 million yr, a time similar to a recent phylogenetic estimate of 6 million yr, but much larger than earlier estimates based on isozymes. Two approaches, one of them novel and that considers both FST and difference in allele frequencies between the two domains, were used to identify SNPs potentially under diversifying selection. SNPs from around 20 genes were detected, including genes previously identified as main target for selection, such as PaPRR3 and PaGI.
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21
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Tsuda Y, Chen J, Stocks M, Källman T, Sønstebø JH, Parducci L, Semerikov V, Sperisen C, Politov D, Ronkainen T, Väliranta M, Vendramin GG, Tollefsrud MM, Lascoux M. The extent and meaning of hybridization and introgression between Siberian spruce (Picea obovata) and Norway spruce (Picea abies): cryptic refugia as stepping stones to the west? Mol Ecol 2016; 25:2773-89. [PMID: 27087633 DOI: 10.1111/mec.13654] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 02/23/2016] [Accepted: 04/09/2016] [Indexed: 01/17/2023]
Abstract
Boreal species were repeatedly exposed to ice ages and went through cycles of contraction and expansion while sister species alternated periods of contact and isolation. The resulting genetic structure is consequently complex, and demographic inferences are intrinsically challenging. The range of Norway spruce (Picea abies) and Siberian spruce (Picea obovata) covers most of northern Eurasia; yet their geographical limits and histories remain poorly understood. To delineate the hybrid zone between the two species and reconstruct their joint demographic history, we analysed variation at nuclear SSR and mitochondrial DNA in 102 and 88 populations, respectively. The dynamics of the hybrid zone was analysed with approximate Bayesian computation (ABC) followed by posterior predictive structure plot reconstruction and the presence of barriers across the range tested with estimated effective migration surfaces. To estimate the divergence time between the two species, nuclear sequences from two well-separated populations of each species were analysed with ABC. Two main barriers divide the range of the two species: one corresponds to the hybrid zone between them, and the other separates the southern and northern domains of Norway spruce. The hybrid zone is centred on the Urals, but the genetic impact of Siberian spruce extends further west. The joint distribution of mitochondrial and nuclear variation indicates an introgression of mitochondrial DNA from Norway spruce into Siberian spruce. Overall, our data reveal a demographic history where the two species interacted frequently and where migrants originating from the Urals and the West Siberian Plain recolonized northern Russia and Scandinavia using scattered refugial populations of Norway spruce as stepping stones towards the west.
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Affiliation(s)
- Yoshiaki Tsuda
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden.,CNR, Institute of Biosciences and Bioresources, Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy
| | - Jun Chen
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Michael Stocks
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Thomas Källman
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | | | - Laura Parducci
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Vladimir Semerikov
- Urals Division of the Russian Academy of Sciences, Institute of Plant and Animal Ecology, 8 Marta Str., 202, 620144, Ekaterinburg, Russia
| | - Christoph Sperisen
- Swiss Federal Research Institute for Forest, Snow and Landscape Research (WSL), Zürcherstrasse 111, CH-8903, Birmendsdorf, Switzerland
| | - Dmitry Politov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin str. 3, 119991, Moscow, Russia
| | - Tiina Ronkainen
- Environmental Change Research Unit (ECRU), Department of Environmental Sciences, University of Helsinki, PO Box 65, FI-00014, Helsinki, Finland
| | - Minna Väliranta
- Environmental Change Research Unit (ECRU), Department of Environmental Sciences, University of Helsinki, PO Box 65, FI-00014, Helsinki, Finland
| | - Giovanni Giuseppe Vendramin
- CNR, Institute of Biosciences and Bioresources, Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy
| | | | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
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22
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Millar AJ. The Intracellular Dynamics of Circadian Clocks Reach for the Light of Ecology and Evolution. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:595-618. [PMID: 26653934 DOI: 10.1146/annurev-arplant-043014-115619] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A major challenge for biology is to extend our understanding of molecular regulation from the simplified conditions of the laboratory to ecologically relevant environments. Tractable examples are essential to make these connections for complex, pleiotropic regulators and, to go further, to link relevant genome sequences to field traits. Here, I review the case for the biological clock in higher plants. The gene network of the circadian clock drives pervasive, 24-hour rhythms in metabolism, behavior, and physiology across the eukaryotes and in some prokaryotes. In plants, the scope of chronobiology is now extending from the most tractable, intracellular readouts to the clock's many effects at the whole-organism level and across the life cycle, including biomass and flowering. I discuss five research areas where recent progress might be integrated in the future, to understand not only circadian functions in natural conditions but also the evolution of the clock's molecular mechanisms.
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Affiliation(s)
- Andrew J Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, United Kingdom;
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23
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Lu P, Parker WC, Colombo SJ, Man R. Restructuring tree provenance test data to conform to reciprocal transplant experiments for detecting local adaptation. J Appl Ecol 2016. [DOI: 10.1111/1365-2664.12647] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pengxin Lu
- Ontario Forest Research Institute; Ontario Ministry of Natural Resources and Forestry; 1235 Queen Street East Sault Ste. Marie ON P6A 2E5 Canada
| | - William C. Parker
- Ontario Forest Research Institute; Ontario Ministry of Natural Resources and Forestry; 1235 Queen Street East Sault Ste. Marie ON P6A 2E5 Canada
| | - Stephen J. Colombo
- Ontario Forest Research Institute; Ontario Ministry of Natural Resources and Forestry; 1235 Queen Street East Sault Ste. Marie ON P6A 2E5 Canada
| | - Rongzhou Man
- Ontario Forest Research Institute; Ontario Ministry of Natural Resources and Forestry; 1235 Queen Street East Sault Ste. Marie ON P6A 2E5 Canada
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24
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Pluess AR, Frank A, Heiri C, Lalagüe H, Vendramin GG, Oddou-Muratorio S. Genome-environment association study suggests local adaptation to climate at the regional scale in Fagus sylvatica. THE NEW PHYTOLOGIST 2016; 210:589-601. [PMID: 26777878 DOI: 10.1111/nph.13809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 11/12/2015] [Indexed: 05/09/2023]
Abstract
The evolutionary potential of long-lived species, such as forest trees, is fundamental for their local persistence under climate change (CC). Genome-environment association (GEA) analyses reveal if species in heterogeneous environments at the regional scale are under differential selection resulting in populations with potential preadaptation to CC within this area. In 79 natural Fagus sylvatica populations, neutral genetic patterns were characterized using 12 simple sequence repeat (SSR) markers, and genomic variation (144 single nucleotide polymorphisms (SNPs) out of 52 candidate genes) was related to 87 environmental predictors in the latent factor mixed model, logistic regressions and isolation by distance/environmental (IBD/IBE) tests. SSR diversity revealed relatedness at up to 150 m intertree distance but an absence of large-scale spatial genetic structure and IBE. In the GEA analyses, 16 SNPs in 10 genes responded to one or several environmental predictors and IBE, corrected for IBD, was confirmed. The GEA often reflected the proposed gene functions, including indications for adaptation to water availability and temperature. Genomic divergence and the lack of large-scale neutral genetic patterns suggest that gene flow allows the spread of advantageous alleles in adaptive genes. Thereby, adaptation processes are likely to take place in species occurring in heterogeneous environments, which might reduce their regional extinction risk under CC.
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Affiliation(s)
- Andrea R Pluess
- Swiss Federal Institute of Forest, Snow and Landscape Research WSL, Zurcherstrasse 111, 8903, Birmensdorf, Switzerland
- Swiss Federal Institute of Technology ETH, Universitatstrasse 16, 8092, Zurich, Switzerland
| | - Aline Frank
- Swiss Federal Institute of Forest, Snow and Landscape Research WSL, Zurcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Caroline Heiri
- Swiss Federal Institute of Forest, Snow and Landscape Research WSL, Zurcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Hadrien Lalagüe
- INRA, UR629 Ecologie des Forêts Méditerranéennes (URFM), F-84914, Avignon, France
- INRA, Institut National de la Recherche Agronomique, Avenue the France, 97310, Kourou, France
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino (FI), Italy
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25
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Mattila TM, Aalto EA, Toivainen T, Niittyvuopio A, Piltonen S, Kuittinen H, Savolainen O. Selection for population-specific adaptation shaped patterns of variation in the photoperiod pathway genes in Arabidopsis lyrata during post-glacial colonization. Mol Ecol 2016; 25:581-97. [PMID: 26600237 DOI: 10.1111/mec.13489] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 11/16/2015] [Accepted: 11/18/2015] [Indexed: 12/20/2022]
Abstract
Spatially varying selection can lead to population-specific adaptation, which is often recognized at the phenotypic level; however, the genetic evidence is weaker in many groups of organisms. In plants, environmental shifts that occur due to colonization of a novel environment may require adaptive changes in the timing of growth and flowering, which are often governed by location-specific environmental cues such as day length. We studied locally varying selection in 19 flowering time loci in nine populations of the perennial herb Arabidopsis lyrata, which has a wide but patchy distribution in temperate and boreal regions of the northern hemisphere. The populations differ in their recent population demographic and colonization histories and current environmental conditions, especially in the growing season length. We searched for population-specific molecular signatures of directional selection by comparing a set of candidate flowering time loci with a genomic reference set within each population using multiple approaches and contrasted the patterns of different populations. The candidate loci possessed approximately 20% of the diversity of the reference loci. On average the flowering time loci had more rare alleles (a smaller Tajima's D) and an excess of highly differentiated sites relative to the reference, suggesting positive selection. The strongest signal of selection was detected in photoperiodic pathway loci in the colonizing populations of Northwestern Europe, whereas no evidence of positive selection was detected in the Central European populations. These findings emphasized the population-specific nature of selection and suggested that photoperiodic adaptation was important during postglacial colonization of the species.
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Affiliation(s)
- Tiina M Mattila
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Esa A Aalto
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Tuomas Toivainen
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland.,Biocenter Oulu, University of Oulu, 90014, Oulu, Finland
| | - Anne Niittyvuopio
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Susanna Piltonen
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Helmi Kuittinen
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Outi Savolainen
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland.,Biocenter Oulu, University of Oulu, 90014, Oulu, Finland
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26
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Mishra P, Panigrahi KC. GIGANTEA - an emerging story. FRONTIERS IN PLANT SCIENCE 2015; 6:8. [PMID: 25674098 PMCID: PMC4306306 DOI: 10.3389/fpls.2015.00008] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 01/06/2015] [Indexed: 05/02/2023]
Abstract
GIGANTEA (GI) is a plant specific nuclear protein and functions in diverse physiological processes such as flowering time regulation, light signaling, hypocotyl elongation, control of circadian rhythm, sucrose signaling, starch accumulation, chlorophyll accumulation, transpiration, herbicide tolerance, cold tolerance, drought tolerance, and miRNA processing. It has been five decades since its discovery but the biochemical function of GI and its different domains are still unclear. Although it is known that both GI transcript and GI protein are clock controlled, the regulation of its abundance and functions at the molecular level are still some of the unexplored areas of intensive research. Since GI has many important pleotropic functions as described above scattered through literature, it is worthwhile and about time to encapsulate the available information in a concise review. Therefore, in this review, we are making an attempt to summarize (i) the various interconnected roles that GI possibly plays in the fine-tuning of plant development, and (ii) the known mutations of GI that have been instrumental in understanding its role in distinct physiological processes.
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Affiliation(s)
| | - Kishore C. Panigrahi
- *Correspondence: Kishore C. Panigrahi, Plant Science Lab, School of Biological Sciences, National Institute of Science Education and Research, IOP campus, Sachivalaya Marg, P.O. Sainik School, Bhubaneshwar 751005, Orissa, India e-mail:
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27
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Molecular proxies for climate maladaptation in a long-lived tree (Pinus pinaster Aiton, Pinaceae). Genetics 2014; 199:793-807. [PMID: 25549630 DOI: 10.1534/genetics.114.173252] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Understanding adaptive genetic responses to climate change is a main challenge for preserving biological diversity. Successful predictive models for climate-driven range shifts of species depend on the integration of information on adaptation, including that derived from genomic studies. Long-lived forest trees can experience substantial environmental change across generations, which results in a much more prominent adaptation lag than in annual species. Here, we show that candidate-gene SNPs (single nucleotide polymorphisms) can be used as predictors of maladaptation to climate in maritime pine (Pinus pinaster Aiton), an outcrossing long-lived keystone tree. A set of 18 SNPs potentially associated with climate, 5 of them involving amino acid-changing variants, were retained after performing logistic regression, latent factor mixed models, and Bayesian analyses of SNP-climate correlations. These relationships identified temperature as an important adaptive driver in maritime pine and highlighted that selective forces are operating differentially in geographically discrete gene pools. The frequency of the locally advantageous alleles at these selected loci was strongly correlated with survival in a common garden under extreme (hot and dry) climate conditions, which suggests that candidate-gene SNPs can be used to forecast the likely destiny of natural forest ecosystems under climate change scenarios. Differential levels of forest decline are anticipated for distinct maritime pine gene pools. Geographically defined molecular proxies for climate adaptation will thus critically enhance the predictive power of range-shift models and help establish mitigation measures for long-lived keystone forest trees in the face of impending climate change.
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Tiffin P, Ross-Ibarra J. Advances and limits of using population genetics to understand local adaptation. Trends Ecol Evol 2014; 29:673-80. [DOI: 10.1016/j.tree.2014.10.004] [Citation(s) in RCA: 248] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/08/2014] [Accepted: 10/10/2014] [Indexed: 01/09/2023]
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