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Archambeau J, Benito Garzón M, de Miguel M, Brachi B, Barraquand F, González-Martínez SC. Reduced within-population quantitative genetic variation is associated with climate harshness in maritime pine. Heredity (Edinb) 2023; 131:68-78. [PMID: 37221230 PMCID: PMC10313832 DOI: 10.1038/s41437-023-00622-9] [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: 09/10/2021] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 05/25/2023] Open
Abstract
How evolutionary forces interact to maintain genetic variation within populations has been a matter of extensive theoretical debates. While mutation and exogenous gene flow increase genetic variation, stabilizing selection and genetic drift are expected to deplete it. To date, levels of genetic variation observed in natural populations are hard to predict without accounting for other processes, such as balancing selection in heterogeneous environments. We aimed to empirically test three hypotheses: (i) admixed populations have higher quantitative genetic variation due to introgression from other gene pools, (ii) quantitative genetic variation is lower in populations from harsher environments (i.e., experiencing stronger selection), and (iii) quantitative genetic variation is higher in populations from heterogeneous environments. Using growth, phenological and functional trait data from three clonal common gardens and 33 populations (522 clones) of maritime pine (Pinus pinaster Aiton), we estimated the association between the population-specific total genetic variances (i.e., among-clone variances) for these traits and ten population-specific indices related to admixture levels (estimated based on 5165 SNPs), environmental temporal and spatial heterogeneity and climate harshness. Populations experiencing colder winters showed consistently lower genetic variation for early height growth (a fitness-related trait in forest trees) in the three common gardens. Within-population quantitative genetic variation was not associated with environmental heterogeneity or population admixture for any trait. Our results provide empirical support for the potential role of natural selection in reducing genetic variation for early height growth within populations, which indirectly gives insight into the adaptive potential of populations to changing environments.
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Affiliation(s)
- Juliette Archambeau
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France.
- UK Centre for Ecology & Hydrology, Bush Estate, Penicuik, UK.
| | | | - Marina de Miguel
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
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Müller M, Kües U, Budde KB, Gailing O. Applying molecular and genetic methods to trees and their fungal communities. Appl Microbiol Biotechnol 2023; 107:2783-2830. [PMID: 36988668 PMCID: PMC10106355 DOI: 10.1007/s00253-023-12480-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023]
Abstract
Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.
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Affiliation(s)
- Markus Müller
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany.
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany.
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Katharina B Budde
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
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Chamberlain C, Wolkovich E. Variation across space, species and methods in models of spring phenology. CLIMATE CHANGE ECOLOGY 2023. [DOI: 10.1016/j.ecochg.2023.100071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
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Galeano E, Thomas BR. Unraveling genetic variation among white spruce families generated through different breeding strategies: Heritability, growth, physiology, hormones and gene expression. FRONTIERS IN PLANT SCIENCE 2023; 14:1052425. [PMID: 37077625 PMCID: PMC10106773 DOI: 10.3389/fpls.2023.1052425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/15/2023] [Indexed: 05/03/2023]
Abstract
Tree improvement programs select genotypes for faster growth, at both early and late stages, to increase yields over unimproved material, and the improvement is frequently attributed to genetic control in growth parameters among genotypes. Underutilized genetic variability among genotypes also has the potential to ensure future gains are possible. However, the genetic variation in growth, physiology and hormone control among genotypes generated from different breeding strategies has not been well characterized in conifers. We assessed growth, biomass, gas exchange, gene expression and hormone levels in white spruce seedlings obtained from three different breeding strategies (controlled crosses, polymix pollination, open pollination) using parents grafted into a clonal seed orchard in Alberta, Canada. A pedigree-based best linear unbiased prediction (ABLUP) mixed model was implemented to quantify variability and narrow-sense heritability for target traits. The levels of several hormones and expression of gibberellin-related genes in apical internodes were also determined. Over the first two years of development, the estimated heritabilities for height, volume, total dry biomass, above ground dry biomass, root:shoot ratio and root length, varied between 0.10 and 0.21, with height having the highest value. The ABLUP values showed large genetic variability in growth and physiology traits both between families from different breeding strategies, and within families. The principal component analysis showed that developmental and hormonal traits explained 44.2% and 29.4% of the total phenotypic variation between the three different breeding strategies and two growth groups. In general, controlled crosses from the fast growth group showed the best apical growth, with more accumulation of indole-3-acetic acid, abscisic acid, phaseic acid, and a 4-fold greater gene expression of PgGA3ox1 in genotypes from controlled crosses versus those from open pollination. However, in some cases, open pollination from the fast and slow growth groups showed the best root development, higher water use efficiency (iWUE and δ13C) and more accumulation of zeatin and isopentenyladenosine. In conclusion, tree domestication can lead to trade-offs between growth, carbon allocation, photosynthesis, hormone levels and gene expression, and we encourage the use of this phenotypic variation identified in improved and unimproved trees to advance white spruce tree improvement programs.
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Affiliation(s)
- Esteban Galeano
- Department of Forestry, Mississippi State University, Starkville, MS, United States
- Department of Renewable Resources, University of Alberta, Edmonton, AB, Canada
- *Correspondence: Esteban Galeano,
| | - Barb R. Thomas
- Department of Renewable Resources, University of Alberta, Edmonton, AB, Canada
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Du C, Sun P, Cheng X, Zhang L, Wang L, Hu J. QTL mapping of drought-related traits in the hybrids of Populus deltoides 'Danhong'×Populus simonii 'Tongliao1'. BMC PLANT BIOLOGY 2022; 22:238. [PMID: 35545765 PMCID: PMC9092850 DOI: 10.1186/s12870-022-03613-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Poplar trees provide a large amount of wood material, but many parts of the world are arid or semi-arid areas because of insufficient annual precipitation, which seriously affects the growth of poplar trees. Populus simonii 'Tongliao1' shows strong tolerance to stress environments, and Populus deltoides 'Danhong' shows a stronger growth rate in a suitable environment. To identify drought tolerance-related QTLs and genes, an F1 population derived from the cross between the 'Danhong' and 'Tongliao 1' Populus was assessed under drought stress. RESULTS We measured drought-related traits such as the relative height growth, relative diameter growth, leaf senescence number, specific leaf area, and leaf relative water content in the population under control and drought environments. The results showed that drought stress reduced the plant height relative growth, ground diameter relative growth, specific leaf area and leaf relative water content and increased the number of leaf drops. A total of 208 QTLs were identified by QTL mapping analysis, and they consisted of 92, 63 and 53 QTLs under control, drought stress treatment and drought index conditions, respectively. A molecular identification marker for drought tolerance, np2841, which was associated with a QTL (qDLRWC-LG10-1) for relative leaf water content, was initially developed. We mined 187 candidate genes for QTL regions of five traits under a drought environment. The reference genome annotation for Populus trichocarpa and a homologous gene analysis of Arabidopsis thaliana identified two candidate genes, Potri.003G171300 and Potri.012G123900, with significant functions in response to drought stress. We identified five key regulatory genes (Potri.006G273500, Potri.007G111500, Potri.007G111600, Potri.007G111700, and Potri.007G111800) related to drought tolerance through the poplar coexpression network. CONCLUSION In this study, our results indicate that the QTLs can effectively enhance the drought tolerance of poplar. It is a step closer towards unravelling the genetic basis of poplar drought tolerance-related traits, and to providing validated candidate genes and molecular markers for future genetic improvement.
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Affiliation(s)
- Changjian Du
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Pei Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China
| | - Xingqi Cheng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Lei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Lijuan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
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Perry A, Wachowiak W, Beaton J, Iason G, Cottrell J, Cavers S. Identifying and testing marker‐trait associations for growth and phenology in three pine species: implications for genomic prediction. Evol Appl 2022; 15:330-348. [PMID: 35233251 PMCID: PMC8867712 DOI: 10.1111/eva.13345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/02/2022] Open
Abstract
In tree species, genomic prediction offers the potential to forecast mature trait values in early growth stages, if robust marker–trait associations can be identified. Here we apply a novel multispecies approach using genotypes from a new genotyping array, based on 20,795 single nucleotide polymorphisms (SNPs) from three closely related pine species (Pinus sylvestris, Pinus uncinata and Pinus mugo), to test for associations with growth and phenology data from a common garden study. Predictive models constructed using significantly associated SNPs were then tested and applied to an independent multisite field trial of P. sylvestris and the capability to predict trait values was evaluated. One hundred and eighteen SNPs showed significant associations with the traits in the pine species. Common SNPs (MAF > 0.05) associated with bud set were only found in genes putatively involved in growth and development, whereas those associated with growth and budburst were also located in genes putatively involved in response to environment and, to a lesser extent, reproduction. At one of the two independent sites, the model we developed produced highly significant correlations between predicted values and observed height data (YA, height 2020: r = 0.376, p < 0.001). Predicted values estimated with our budburst model were weakly but positively correlated with duration of budburst at one of the sites (GS, 2015: r = 0.204, p = 0.034; 2018: r = 0.205, p = 0.034–0.037) and negatively associated with budburst timing at the other (YA: r = −0.202, p = 0.046). Genomic prediction resulted in the selection of sets of trees whose mean height was taller than the average for each site. Our results provide tentative support for the capability of prediction models to forecast trait values in trees, while highlighting the need for caution in applying them to trees grown in different environments.
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Affiliation(s)
- Annika Perry
- UK Centre for Ecology & Hydrology Edinburgh Penicuik Midlothian EH26 0QB UK
| | - Witold Wachowiak
- Institute of Environmental Biology Faculty of Biology Adam Mickiewicz University Poznań Poland
| | - Joan Beaton
- James Hutton Institute Craigiebuckler, Aberdeen AB15 8QH UK
| | - Glenn Iason
- James Hutton Institute Craigiebuckler, Aberdeen AB15 8QH UK
| | - Joan Cottrell
- Northern Research Station, Forest Research Roslin EH25 9SY UK
| | - Stephen Cavers
- UK Centre for Ecology & Hydrology Edinburgh Penicuik Midlothian EH26 0QB UK
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Genetic Diversity and Differentiation of Pedunculate Oak (Quercus robur L.) Populations at the Southern Margin of Its Distribution Range—Implications for Conservation. DIVERSITY 2021. [DOI: 10.3390/d13080371] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Understanding intraspecific genetic variation is one of the principal requirements for the evaluation of tree species capacity to cope with intensive climatic changes, as well as designing long-term conservation programs. Herein, we evaluated the genetic diversity and genetic structure of seven pedunculate oak (Quercus robur L.) populations, located at the southern margin of its distribution range on the Balkan Peninsula (Serbia). The objective of the study was to propose future in situ conservation measures aimed at protection of pedunculate oak adaptive and neutral genetic diversity at the species rear-edge. Genetic diversity and structure were estimated using twelve highly polymorphic simple sequence repeat (SSR) markers. The mean expected heterozygosity (He) was 0.769, allelic richness (AR) 9.63, and private allelic richness (pAR) 0.79, indicating high genetic diversity in the studied populations. Genetic differentiation among the populations was low (Fst = 0.032). Structure analysis, the unweighted pair group method with arithmetic mean (UPGMA) showed the existence of two gene pools unrelated to the populations’ area of occurrence. Taking into consideration the results of the current study and previous conservation activities on the pedunculate oak in Serbia, as well as the importance of rear-edge populations in the long-term conservation of the species genetic diversity, we suggested establishing three additional gene conservation units for securing long-term sustainability of the species.
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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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Varying Levels of Genetic Control and Phenotypic Plasticity in Timing of Bud Burst, Flower Opening, Leaf Senescence and Leaf Fall in Two Common Gardens of Prunus padus L.
. FORESTS 2020. [DOI: 10.3390/f11101070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Several phenological phases mark the seasonal growth pattern in temperate woody perennials. To gain further insight into the way these phases react on an altering growth environment, we tested whether vegetative and reproductive phenophases in a shrub species respond differentially among different genetic entities and between two different planting sites. We scored leaf bud burst, flower opening, leaf senescence and leaf fall on 267 ramets of Prunus padus L. belonging to 53 genotypes that were sampled in 9 local populations, and that were planted in 2 common gardens in the northern part of Belgium. The data were processed with cumulative logistic regression. The contribution of genetic and non-genetic components to the total variability varied between the four studied seasonal phenophases. The timing of flower opening displayed the smallest relative amount of intragenotypic variance (between ramets), suggesting a stronger genetic control and a lesser need at the individual plant level for plastic fine tuning to the micro-environment. In addition, whereas leaf bud burst showed the highest relative variance at the interpopulation level among all phenophases, probably at least partly attributable to local adaptation, flower opening displayed the highest intergenotypic variance, which may have been promoted more by assortative mating. Spring phenophases were strongly correlated (r = 0.89) as well as the autumnal phenophases (r = 0.72). Flower opening was not correlated with the autumnal phenophases. Timing of leaf bud burst and leaf senescence were negatively correlated, demonstrating that the length of the growing season enlarged or diminished among the studied genotypes. Although the two planting sites were only 24 km apart, all phenophases were advanced at the less exposed site, indicating a phenotypic plastic response. Together, our results suggest that in P. padus, flowering is less sensitive to environmental variation than leaf bud break and may show a lesser impact of a changing environment on this reproductive phenophase.
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Berzaghi F, Wright IJ, Kramer K, Oddou-Muratorio S, Bohn FJ, Reyer CPO, Sabaté S, Sanders TGM, Hartig F. Towards a New Generation of Trait-Flexible Vegetation Models. Trends Ecol Evol 2019; 35:191-205. [PMID: 31882280 DOI: 10.1016/j.tree.2019.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/15/2019] [Accepted: 11/25/2019] [Indexed: 12/17/2022]
Abstract
Plant trait variability, emerging from eco-evolutionary dynamics that range from alleles to macroecological scales, is one of the most elusive, but possibly most consequential, aspects of biodiversity. Plasticity, epigenetics, and genetic diversity are major determinants of how plants will respond to climate change, yet these processes are rarely represented in current vegetation models. Here, we provide an overview of the challenges associated with understanding the causes and consequences of plant trait variability, and review current developments to include plasticity and evolutionary mechanisms in vegetation models. We also present a roadmap of research priorities to develop a next generation of vegetation models with flexible traits. Including trait variability in vegetation models is necessary to better represent biosphere responses to global change.
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Affiliation(s)
- Fabio Berzaghi
- Laboratory for Sciences of Climate and Environment (LSCE) - UMR CEA/CNRS/UVSQ, Gif-sur-Yvette 91191, France; Department of Biological Sciences, Macquarie University, Sydney, NSW 2022, Australia; Dipartimento per la Innovazione nei sistemi Biologici, Agroalimentari e Forestali, University of Tuscia, Viterbo 01100, Italy.
| | - Ian J Wright
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2022, Australia
| | - Koen Kramer
- Wageningen University and Research, Droevendaalse steeg 4, 6700AA Wageningen, The Netherlands
| | | | - Friedrich J Bohn
- Karlsruhe Institute of Technology, Institute for Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU), Kreuzeckbahnstrasse 19, Garmisch-Partenkirchen 82467, Germany; Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, Leipzig 04318, Germany
| | - Christopher P O Reyer
- Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, PO Box 60 12 03, D-14412 Potsdam, Germany
| | - Santiago Sabaté
- Department of Evolutionary Biology, Ecology, and Environmental Sciences, University of Barcelona (UB), Barcelona 08028, Spain; CREAF (Center for Ecological Research and Forestry Applications), Cerdanyola del Vallès 08193, Spain
| | - Tanja G M Sanders
- Thuenen Institut of Forest Ecosystems, Alfred-Moeller-Str. 1, Haus 41/42, 16225 Eberswalde, Germany
| | - Florian Hartig
- Theoretical Ecology, Faculty of Biology and Preclinical Medicine, University of Regensburg, Universitätsstraße 3, 93053, Regensburg, Germany
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Calleja-Rodriguez A, Li Z, Hallingbäck HR, Sillanpää MJ, Wu HX, Abrahamsson S, García-Gil MR. Analysis of phenotypic- and Estimated Breeding Values (EBV) to dissect the genetic architecture of complex traits in a Scots pine three-generation pedigree design. J Theor Biol 2019; 462:283-292. [PMID: 30423305 DOI: 10.1016/j.jtbi.2018.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/17/2018] [Accepted: 11/09/2018] [Indexed: 11/28/2022]
Abstract
In forest tree breeding, family-based Quantitative Trait Loci (QTL) studies are valuable as methods to dissect the complexity of a trait and as a source of candidate genes. In the field of conifer research, our study contributes to the evaluation of phenotypic and predicted breeding values for the identification of QTL linked to complex traits in a three-generation pedigree population in Scots pine (Pinus sylvestris L.). A total of 11 470 open pollinated F2-progeny trees established at three different locations, were measured for growth and adaptive traits. Breeding values were predicted for their 360 mothers, originating from a single cross of two grand-parents. A multilevel LASSO association analysis was conducted to detect QTL using genotypes of the mothers with the corresponding phenotypes and Estimated Breeding Values (EBV). Different levels of genotype-by-environment (G × E) effects among sites at different years, were detected for survival and height. Moderate-to-low narrow sense heritabilities and EBV accuracies were found for all traits and all sites. We identified 18 AFLPs and 12 SNPs to be associated with QTL for one or more traits. 62 QTL were significant with percentages of variance explained ranging from 1.7 to 18.9%. In those cases where the same marker was associated to a phenotypic or an ebvQTL, the ebvQTL always explained higher proportion of the variance, maybe due to the more accurate nature of Estimated Breeding Values (EBV). Two SNP-QTL showed pleiotropic effects for traits related with hardiness, seed, cone and flower production. Furthermore, we detected several QTL with significant effects across multiple ages, which could be considered as strong candidate loci for early selection. The lack of reproducibility of some QTL detected across sites may be due to environmental heterogeneity reflected by the genotype- and QTL-by-environment effects.
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Affiliation(s)
- Ainhoa Calleja-Rodriguez
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå SE-901 83, Sweden; Skogforsk, Box 3, Sävar SE-91821, Sweden
| | - Zitong Li
- Melbourne Integrative Genomics and School of Mathematics and Statistics, the University of Melbourne, Parkville, Victoria 3010, Australia; Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki FI-00014, Finland
| | - Henrik R Hallingbäck
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå SE-901 83, Sweden; Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Science, Uppsala SE-75007, Sweden
| | - Mikko J Sillanpää
- Department of Mathematical Sciences and Biocenter Oulu, University of Oulu, Oulu FI-90014, Finland
| | - Harry X Wu
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå SE-901 83, Sweden
| | | | - Maria Rosario García-Gil
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå SE-901 83, Sweden.
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Caignard T, Delzon S, Bodénès C, Dencausse B, Kremer A. Heritability and genetic architecture of reproduction-related traits in a temperate oak species. TREE GENETICS & GENOMES 2019; 15:1. [PMID: 30546292 PMCID: PMC6287713 DOI: 10.1007/s11295-018-1309-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/23/2018] [Accepted: 11/26/2018] [Indexed: 05/12/2023]
Abstract
Reproduction, one of the main components of plant fitness, is highly variable in response to environmental cues, but little is known about the genetic determinism underlying reproduction-related traits in forest tree species. There is therefore an urgent need to characterize the genetic architecture of those traits if we are to predict the evolutionary trajectories of forest populations facing rapidly changing environment and mitigate their impacts. Using a full-sib family of pedunculate oak (Quercus robur), we investigated the within population variability of seed production and mean seed mass during four consecutive years. Reproductive traits were highly variable between trees and between years. The high narrow sense heritability and evolvability estimated underline the important genetic effect on the variability in seed production and mean seed mass. Despite a large variability over years, reproductive traits show significant genetic correlation between years. Furthermore, for the first time in forest tree species, quantitative trait loci (QTLs) associated with seed production and mean mass of a seed have been identified. While it is commonly assumed and observed that fitness-traits have low narrow sense heritabilities, our findings show that reproduction-related traits may undergo evolutionary changes under selective pressure and may be determinant for tree adaptation.
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Affiliation(s)
- Thomas Caignard
- UMR BIOGECO 1202-INRA, University of Bordeaux, 33615, Pessac,
France
| | - Sylvain Delzon
- UMR BIOGECO 1202-INRA, University of Bordeaux, 33615, Pessac,
France
| | - Catherine Bodénès
- UMR BIOGECO 1202-INRA, University of Bordeaux, 33615, Pessac,
France
| | | | - Antoine Kremer
- UMR BIOGECO 1202-INRA, University of Bordeaux, 33615, Pessac,
France
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13
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Plomion C, Aury JM, Amselem J, Leroy T, Murat F, Duplessis S, Faye S, Francillonne N, Labadie K, Le Provost G, Lesur I, Bartholomé J, Faivre-Rampant P, Kohler A, Leplé JC, Chantret N, Chen J, Diévart A, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Bogeat-Triboulot MB, Bouffaud ML, Brachi B, Chancerel E, Cohen D, Couloux A, Da Silva C, Dossat C, Ehrenmann F, Gaspin C, Grima-Pettenati J, Guichoux E, Hecker A, Herrmann S, Hugueney P, Hummel I, Klopp C, Lalanne C, Lascoux M, Lasserre E, Lemainque A, Desprez-Loustau ML, Luyten I, Madoui MA, Mangenot S, Marchal C, Maumus F, Mercier J, Michotey C, Panaud O, Picault N, Rouhier N, Rué O, Rustenholz C, Salin F, Soler M, Tarkka M, Velt A, Zanne AE, Martin F, Wincker P, Quesneville H, Kremer A, Salse J. Oak genome reveals facets of long lifespan. NATURE PLANTS 2018; 4:440-452. [PMID: 29915331 PMCID: PMC6086335 DOI: 10.1038/s41477-018-0172-3] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 05/08/2018] [Indexed: 05/18/2023]
Abstract
Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times2. With 450 species spread throughout Asia, Europe and America3, oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical4 and modelling5 approaches have shown that intra-organismal genetic heterogeneity can be selected for6 and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes7. However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.
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Affiliation(s)
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | | | | | - Sébastien Faye
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | - Isabelle Lesur
- BIOGECO, INRA, Université de Bordeaux, Cestas, France
- HelixVenture, Mérignac, France
| | | | | | | | | | - Nathalie Chantret
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Jun Chen
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anne Diévart
- CIRAD, UMR AGAP, Montpellier, France
- Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Valérie Barbe
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Caroline Belser
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | | | - Marie-Lara Bouffaud
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle/Saale, Germany
| | | | | | - David Cohen
- UMR Silva, INRA, Université de Lorraine, AgroPariTech, Nancy, France
| | - Arnaud Couloux
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Carole Dossat
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | - Christine Gaspin
- Plateforme bioinformatique Toulouse Midi-Pyrénées, INRA, Auzeville Castanet-Tolosan, France
| | | | | | - Arnaud Hecker
- IAM, INRA, Université de Lorraine, Champenoux, France
| | - Sylvie Herrmann
- German Centre for Integrative Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | | | - Irène Hummel
- UMR Silva, INRA, Université de Lorraine, AgroPariTech, Nancy, France
| | - Christophe Klopp
- Plateforme bioinformatique Toulouse Midi-Pyrénées, INRA, Auzeville Castanet-Tolosan, France
| | | | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Eric Lasserre
- Université de Perpignan, UMR 5096, Perpignan, France
| | - Arnaud Lemainque
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | - Mohammed-Amin Madoui
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Sophie Mangenot
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | - Jonathan Mercier
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | | | | | - Olivier Rué
- Plateforme bioinformatique Toulouse Midi-Pyrénées, INRA, Auzeville Castanet-Tolosan, France
| | | | - Franck Salin
- BIOGECO, INRA, Université de Bordeaux, Cestas, France
| | - Marçal Soler
- Université de Toulouse, CNRS, UMR 5546, LRSV, Castanet-Tolosan, France
- Laboratori del Suro, University of Girona, Girona, Spain
| | - Mika Tarkka
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle/Saale, Germany
| | - Amandine Velt
- SVQV, Université de Strasbourg, INRA, Colmar, France
| | - Amy E Zanne
- Department of Biological Sciences, George Washington University, Washington, DC, USA
| | | | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université d'Evry, Université Paris-Saclay, Evry, France
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14
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Torello Marinoni D, Valentini N, Portis E, Acquadro A, Beltramo C, Mehlenbacher SA, Mockler TC, Rowley ER, Botta R. High density SNP mapping and QTL analysis for time of leaf budburst in Corylus avellana L. PLoS One 2018; 13:e0195408. [PMID: 29608620 PMCID: PMC5880404 DOI: 10.1371/journal.pone.0195408] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 03/21/2018] [Indexed: 01/25/2023] Open
Abstract
The growing area of European hazelnut (Corylus avellana L.) is increasing, as well as the number of producing countries, and there is a pressing need for new improved cultivars. Hazelnut conventional breeding process is slow, due to the length of juvenile phase and the high heterozygosity level. The development of genetic linkage maps and the identification of molecular markers tightly linked to QTL (quantitative trait loci) of agronomic interest are essential tools for speeding up the selection of seedlings carrying desired traits through marker-assisted selection. The objectives of this study were to enrich a previous linkage map and confirm QTL related to time of leaf budburst, using an F1 population obtained by crossing Tonda Gentile delle Langhe with Merveille de Bollwiller. Genotyping-by-Sequencing was used to identify a total of 9,999 single nucleotide polymorphism markers. Well saturated linkage maps were constructed for each parent using the double pseudo-testcross mapping strategy. A reciprocal translocation was detected in Tonda Gentile delle Langhe between two non-homologous chromosomes. Applying a bioinformatic approach, we were able to disentangle ‘pseudo-linkage’ between markers, removing markers around the translocation breakpoints and obtain a linear order of the markers for the two chromosomes arms, for each linkage group involved in the translocation. Twenty-nine QTL for time of leaf budburst were identified, including a stably expressed region on LG_02 of the Tonda Gentile delle Langhe map. The stability of these QTL and their coding sequence content indicates promise for the identification of specific chromosomal regions carrying key genes involved in leaf budburst.
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Affiliation(s)
- Daniela Torello Marinoni
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
| | - Nadia Valentini
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
- * E-mail:
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
| | - Chiara Beltramo
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
| | - Shawn A. Mehlenbacher
- Department of Horticulture, Oregon State University, Corvallis, Oregon, United States of America
| | - Todd C. Mockler
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Erik R. Rowley
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Roberto Botta
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
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15
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Comprehensive Analysis of the Cork Oak (Quercus suber) Transcriptome Involved in the Regulation of Bud Sprouting. FORESTS 2017. [DOI: 10.3390/f8120486] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Cole EF, Sheldon BC. The shifting phenological landscape: Within- and between-species variation in leaf emergence in a mixed-deciduous woodland. Ecol Evol 2017; 7:1135-1147. [PMID: 28303184 PMCID: PMC5305997 DOI: 10.1002/ece3.2718] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 11/30/2016] [Accepted: 12/18/2016] [Indexed: 12/20/2022] Open
Abstract
Many organisms rely on synchronizing the timing of their life-history events with those of other trophic levels-known as phenological matching-for survival or successful reproduction. In temperate deciduous forests, the extent of matching with the budburst date of key tree species is of particular relevance for many herbivorous insects and, in turn, insectivorous birds. In order to understand the ecological and evolutionary forces operating in these systems, we require knowledge of the factors influencing leaf emergence of tree communities. However, little is known about how phenology at the level of individual trees varies across landscapes, or how consistent this spatial variation is between different tree species. Here, we use field observations, collected over 2 years, to characterize within- and between-species differences in spring phenology for 825 trees of six species (Quercus robur, Fraxinus excelsior, Fagus sylvatica, Betula pendula, Corylus avellana, and Acer pseudoplatanus) in a 385-ha woodland. We explore environmental predictors of individual variation in budburst date and bud development rate and establish how these phenological traits vary over space. Trees of all species showed markedly consistent individual differences in their budburst timing. Bud development rate also varied considerably between individuals and was repeatable in oak, beech, and sycamore. We identified multiple predictors of budburst date including altitude, local temperature, and soil type, but none were universal across species. Furthermore, we found no evidence for interspecific covariance of phenology over space within the woodland. These analyses suggest that phenological landscapes are highly complex, varying over small spatial scales both within and between species. Such spatial variation in vegetation phenology is likely to influence patterns of selection on phenology within populations of consumers. Knowledge of the factors shaping the phenological environments experienced by animals is therefore likely to be key in understanding how these evolutionary processes operate.
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Affiliation(s)
- Ella F Cole
- Edward Grey Institute Department of Zoology University of Oxford Oxford UK
| | - Ben C Sheldon
- Edward Grey Institute Department of Zoology University of Oxford Oxford UK
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17
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Jakuschkin B, Fievet V, Schwaller L, Fort T, Robin C, Vacher C. Deciphering the Pathobiome: Intra- and Interkingdom Interactions Involving the Pathogen Erysiphe alphitoides. MICROBIAL ECOLOGY 2016; 72:870-880. [PMID: 27147439 DOI: 10.1007/s00248-016-0777-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 04/21/2016] [Indexed: 05/13/2023]
Abstract
Plant-inhabiting microorganisms interact directly with each other, forming complex microbial interaction networks. These interactions can either prevent or facilitate the establishment of new microbial species, such as a pathogen infecting the plant. Here, our aim was to identify the most likely interactions between Erysiphe alphitoides, the causal agent of oak powdery mildew, and other foliar microorganisms of pedunculate oak (Quercus robur L.). We combined metabarcoding techniques and a Bayesian method of network inference to decipher these interactions. Our results indicate that infection with E. alphitoides is accompanied by significant changes in the composition of the foliar fungal and bacterial communities. They also highlight 13 fungal operational taxonomic units (OTUs) and 13 bacterial OTUs likely to interact directly with E. alphitoides. Half of these OTUs, including the fungal endophytes Mycosphaerella punctiformis and Monochaetia kansensis, could be antagonists of E. alphitoides according to the inferred microbial network. Further studies will be required to validate these potential interactions experimentally. Overall, we showed that a combination of metabarcoding and network inference, by highlighting potential antagonists of pathogen species, could potentially improve the biological control of plant diseases.
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Affiliation(s)
- Boris Jakuschkin
- BIOGECO, INRA, University of Bordeaux, F-33615, Bordeaux, Pessac, France
| | - Virgil Fievet
- BIOGECO, INRA, University of Bordeaux, F-33615, Bordeaux, Pessac, France
| | - Loïc Schwaller
- AgroParisTech, UMR 518 MIA, F-75005, Paris, France
- INRA, UMR 518 MIA, F-75005, Paris, France
| | - Thomas Fort
- BIOGECO, INRA, University of Bordeaux, F-33615, Bordeaux, Pessac, France
| | - Cécile Robin
- BIOGECO, INRA, University of Bordeaux, F-33615, Bordeaux, Pessac, France
| | - Corinne Vacher
- BIOGECO, INRA, University of Bordeaux, F-33615, Bordeaux, Pessac, France.
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18
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Beltramo C, Valentini N, Portis E, Torello Marinoni D, Boccacci P, Sandoval Prando MA, Botta R. Genetic mapping and QTL analysis in European hazelnut (Corylus avellana L.). MOLECULAR BREEDING 2016; 36:27. [PMID: 0 DOI: 10.1007/s11032-016-0450-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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19
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George JP, Schueler S, Karanitsch-Ackerl S, Mayer K, Klumpp RT, Grabner M. Inter- and intra-specific variation in drought sensitivity in Abies spec. and its relation to wood density and growth traits. AGRICULTURAL AND FOREST METEOROLOGY 2015; 214-215:430-443. [PMID: 27713591 PMCID: PMC5049588 DOI: 10.1016/j.agrformet.2015.08.268] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Understanding drought sensitivity of tree species and its intra-specific variation is required to estimate the effects of climate change on forest productivity, carbon sequestration and tree mortality as well as to develop adaptive forest management measures. Here, we studied the variation of drought reaction of six European Abies species and ten provenances of Abies alba planted in the drought prone eastern Austria. Tree-ring and X-ray densitometry data were used to generate early- and latewood measures for ring width and wood density. Moreover, the drought reaction of species and provenances within six distinct drought events between 1970 and 2011, as identified by the standardized precipitation index, was determined by four drought response measures. The mean reaction of species and provenances to drought events was strongly affected by the seasonal occurrence of the drought: a short, strong drought at the beginning of the growing season resulted in growth reductions up to 50%, while droughts at the end of the growing season did not affect annual increment. Wood properties and drought response measures showed significant variation among Abies species as well as among A. alba provenances. Whereas A. alba provenances explained significant parts in the variation of ring width measures, the Abies species explained significant parts in the variation of wood density parameters. A consistent pattern in drought response across the six drought events was observed only at the inter-specific level, where A. nordmanniana showed the highest resistance and A. cephalonica showed the best recovery after drought. In contrast, differences in drought reaction among provenances were only found for the milder drought events in 1986, 1990, 1993 and 2000 and the ranking of provenances varied at each drought event. This indicates that genetic variation in drought response within A. alba is more limited than among Abies species. Low correlations between wood density parameters and drought response measures suggest that wood density is a poor predictor of drought sensitivity in Abies spec.
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Affiliation(s)
- Jan-Peter George
- Federal Research and Training Centre for Forests, Natural Hazards and Landscape (BFW), Department of Forest Genetics, Seckendorff-Gudent-Weg 8, 1131 Vienna, Austria
| | - Silvio Schueler
- Federal Research and Training Centre for Forests, Natural Hazards and Landscape (BFW), Department of Forest Genetics, Seckendorff-Gudent-Weg 8, 1131 Vienna, Austria
- Corresponding author. (S. Schueler)
| | - Sandra Karanitsch-Ackerl
- University of Natural Resources and Life Sciences (BOKU), Institute of Wood Science and Technology, Konrad-Lorenz-Straβe 24, 3430 Tulln an der Donau, Austria
| | - Konrad Mayer
- University of Natural Resources and Life Sciences (BOKU), Institute of Wood Science and Technology, Konrad-Lorenz-Straβe 24, 3430 Tulln an der Donau, Austria
| | - Raphael T. Klumpp
- University of Natural Resources and Life Sciences (BOKU), Institute of Silviculture, Peter-Jordan-Straβe 82, 1190 Vienna, Austria
| | - Michael Grabner
- University of Natural Resources and Life Sciences (BOKU), Institute of Wood Science and Technology, Konrad-Lorenz-Straβe 24, 3430 Tulln an der Donau, Austria
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20
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Plomion C, Aury JM, Amselem J, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Boudet N, Boury C, Canaguier A, Couloux A, Da Silva C, Duplessis S, Ehrenmann F, Estrada-Mairey B, Fouteau S, Francillonne N, Gaspin C, Guichard C, Klopp C, Labadie K, Lalanne C, Le Clainche I, Leplé JC, Le Provost G, Leroy T, Lesur I, Martin F, Mercier J, Michotey C, Murat F, Salin F, Steinbach D, Faivre-Rampant P, Wincker P, Salse J, Quesneville H, Kremer A. Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. Mol Ecol Resour 2015; 16:254-65. [PMID: 25944057 DOI: 10.1111/1755-0998.12425] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/27/2015] [Accepted: 04/30/2015] [Indexed: 12/31/2022]
Abstract
The 1.5 Gbp/2C genome of pedunculate oak (Quercus robur) has been sequenced. A strategy was established for dealing with the challenges imposed by the sequencing of such a large, complex and highly heterozygous genome by a whole-genome shotgun (WGS) approach, without the use of costly and time-consuming methods, such as fosmid or BAC clone-based hierarchical sequencing methods. The sequencing strategy combined short and long reads. Over 49 million reads provided by Roche 454 GS-FLX technology were assembled into contigs and combined with shorter Illumina sequence reads from paired-end and mate-pair libraries of different insert sizes, to build scaffolds. Errors were corrected and gaps filled with Illumina paired-end reads and contaminants detected, resulting in a total of 17,910 scaffolds (>2 kb) corresponding to 1.34 Gb. Fifty per cent of the assembly was accounted for by 1468 scaffolds (N50 of 260 kb). Initial comparison with the phylogenetically related Prunus persica gene model indicated that genes for 84.6% of the proteins present in peach (mean protein coverage of 90.5%) were present in our assembly. The second and third steps in this project are genome annotation and the assignment of scaffolds to the oak genetic linkage map. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement, the oak genome data have been released into public sequence repositories in advance of publication. In this presubmission paper, the oak genome consortium describes its principal lines of work and future directions for analyses of the nature, function and evolution of the oak genome.
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Affiliation(s)
- Christophe Plomion
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Joëlle Amselem
- INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France
| | - Tina Alaeitabar
- INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France
| | - Valérie Barbe
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Caroline Belser
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | | | - Catherine Bodénès
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | | | - Christophe Boury
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | | | - Arnaud Couloux
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Sébastien Duplessis
- INRA, UMR1136 INRA-Université de Lorraine, Interactions Arbres/Micro-organismes, Laboratoire d'Excellence ARBRE, Champenoux, F-54280, France
| | - François Ehrenmann
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Barbara Estrada-Mairey
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Stéphanie Fouteau
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | | | - Christine Gaspin
- Plateforme bioinformatique Toulouse Midi-Pyrénées, UBIA, INRA, Castanet-Tolosan, F-31326, France
| | | | - Christophe Klopp
- Plateforme bioinformatique Toulouse Midi-Pyrénées, UBIA, INRA, Castanet-Tolosan, F-31326, France
| | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Céline Lalanne
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | | | - Jean-Charles Leplé
- INRA, UR0588 Amélioration Génétique et Physiologie Forestières, Orléans, F-45075, France
| | - Grégoire Le Provost
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Thibault Leroy
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Isabelle Lesur
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Francis Martin
- INRA, UMR1136 INRA-Université de Lorraine, Interactions Arbres/Micro-organismes, Laboratoire d'Excellence ARBRE, Champenoux, F-54280, France
| | - Jonathan Mercier
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Célia Michotey
- INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France
| | - Florent Murat
- INRA/UBP UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, Clermont-Ferrand, F-63039, France
| | - Franck Salin
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Delphine Steinbach
- INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France
| | | | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France.,Université d'Evry Val d'Essone, UMR 8030, Evry, CP5706, France.,Centre National de Recherche Scientifique (CNRS), UMR 8030, Evry, CP5706, France
| | - Jérôme Salse
- INRA/UBP UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, Clermont-Ferrand, F-63039, France
| | - Hadi Quesneville
- INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France
| | - Antoine Kremer
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
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Howe GT, Horvath DP, Dharmawardhana P, Priest HD, Mockler TC, Strauss SH. Extensive Transcriptome Changes During Natural Onset and Release of Vegetative Bud Dormancy in Populus. FRONTIERS IN PLANT SCIENCE 2015; 6:989. [PMID: 26734012 PMCID: PMC4681841 DOI: 10.3389/fpls.2015.00989] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 10/29/2015] [Indexed: 05/19/2023]
Abstract
To survive winter, many perennial plants become endodormant, a state of suspended growth maintained even in favorable growing environments. To understand vegetative bud endodormancy, we collected paradormant, endodormant, and ecodormant axillary buds from Populus trees growing under natural conditions. Of 44,441 Populus gene models analyzed using NimbleGen microarrays, we found that 1,362 (3.1%) were differentially expressed among the three dormancy states, and 429 (1.0%) were differentially expressed during only one of the two dormancy transitions (FDR p-value < 0.05). Of all differentially expressed genes, 69% were down-regulated from paradormancy to endodormancy, which was expected given the lower metabolic activity associated with endodormancy. Dormancy transitions were accompanied by changes in genes associated with DNA methylation (via RNA-directed DNA methylation) and histone modifications (via Polycomb Repressive Complex 2), confirming and extending knowledge of chromatin modifications as major features of dormancy transitions. Among the chromatin-associated genes, two genes similar to SPT (SUPPRESSOR OF TY) were strongly up-regulated during endodormancy. Transcription factor genes and gene sets that were atypically up-regulated during endodormancy include a gene that seems to encode a trihelix transcription factor and genes associated with proteins involved in responses to ethylene, cold, and other abiotic stresses. These latter transcription factors include ETHYLENE INSENSITIVE 3 (EIN3), ETHYLENE-RESPONSIVE ELEMENT BINDING PROTEIN (EBP), ETHYLENE RESPONSE FACTOR (ERF), ZINC FINGER PROTEIN 10 (ZAT10), ZAT12, and WRKY DNA-binding domain proteins. Analyses of phytohormone-associated genes suggest important changes in responses to ethylene, auxin, and brassinosteroids occur during endodormancy. We found weaker evidence for changes in genes associated with salicylic acid and jasmonic acid, and little evidence for important changes in genes associated with gibberellins, abscisic acid, and cytokinin. We identified 315 upstream sequence motifs associated with eight patterns of gene expression, including novel motifs and motifs associated with the circadian clock and responses to photoperiod, cold, dehydration, and ABA. Analogies between flowering and endodormancy suggest important roles for genes similar to SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL), DORMANCY ASSOCIATED MADS-BOX (DAM), and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1).
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Affiliation(s)
- Glenn T. Howe
- Department of Forest Ecosystems and Society, Oregon State UniversityCorvallis, OR, USA
| | - David P. Horvath
- Biosciences Research Laboratory, United States Department of Agriculture-Agricultural Research ServiceFargo, ND, USA
| | - Palitha Dharmawardhana
- Department of Forest Ecosystems and Society, Oregon State UniversityCorvallis, OR, USA
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
| | - Henry D. Priest
- Donald Danforth Plant Science CenterSaint Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University in Saint LouisSaint Louis, MO, USA
| | - Todd C. Mockler
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
- Donald Danforth Plant Science CenterSaint Louis, MO, USA
| | - Steven H. Strauss
- Department of Forest Ecosystems and Society, Oregon State UniversityCorvallis, OR, USA
- *Correspondence: Steven H. Strauss,
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22
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A linkage disequilibrium perspective on the genetic mosaic of speciation in two hybridizing Mediterranean white oaks. Heredity (Edinb) 2014; 114:373-86. [PMID: 25515016 DOI: 10.1038/hdy.2014.113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 10/11/2014] [Accepted: 11/12/2014] [Indexed: 01/09/2023] Open
Abstract
We analyzed the genetic mosaic of speciation in two hybridizing Mediterranean white oaks from the Iberian Peninsula (Quercus faginea Lamb. and Quercus pyrenaica Willd.). The two species show ecological divergence in flowering phenology, leaf morphology and composition, and in their basic or acidic soil preferences. Ninety expressed sequence tag-simple sequence repeats (EST-SSRs) and eight nuclear SSRs were genotyped in 96 trees from each species. Genotyping was designed in two steps. First, we used 69 markers evenly distributed over the 12 linkage groups (LGs) of the oak linkage map to confirm the species genetic identity of the sampled genotypes, and searched for differentiation outliers. Then, we genotyped 29 additional markers from the chromosome bins containing the outliers and repeated the multilocus scans. We found one or two additional outliers within four saturated bins, thus confirming that outliers are organized into clusters. Linkage disequilibrium (LD) was extensive; even for loosely linked and for independent markers. Consequently, score tests for association between two-marker haplotypes and the 'species trait' showed a broad genomic divergence, although substantial variation across the genome and within LGs was also observed. We discuss the influence of several confounding effects on neutrality tests and review the evolutionary processes leading to extensive LD. Finally, we examine how LD analyses within regions that contain outlier clusters and quantitative trait loci can help to identify regions of divergence and/or genomic hitchhiking in the light of predictions from ecological speciation theory.
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Vranckx G, Jacquemyn H, Mergeay J, Cox K, Janssens P, Gielen BAS, Muys B, Honnay O. The effect of drought stress on heterozygosity-fitness correlations in pedunculate oak (Quercus robur). ANNALS OF BOTANY 2014; 113:1057-69. [PMID: 24638819 PMCID: PMC3997642 DOI: 10.1093/aob/mcu025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 02/07/2014] [Indexed: 05/15/2023]
Abstract
BACKGROUND AND AIMS The interaction between forest fragmentation and predicted climate change may pose a serious threat to tree populations. In small and spatially isolated forest fragments, increased homozygosity may directly affect individual tree fitness through the expression of deleterious alleles. Climate change-induced drought stress may exacerbate these detrimental genetic consequences of forest fragmentation, as the fitness response to low levels of individual heterozygosity is generally thought to be stronger under environmental stress than under optimal conditions. METHODS To test this hypothesis, a greenhouse experiment was performed in which various transpiration and growth traits of 6-month-old seedlings of Quercus robur differing in multilocus heterozygosity (MLH) were recorded for 3 months under a well-watered and a drought stress treatment. Heterozygosity-fitness correlations (HFC) were examined by correlating the recorded traits of individual seedlings to their MLH and by studying their response to drought stress. KEY RESULTS Weak, but significant, effects of MLH on several fitness traits were obtained, which were stronger for transpiration variables than for the recorded growth traits. High atmospheric stress (measured as vapour pressure deficit) influenced the strength of the HFCs of the transpiration variables, whereas only a limited effect of the irrigation treatment on the HFCs was observed. CONCLUSIONS Under ongoing climate change, increased atmospheric stress in the future may strengthen the negative fitness responses of trees to low MLH. This indicates the necessity to maximize individual multilocus heterozygosity in forest tree breeding programmes.
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Affiliation(s)
- Guy Vranckx
- Plant Conservation and Population Biology, Biology Department, University of Leuven, Kasteelpark Arenberg 31, Box 2435, 3001 Leuven, Belgium
| | - Hans Jacquemyn
- Plant Conservation and Population Biology, Biology Department, University of Leuven, Kasteelpark Arenberg 31, Box 2435, 3001 Leuven, Belgium
| | - Joachim Mergeay
- Research Institute for Nature and Forest (INBO), Flemish Government, Gaverstraat 4, 9500 Geraardsbergen, Belgium
| | - Karen Cox
- Research Institute for Nature and Forest (INBO), Flemish Government, Gaverstraat 4, 9500 Geraardsbergen, Belgium
| | - Pieter Janssens
- Soil Service of Belgium, Willem de Croylaan 48, 3001 Leuven, Belgium
| | - Bie An Sofie Gielen
- Division of Forest, Nature and Landscape, University of Leuven, Celestijnenlaan 200E, Box 2411, 3001 Leuven, Belgium
| | - Bart Muys
- Division of Forest, Nature and Landscape, University of Leuven, Celestijnenlaan 200E, Box 2411, 3001 Leuven, Belgium
| | - Olivier Honnay
- Plant Conservation and Population Biology, Biology Department, University of Leuven, Kasteelpark Arenberg 31, Box 2435, 3001 Leuven, Belgium
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24
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Brousseau L, Bonal D, Cigna J, Scotti I. Highly local environmental variability promotes intrapopulation divergence of quantitative traits: an example from tropical rain forest trees. ANNALS OF BOTANY 2013; 112:1169-79. [PMID: 24023042 PMCID: PMC3783240 DOI: 10.1093/aob/mct176] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 06/20/2013] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS In habitat mosaics, plant populations face environmental heterogeneity over short geographical distances. Such steep environmental gradients can induce ecological divergence. Lowland rainforests of the Guiana Shield are characterized by sharp, short-distance environmental variations related to topography and soil characteristics (from waterlogged bottomlands on hydromorphic soils to well-drained terra firme on ferralitic soils). Continuous plant populations distributed along such gradients are an interesting system to study intrapopulation divergence at highly local scales. This study tested (1) whether conspecific populations growing in different habitats diverge at functional traits, and (2) whether they diverge in the same way as congeneric species having different habitat preferences. METHODS Phenotypic differentiation was studied within continuous populations occupying different habitats for two congeneric, sympatric, and ecologically divergent tree species (Eperua falcata and E. grandiflora, Fabaceae). Over 3000 seeds collected from three habitats were germinated and grown in a common garden experiment, and 23 morphological, biomass, resource allocation and physiological traits were measured. KEY RESULTS In both species, seedling populations native of different habitats displayed phenotypic divergence for several traits (including seedling growth, biomass allocation, leaf chemistry, photosynthesis and carbon isotope composition). This may occur through heritable genetic variation or other maternally inherited effects. For a sub-set of traits, the intraspecific divergence associated with environmental variation coincided with interspecific divergence. CONCLUSIONS The results indicate that mother trees from different habitats transmit divergent trait values to their progeny, and suggest that local environmental variation selects for different trait optima even at a very local spatial scale. Traits for which differentiation within species follows the same pattern as differentiation between species indicate that the same ecological processes underlie intra- and interspecific variation.
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Affiliation(s)
- Louise Brousseau
- INRA, UMR ‘Ecologie des Forêts de Guyane’, Campus agronomique, BP 709, 97387 Kourou cedex, French Guiana
- INRA, UMR 1137 ‘Ecologie et Ecophysiologie Forestières’, 54280 Champenoux, France
- Université de Lorraine, UMR 1137 ‘Ecologie et Ecophysiologie Forestières’, Faculté des Sciences, Vandœuvre-lès-Nancy, France
| | - Damien Bonal
- INRA, UMR ‘Ecologie des Forêts de Guyane’, Campus agronomique, BP 709, 97387 Kourou cedex, French Guiana
- INRA, UMR 1137 ‘Ecologie et Ecophysiologie Forestières’, 54280 Champenoux, France
- Université de Lorraine, UMR 1137 ‘Ecologie et Ecophysiologie Forestières’, Faculté des Sciences, Vandœuvre-lès-Nancy, France
| | - Jeremy Cigna
- INRA, UMR ‘Ecologie des Forêts de Guyane’, Campus agronomique, BP 709, 97387 Kourou cedex, French Guiana
| | - Ivan Scotti
- INRA, UMR ‘Ecologie des Forêts de Guyane’, Campus agronomique, BP 709, 97387 Kourou cedex, French Guiana
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Prunier J, Pelgas B, Gagnon F, Desponts M, Isabel N, Beaulieu J, Bousquet J. The genomic architecture and association genetics of adaptive characters using a candidate SNP approach in boreal black spruce. BMC Genomics 2013; 14:368. [PMID: 23724860 PMCID: PMC3674900 DOI: 10.1186/1471-2164-14-368] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 05/24/2013] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The genomic architecture of adaptive traits remains poorly understood in non-model plants. Various approaches can be used to bridge this gap, including the mapping of quantitative trait loci (QTL) in pedigrees, and genetic association studies in non-structured populations. Here we present results on the genomic architecture of adaptive traits in black spruce, which is a widely distributed conifer of the North American boreal forest. As an alternative to the usual candidate gene approach, a candidate SNP approach was developed for association testing. RESULTS A genetic map containing 231 gene loci was used to identify QTL that were related to budset timing and to tree height assessed over multiple years and sites. Twenty-two unique genomic regions were identified, including 20 that were related to budset timing and 6 that were related to tree height. From results of outlier detection and bulk segregant analysis for adaptive traits using DNA pool sequencing of 434 genes, 52 candidate SNPs were identified and subsequently tested in genetic association studies for budset timing and tree height assessed over multiple years and sites. A total of 34 (65%) SNPs were significantly associated with budset timing, or tree height, or both. Although the percentages of explained variance (PVE) by individual SNPs were small, several significant SNPs were shared between sites and among years. CONCLUSIONS The sharing of genomic regions and significant SNPs between budset timing and tree height indicates pleiotropic effects. Significant QTLs and SNPs differed quite greatly among years, suggesting that different sets of genes for the same characters are involved at different stages in the tree's life history. The functional diversity of genes carrying significant SNPs and low observed PVE further indicated that a large number of polymorphisms are involved in adaptive genetic variation. Accordingly, for undomesticated species such as black spruce with natural populations of large effective size and low linkage disequilibrium, efficient marker systems that are predictive of adaptation should require the survey of large numbers of SNPs. Candidate SNP approaches like the one developed in the present study could contribute to reducing these numbers.
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Affiliation(s)
- Julien Prunier
- Centre for Forest Research, and Institute for Systems and Integrative Biology, Université Laval, Québec, Québec G1V 0A6, Canada.
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26
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Bodénès C, Chancerel E, Gailing O, Vendramin GG, Bagnoli F, Durand J, Goicoechea PG, Soliani C, Villani F, Mattioni C, Koelewijn HP, Murat F, Salse J, Roussel G, Boury C, Alberto F, Kremer A, Plomion C. Comparative mapping in the Fagaceae and beyond with EST-SSRs. BMC PLANT BIOLOGY 2012; 12:153. [PMID: 22931513 PMCID: PMC3493355 DOI: 10.1186/1471-2229-12-153] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 08/22/2012] [Indexed: 05/02/2023]
Abstract
BACKGROUND Genetic markers and linkage mapping are basic prerequisites for comparative genetic analyses, QTL detection and map-based cloning. A large number of mapping populations have been developed for oak, but few gene-based markers are available for constructing integrated genetic linkage maps and comparing gene order and QTL location across related species. RESULTS We developed a set of 573 expressed sequence tag-derived simple sequence repeats (EST-SSRs) and located 397 markers (EST-SSRs and genomic SSRs) on the 12 oak chromosomes (2n = 2x = 24) on the basis of Mendelian segregation patterns in 5 full-sib mapping pedigrees of two species: Quercus robur (pedunculate oak) and Quercus petraea (sessile oak). Consensus maps for the two species were constructed and aligned. They showed a high degree of macrosynteny between these two sympatric European oaks. We assessed the transferability of EST-SSRs to other Fagaceae genera and a subset of these markers was mapped in Castanea sativa, the European chestnut. Reasonably high levels of macrosynteny were observed between oak and chestnut. We also obtained diversity statistics for a subset of EST-SSRs, to support further population genetic analyses with gene-based markers. Finally, based on the orthologous relationships between the oak, Arabidopsis, grape, poplar, Medicago, and soybean genomes and the paralogous relationships between the 12 oak chromosomes, we propose an evolutionary scenario of the 12 oak chromosomes from the eudicot ancestral karyotype. CONCLUSIONS This study provides map locations for a large set of EST-SSRs in two oak species of recognized biological importance in natural ecosystems. This first step toward the construction of a gene-based linkage map will facilitate the assignment of future genome scaffolds to pseudo-chromosomes. This study also provides an indication of the potential utility of new gene-based markers for population genetics and comparative mapping within and beyond the Fagaceae.
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Affiliation(s)
- Catherine Bodénès
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Emilie Chancerel
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding Büsgen Institute Faculty of Forest Sciences and Forest Ecology Göttingen University, Büsgenweg 2, 37077, Göttingen, Germany
- New address: School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Giovanni G Vendramin
- Plant Genetics Institute, National Research Council, Via Madonna del Piano 10, Sesto Fiorentino, FI, 50019, Italy
| | - Francesca Bagnoli
- Plant Protection Institute, National Research Council, Via Madonna del Piano 10, Sesto Fiorentino, FI, 50019, Italy
| | - Jerome Durand
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Pablo G Goicoechea
- NEIKER-Tecnalia, Dpto Biotecnologia, PO Box 46, Vitoria-Gasteiz, 01080, Spain
| | - Carolina Soliani
- Unidad de Genética Ecológica y Mejoramiento Forestal, INTA EEA Bariloche, Bariloche, CC277 8400, Argentina
| | - Fiorella Villani
- CNR Istituto di Biologia Agroambientale e Forestale, Porano, TR, 05010, Italy
| | - Claudia Mattioni
- CNR Istituto di Biologia Agroambientale e Forestale, Porano, TR, 05010, Italy
| | | | - Florent Murat
- INRA, UMR1095 GDEC, Clermont-Ferrand, F-63100, France
| | - Jerome Salse
- INRA, UMR1095 GDEC, Clermont-Ferrand, F-63100, France
| | - Guy Roussel
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Christophe Boury
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Florian Alberto
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Antoine Kremer
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Christophe Plomion
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
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Meier AR, Saunders MR, Michler CH. Epicormic buds in trees: a review of bud establishment, development and dormancy release. TREE PHYSIOLOGY 2012; 32:565-84. [PMID: 22555307 DOI: 10.1093/treephys/tps040] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The formation of epicormic sprouts on the boles of trees is a phenomenon that has, until recently, been poorly understood. Renewed interest in the topic in the last two decades has led to significant advances in our knowledge of the subject, especially in regard to bud anatomy, morphology and ontogeny. There exists, however, no comprehensive synthesis of results from different disciplines across genera and geographical areas; this review seeks to fill that void and provide a comprehensive framework capable of guiding future research. A tree's potential for producing epicormic branches is dependent on the number of buds that are produced on a growing shoot, the development of those buds and associated meristems over time and the factors that promote sprout formation or bud death. Based on the descriptions of a limited number of researched species, we were able to describe four different developmental strategies for epicormics based on characteristics of meristem development. Control over epicormic bud dormancy is complex, but it is clear that the traditional view of auxin-mediated dormancy release is incomplete. Genetic control over epicormic development is yet to be empirically proven. Future research should focus on clarifying these physiological and genetic controls of epicormic bud development as well as developing more robust methods for tracking epicormics in ecological and silvicultural studies.
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Affiliation(s)
- Andrew R Meier
- Hardwood Tree Improvement and Regeneration Center, Department of Forestry and Natural Resources, Purdue University, 715 State Street, West Lafayette, IN 47907-2061, USA
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28
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Marguerit E, Brendel O, Lebon E, Van Leeuwen C, Ollat N. Rootstock control of scion transpiration and its acclimation to water deficit are controlled by different genes. THE NEW PHYTOLOGIST 2012; 194:416-429. [PMID: 22335501 DOI: 10.1111/j.1469-8137.2012.04059.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The stomatal control of transpiration is one of the major strategies by which plants cope with water stress. Here, we investigated the genetic architecture of the rootstock control of scion transpiration-related traits over a period of 3 yr. The rootstocks studied were full sibs from a controlled interspecific cross (Vitis vinifera cv. Cabernet Sauvignon × Vitis riparia cv. Gloire de Montpellier), onto which we grafted a single scion genotype. After 10 d without stress, the water supply was progressively limited over a period of 10 d, and a stable water deficit was then applied for 15 d. Transpiration rate was estimated daily and a mathematical curve was fitted to its response to water deficit intensity. We also determined δ(13) C values in leaves, transpiration efficiency and water extraction capacity. These traits were then analysed in a multienvironment (year and water status) quantitative trait locus (QTL) analysis. Quantitative trait loci, independent of year and water status, were detected for each trait. One genomic region was specifically implicated in the acclimation of scion transpiration induced by the rootstock. The QTLs identified colocalized with genes involved in water deficit responses, such as those relating to ABA and hydraulic regulation. Scion transpiration rate and its acclimation to water deficit are thus controlled genetically by the rootstock, through different genetic architectures.
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Affiliation(s)
- Elisa Marguerit
- Bordeaux Sciences Agro, ISVV, EGFV, UMR 1287, F-33175 Gradignan, France
- Univ. Bordeaux, ISVV, EGFV, UMR 1287, F-33140 Villenave d'Ornon, France
- INRA, ISVV, EGFV, UMR 1287, F-33140 Villenave d'Ornon, France
| | - Oliver Brendel
- INRA, UMR 1137 Ecologie et Ecophysiologie Forestières, 54280 Champenoux, France
- Université de Lorraine, UMR 1137 Ecologie et Ecophysiologie Forestières, 54506 Vandoeuvre-les-Nancy, France
| | - Eric Lebon
- INRA, UMR 759 Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, 34060 Montpellier, France
| | - Cornelis Van Leeuwen
- Bordeaux Sciences Agro, ISVV, EGFV, UMR 1287, F-33175 Gradignan, France
- Univ. Bordeaux, ISVV, EGFV, UMR 1287, F-33140 Villenave d'Ornon, France
- INRA, ISVV, EGFV, UMR 1287, F-33140 Villenave d'Ornon, France
| | - Nathalie Ollat
- Bordeaux Sciences Agro, ISVV, EGFV, UMR 1287, F-33175 Gradignan, France
- Univ. Bordeaux, ISVV, EGFV, UMR 1287, F-33140 Villenave d'Ornon, France
- INRA, ISVV, EGFV, UMR 1287, F-33140 Villenave d'Ornon, France
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29
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Abadie P, Roussel G, Dencausse B, Bonnet C, Bertocchi E, Louvet JM, Kremer A, Garnier-Géré P. Strength, diversity and plasticity of postmating reproductive barriers between two hybridizing oak species (Quercus robur L. and Quercus petraea (Matt) Liebl.). J Evol Biol 2011; 25:157-73. [PMID: 22092648 DOI: 10.1111/j.1420-9101.2011.02414.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Very little is known about the nature and strength of reproductive isolation (RI) in Quercus species, despite extensive research on the estimation and evolutionary significance of hybridization rates. We characterized postmating pre- and postzygotic RI between two hybridizing oak species, Quercus robur and Quercus petraea, using a large set of controlled crosses between different genotypes. Various traits potentially associated with reproductive barriers were quantified at several life history stages, from pollen-pistil interactions to seed set and progeny fitness-related traits. Results indicate strong intrinsic postmating prezygotic barriers, with significant barriers also at the postzygotic level, but relatively weaker extrinsic barriers on early hybrid fitness measures assessed in controlled conditions. Using general linear modelling of common garden data with clonal replicates, we showed that most traits exhibited important genotypic differences, as well as different levels of sensitivity to micro-environmental heterogeneity. These new findings suggest a large potential genetic diversity and plasticity of reproductive barriers and are confronted with hybridization evidence in these oak species.
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Affiliation(s)
- P Abadie
- INRA, UMR 1202 BIOGECO, 69 route d'Arcachon, F-33612 Cestas, France
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Reviewing the Science and Implementation of Climate Change Adaptation Measures in European Forestry. FORESTS 2011. [DOI: 10.3390/f2040961] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Lauri PÉ, Gorza O, Cochard H, Martinez S, Celton JM, Ripetti V, Lartaud M, Bry X, Trottier C, Costes E. Genetic determinism of anatomical and hydraulic traits within an apple progeny. PLANT, CELL & ENVIRONMENT 2011; 34:1276-90. [PMID: 21477120 DOI: 10.1111/j.1365-3040.2011.02328.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The apple tree is known to have an isohydric behaviour, maintaining rather constant leaf water potential in soil with low water status and/or under high evaporative demand. However, little is known on the xylem water transport from roots to leaves from the two perspectives of efficiency and safety, and on its genetic variability. We analysed 16 traits related to hydraulic efficiency and safety, and anatomical traits in apple stems, and the relationships between them. Most variables were found heritable, and we investigated the determinism underlying their genetic control through a quantitative trait loci (QTL) analysis on 90 genotypes from the same progeny. Principal component analysis (PCA) revealed that all traits related to efficiency, whether hydraulic conductivity, vessel number and area or wood area, were included in the first PC, whereas the second PC included the safety variables, thus confirming the absence of trade-off between these two sets of traits. Our results demonstrated that clustered variables were characterized by common genomic regions. Together with previous results on the same progeny, our study substantiated that hydraulic efficiency traits co-localized with traits identified for tree growth and fruit production.
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Gion JM, Carouché A, Deweer S, Bedon F, Pichavant F, Charpentier JP, Baillères H, Rozenberg P, Carocha V, Ognouabi N, Verhaegen D, Grima-Pettenati J, Vigneron P, Plomion C. Comprehensive genetic dissection of wood properties in a widely-grown tropical tree: Eucalyptus. BMC Genomics 2011; 12:301. [PMID: 21651758 PMCID: PMC3130712 DOI: 10.1186/1471-2164-12-301] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 06/08/2011] [Indexed: 11/16/2022] Open
Abstract
Background Eucalyptus is an important genus in industrial plantations throughout the world and is grown for use as timber, pulp, paper and charcoal. Several breeding programmes have been launched worldwide to concomitantly improve growth performance and wood properties (WPs). In this study, an interspecific cross between Eucalyptus urophylla and E. grandis was used to identify major genomic regions (Quantitative Trait Loci, QTL) controlling the variability of WPs. Results Linkage maps were generated for both parent species. A total of 117 QTLs were detected for a series of wood and end-use related traits, including chemical, technological, physical, mechanical and anatomical properties. The QTLs were mainly clustered into five linkage groups. In terms of distribution of QTL effects, our result agrees with the typical L-shape reported in most QTL studies, i.e. most WP QTLs had limited effects and only a few (13) had major effects (phenotypic variance explained > 15%). The co-locations of QTLs for different WPs as well as QTLs and candidate genes are discussed in terms of phenotypic correlations between traits, and of the function of the candidate genes. The major wood property QTL harbours a gene encoding a Cinnamoyl CoA reductase (CCR), a structural enzyme of the monolignol-specific biosynthesis pathway. Conclusions Given the number of traits analysed, this study provides a comprehensive understanding of the genetic architecture of wood properties in this Eucalyptus full-sib pedigree. At the dawn of Eucalyptus genome sequence, it will provide a framework to identify the nature of genes underlying these important quantitative traits.
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Affiliation(s)
- Jean-Marc Gion
- CIRAD, Department of Biological System, Research Unit "Genetic improvement and adaptation of mediterranean and tropical plants" TA A-108/C, Campus International de Baillarguet, 34398 Montpellier Cedex, France.
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Alberto F, Bouffier L, Louvet JM, Lamy JB, Delzon S, Kremer A. Adaptive responses for seed and leaf phenology in natural populations of sessile oak along an altitudinal gradient. J Evol Biol 2011; 24:1442-54. [PMID: 21507119 DOI: 10.1111/j.1420-9101.2011.02277.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We assessed the adaptive potential of seed and leaf phenology in 10 natural populations of sessile oak (Quercus petraea) sampled along two altitudinal transects using common garden experiments. Population differentiation for both phenological traits was observed with high-altitude populations germinating and flushing later than low altitude ones. However, high genetic variation and heritability values were also maintained within populations, despite slightly decreasing for dates of leaf unfolding with increasing altitude. We suggest that biotic and abiotic fluctuating selection pressures within populations and high gene flow are the main mechanisms maintaining high genetic variation for these fitness related traits. Moreover, changes in selection intensity and/or selection pressures along the altitudinal gradient can explain the reduction in genetic variation observed for leaf phenology. We anticipate that the maintenance of high genetic variation will be a valuable resource for future adaptation of sessile oak populations undergoing an upslope shift caused by climate change.
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Affiliation(s)
- F Alberto
- INRA, UMR1202 Biodiversité Gènes et Communautés, Cestas, France
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Pelgas B, Bousquet J, Meirmans PG, Ritland K, Isabel N. QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environments. BMC Genomics 2011; 12:145. [PMID: 21392393 PMCID: PMC3068112 DOI: 10.1186/1471-2164-12-145] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 03/10/2011] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The genomic architecture of bud phenology and height growth remains poorly known in most forest trees. In non model species, QTL studies have shown limited application because most often QTL data could not be validated from one experiment to another. The aim of our study was to overcome this limitation by basing QTL detection on the construction of genetic maps highly-enriched in gene markers, and by assessing QTLs across pedigrees, years, and environments. RESULTS Four saturated individual linkage maps representing two unrelated mapping populations of 260 and 500 clonally replicated progeny were assembled from 471 to 570 markers, including from 283 to 451 gene SNPs obtained using a multiplexed genotyping assay. Thence, a composite linkage map was assembled with 836 gene markers.For individual linkage maps, a total of 33 distinct quantitative trait loci (QTLs) were observed for bud flush, 52 for bud set, and 52 for height growth. For the composite map, the corresponding numbers of QTL clusters were 11, 13, and 10. About 20% of QTLs were replicated between the two mapping populations and nearly 50% revealed spatial and/or temporal stability. Three to four occurrences of overlapping QTLs between characters were noted, indicating regions with potential pleiotropic effects. Moreover, some of the genes involved in the QTLs were also underlined by recent genome scans or expression profile studies.Overall, the proportion of phenotypic variance explained by each QTL ranged from 3.0 to 16.4% for bud flush, from 2.7 to 22.2% for bud set, and from 2.5 to 10.5% for height growth. Up to 70% of the total character variance could be accounted for by QTLs for bud flush or bud set, and up to 59% for height growth. CONCLUSIONS This study provides a basic understanding of the genomic architecture related to bud flush, bud set, and height growth in a conifer species, and a useful indicator to compare with Angiosperms. It will serve as a basic reference to functional and association genetic studies of adaptation and growth in Picea taxa. The putative QTNs identified will be tested for associations in natural populations, with potential applications in molecular breeding and gene conservation programs. QTLs mapping consistently across years and environments could also be the most important targets for breeding, because they represent genomic regions that may be least affected by G × E interactions.
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Affiliation(s)
- Betty Pelgas
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, Québec, G1V 4C7, Canada
- Arborea and Canada Research Chair in Forest and Environmental Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, Québec, G1V OA6, Canada
| | - Jean Bousquet
- Arborea and Canada Research Chair in Forest and Environmental Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, Québec, G1V OA6, Canada
| | - Patrick G Meirmans
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, Québec, G1V 4C7, Canada
- Current address: Institute of Biodiversity and Ecosystem Dynamics, Universiteit van Amsterdam, PO Box 94248, 1090GE Amsterdam, The Netherlands
| | - Kermit Ritland
- Department of Forest Science, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, Québec, G1V 4C7, Canada
- Arborea and Canada Research Chair in Forest and Environmental Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, Québec, G1V OA6, Canada
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Prunier J, Laroche J, Beaulieu J, Bousquet J. Scanning the genome for gene SNPs related to climate adaptation and estimating selection at the molecular level in boreal black spruce. Mol Ecol 2011; 20:1702-16. [PMID: 21375634 DOI: 10.1111/j.1365-294x.2011.05045.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Outlier detection methods were used to scan the genome of the boreal conifer black spruce (Picea mariana [Mill.] B.S.P.) for gene single-nucleotide polymorphisms (SNPs) potentially involved in adaptations to temperature and precipitation variations. The scan involved 583 SNPs from 313 genes potentially playing adaptive roles. Differentiation estimates among population groups defined following variation in temperature and precipitation were moderately high for adaptive quantitative characters such as the timing of budset or tree height (Q(ST) = 0.189-0.314). Average differentiation estimates for gene SNPs were null, with F(ST) values of 0.005 and 0.006, respectively, among temperature and precipitation population groups. Using two detection approaches, a total of 26 SNPs from 25 genes distributed among 11 of the 12 linkage groups of black spruce were detected as outliers with F(ST) as high as 0.078. Nearly half of the outlier SNPs were located in exons and half of those were nonsynonymous. The functional annotations of genes carrying outlier SNPs and regression analyses between the frequencies of these SNPs and climatic variables supported their implication in adaptive processes. Several genes carrying outlier SNPs belonged to gene families previously found to harbour outlier SNPs in a reproductively isolated but largely sympatric congeneric species, suggesting differential subfunctionalization of gene duplicates. Selection coefficient estimates (S) were moderate but well above the magnitude of drift (>>1/N(e)), indicating that the signature of natural selection could be detected at the nucleotide level despite the recent establishment of these populations during the Holocene.
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Affiliation(s)
- Julien Prunier
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research 1030 avenue de Médecine, Université Laval, QC G1V 0A6, Canada
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Abstract
Over the past two decades, research in forest tree genomics has lagged behind that of model and agricultural systems. However, genomic research in forest trees is poised to enter into an important and productive phase owing to the advent of next-generation sequencing technologies, the enormous genetic diversity in forest trees and the need to mitigate the effects of climate change. Research on long-lived woody perennials is extending our molecular knowledge of complex life histories and adaptations to the environment - enriching a field that has traditionally drawn biological inference from a few short-lived herbaceous species.
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Affiliation(s)
- David B Neale
- Department of Plant Sciences, University of California, Davis, California 95616, USA.
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Torres-Miranda A, Luna-Vega I, Oyama K. Conservation biogeography of red oaks (Quercus, section Lobatae) in Mexico and Central America. AMERICAN JOURNAL OF BOTANY 2011; 98:290-305. [PMID: 21613118 DOI: 10.3732/ajb.1000218] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
PREMISE OF THE STUDY Oaks are dominant trees and key species in many temperate and subtropical forests in the world. In this study, we analyzed patterns of distribution of red oaks (Quercus, section Lobatae) occurring in Mexico and Central America to determine areas of species richness and endemism to propose areas of conservation. METHODS Patterns of richness and endemism of 75 red oak species were analyzed using three different units. Two complementarity algorithms based on species richness and three algorithms based on species rarity were used to identify important areas for conservation. A simulated annealing analysis was performed to evaluate and formulate effective new reserves for red oaks that are useful for conserving the ecosystems associated with them after the systematic conservation planning approach. KEY RESULTS Two main centers of species richness were detected. The northern Sierra Madre Oriental and Serranías Meridionales of Jalisco had the highest values of endemism. Fourteen areas were considered as priorities for conservation of red oak species based on the 26 priority political entities, 11 floristic units and the priority grid-cells obtained in the complementarity analysis. In the present network of Natural Protected Areas in Mexico and Central America, only 41.3% (31 species) of the red oak species are protected. The simulated annealing analysis indicated that to protect all 75 species of red oaks, 12 current natural protected areas need to be expanded by 120000 ha of additional land, and 26 new natural protected areas with 512500 ha need to be created. CONCLUSIONS Red oaks are a useful model to identify areas for conservation based on species richness and endemism as a result of their wide geographic distribution and a high number of species. We evaluated and reformulated new reserves for red oaks that are also useful for the conservation of ecosystems associated with them.
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Affiliation(s)
- Andrés Torres-Miranda
- Centro de Investigaciones en Ecosistemas, Universidad Nacional Autónoma de México, Ant. Carr. a Pátzcuaro 8701, Col. Ex-Hda. de San José de la Huerta, 58190, Morelia, Michoacán, Mexico
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Durand J, Bodénès C, Chancerel E, Frigerio JM, Vendramin G, Sebastiani F, Buonamici A, Gailing O, Koelewijn HP, Villani F, Mattioni C, Cherubini M, Goicoechea PG, Herrán A, Ikaran Z, Cabané C, Ueno S, Alberto F, Dumoulin PY, Guichoux E, de Daruvar A, Kremer A, Plomion C. A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study. BMC Genomics 2010; 11:570. [PMID: 20950475 PMCID: PMC3091719 DOI: 10.1186/1471-2164-11-570] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Accepted: 10/15/2010] [Indexed: 08/14/2023] Open
Abstract
Background Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut). Results A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference full-sib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher. Conclusion We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance.
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DESPREZ-LOUSTAU ML, VITASSE Y, DELZON S, CAPDEVIELLE X, MARÇAIS B, KREMER A. Are plant pathogen populations adapted for encounter with their host? A case study of phenological synchrony between oak and an obligate fungal parasite along an altitudinal gradient. J Evol Biol 2010; 23:87-97. [DOI: 10.1111/j.1420-9101.2009.01881.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Contrasting relations between diversity of candidate genes and variation of bud burst in natural and segregating populations of European oaks. Heredity (Edinb) 2009; 105:401-11. [PMID: 19997122 DOI: 10.1038/hdy.2009.170] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Nucleotide diversity was assessed within nine candidate genes (in total 4.6 kb) for the time of bud burst in nine sessile oak (Quercus petraea) populations distributed in central and northern Europe. The sampled populations were selected on the basis of their contrasting time of bud burst observed in common garden experiments (provenance tests). The candidate genes were selected according to their expression profiles during the transition from quiescent to developing buds and/or their functional role in model plants. The overall nucleotide diversity was large (π(tot)=6.15 × 10(-3); π(silent)=11.2 × 10(-3)), but population differentiation was not larger than for microsatellites. No outlier single-nucleotide polymorphism (SNP), departing from neutral expectation, was found among the total of 125 SNPs. These results contrasted markedly with the significant associations that were observed between the candidate genes and bud burst in segregating populations. Quantitative trait loci (QTLs) for bud burst were identified for 13 year*site seasonal observations in a cloned mapping pedigree. Nineteen QTLs were detected, and QTLs located on linkage groups 2, 5 and 9 contributed repeatedly to more than 12% of the phenotypic variation of the trait. Eight genes were polymorphic in the two parents of the pedigree and could be mapped on the existing genetic map. Five of them located within the confidence intervals of QTLs for bud burst. Interestingly, four of them located within the three QTLs exhibiting the largest contributions to bud burst.
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Gailing O, Vornam B, Leinemann L, Finkeldey R. Genetic and genomic approaches to assess adaptive genetic variation in plants: forest trees as a model. PHYSIOLOGIA PLANTARUM 2009; 137:509-19. [PMID: 19627554 DOI: 10.1111/j.1399-3054.2009.01263.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
With the increasing availability of sequence information at putatively important genes or regulatory regions, the characterization of adaptive genetic diversity and their association with phenotypic trait variation becomes feasible for many non-model organisms such as forest trees. Especially in predominantly outcrossing forest tree populations with large effective size, a high genetic variation in relevant genes is maintained, that is the raw material for the adaptation to changing and variable environments, and likewise for plant breeding. Oaks (Quercus spp.) are excellent model species to study the adaptation of forest trees to changing environments. They show a wide geographic distribution in Europe as dominant tree species in many forests and grow under a wide range of climatic and edaphic conditions. With the availability of a growing amount of functional and expressional candidate genes, we are now able to test the functional importance of single nucleotide polymorphisms (SNPs) by associating nucleotide variation in these genes with phenotypic variation in adaptive traits in segregating or natural populations. Here, we report on quantitative trait locus (QTL), candidate gene and association mapping approaches that are applicable to characterize gene markers and SNPs associated with variation in adaptive traits, such as bud burst, drought resistance and other traits showing selective responses to environmental change and stress. Because genome-wide association mapping studies are not feasible because of the enormous amount of SNP markers required in outcrossing trees with high recombination rates, the success of such an approach depends largely on the reasonable selection of candidate genes.
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Affiliation(s)
- Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Germany.
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Derory J, Scotti-Saintagne C, Bertocchi E, Le Dantec L, Graignic N, Jauffres A, Casasoli M, Chancerel E, Bodénès C, Alberto F, Kremer A. Contrasting relationships between the diversity of candidate genes and variation of bud burst in natural and segregating populations of European oaks. Heredity (Edinb) 2009; 104:438-48. [DOI: 10.1038/hdy.2009.134] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Roussel M, Dreyer E, Montpied P, Le-Provost G, Guehl JM, Brendel O. The diversity of (13)C isotope discrimination in a Quercus robur full-sib family is associated with differences in intrinsic water use efficiency, transpiration efficiency, and stomatal conductance. JOURNAL OF EXPERIMENTAL BOTANY 2009; 60:2419-31. [PMID: 19380420 DOI: 10.1093/jxb/erp100] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
(13)C discrimination in organic matter with respect to atmospheric CO(2) (Delta(13)C) is under tight genetic control in many plant species, including the pedunculate oak (Quercus robur L.) full-sib progeny used in this study. Delta(13)C is expected to reflect intrinsic water use efficiency, but this assumption requires confirmation due to potential interferences with mesophyll conductance to CO(2), or post-photosynthetic discrimination. In order to dissect the observed Delta(13)C variability in this progeny, six genotypes that have previously been found to display extreme phenotypic values of Delta(13)C [either very high ('high Delta') or low ('low Delta') phenotype] were selected, and transpiration efficiency (TE; accumulated biomass/transpired water), net CO(2) assimilation rate (A), stomatal conductance for water vapour (g(s)), and intrinsic water use efficiency (W(i)=A/g(s)) were compared with Delta(13)C in bulk leaf matter, wood, and cellulose in wood. As expected, 'high Delta' displayed higher values of Delta(13)C not only in bulk leaf matter, but also in wood and cellulose. This confirmed the stability of the genotypic differences in Delta(13)C recorded earlier. 'High Delta' also displayed lower TE, lower W(i), and higher g(s). A small difference was detected in photosynthetic capacity but none in mesophyll conductance to CO(2). 'High Delta' and 'low Delta' displayed very similar leaf anatomy, except for higher stomatal density in 'high Delta'. Finally, diurnal courses of leaf gas exchange revealed a higher g(s) in 'high Delta' in the morning than in the afternoon when the difference decreased. The gene ERECTA, involved in the control of water use efficiency, leaf differentiation, and stomatal density, displayed higher expression levels in 'low Delta'. In this progeny, the variability of Delta(13)C correlated closely with that of W(i) and TE. Genetic differences of Delta(13)C and W(i) can be ascribed to differences in stomatal conductance and stomatal density but not in photosynthetic capacity.
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Affiliation(s)
- Magali Roussel
- INRA, UMR 'Ecologie et Ecophysiologie Forestières', IFR 'Génomique, Ecophysiologie, Ecologie Fonctionnelle', Champenoux, France
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Savolainen O, Pyhäjärvi T, Knürr T. Gene Flow and Local Adaptation in Trees. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2007. [DOI: 10.1146/annurev.ecolsys.38.091206.095646] [Citation(s) in RCA: 787] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Outi Savolainen
- Department of Biology, University of Oulu, FIN-90014 Finland; ;
| | - Tanja Pyhäjärvi
- Department of Biology, University of Oulu, FIN-90014 Finland; ;
| | - Timo Knürr
- Department of Biology, University of Oulu, FIN-90014 Finland; ;
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Parelle J, Zapater M, Scotti-Saintagne C, Kremer A, Jolivet Y, Dreyer E, Brendel O. Quantitative trait loci of tolerance to waterlogging in a European oak (Quercus robur L.): physiological relevance and temporal effect patterns. PLANT, CELL & ENVIRONMENT 2007; 30:422-34. [PMID: 17324229 DOI: 10.1111/j.1365-3040.2006.01629.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Quercus robur L. is a mid-European broadleaved tree species that grows readily on temporary waterlogged soils. An experiment aiming to identify potential markers of tolerance to waterlogging in this species and to assess the degree of genetic control over the corresponding traits was conducted. Quantitative trait loci (QTL) were assessed in an F(1) progeny for responses to waterlogging, and the relevance of the observed traits as markers of tolerance was investigated using a precise description of the time course of their expression. Five significant QTL involved in the response to waterlogging were identified. In particular, QTL were detected for the development of hypertrophied lenticels and for the degree of leaf epinasty, but not for the formation of adventitious roots. A multi-environment QTL model allowed a detailed description of the time course (7 weeks) of the allelic substitution effect of some of these QTL. Correlation clustering identified significant clusters of QTL, at inter-trait as well as at intra-trait level. These clusters suggest the occurrence of a genetically controlled response cascade to waterlogging.
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Affiliation(s)
- Julien Parelle
- UMR INRA-UHP 1137, Ecologie et Ecophysiologie Forestières, Centre INRA de Nancy 54280 Champenoux, et Faculté des Sciences, BP 239, 54506 Vandoeuvre lès Nancy, France
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Yatabe Y, Kane NC, Scotti-Saintagne C, Rieseberg LH. Rampant gene exchange across a strong reproductive barrier between the annual sunflowers, Helianthus annuus and H. petiolaris. Genetics 2007; 175:1883-93. [PMID: 17277373 PMCID: PMC1855124 DOI: 10.1534/genetics.106.064469] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plant species may remain morphologically distinct despite gene exchange with congeners, yet little is known about the genomewide pattern of introgression among species. Here we analyze the effects of persistent gene flow on genomic differentiation between the sympatric sunflower species Helianthus annuus and H. petiolaris. While the species are strongly isolated in testcrosses, genetic distances at 108 microsatellite loci and 14 sequenced genes are highly variable and much lower (on average) than for more closely related but historically allopatric congeners. Our analyses failed to detect a positive association between levels of genetic differentiation and chromosomal rearrangements (as reported in a prior publication) or proximity to QTL for morphological differences or hybrid sterility. However, a significant increase in differentiation was observed for markers within 5 cM of chromosomal breakpoints. Together, these results suggest that islands of differentiation between these two species are small, except in areas of low recombination. Furthermore, only microsatellites associated with ESTs were identified as outlier loci in tests for selection, which might indicate that the ESTs themselves are the targets of selection rather than linked genes (or that coding regions are not randomly distributed). In general, these results indicate that even strong and genetically complex reproductive barriers cannot prevent widespread introgression.
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Affiliation(s)
- Yoko Yatabe
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
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Derory J, Léger P, Garcia V, Schaeffer J, Hauser MT, Salin F, Luschnig C, Plomion C, Glössl J, Kremer A. Transcriptome analysis of bud burst in sessile oak (Quercus petraea). THE NEW PHYTOLOGIST 2006; 170:723-38. [PMID: 16684234 DOI: 10.1111/j.1469-8137.2006.01721.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Expression patterns of hundreds of transcripts in apical buds were monitored during bud flushing in sessile oak (Quercus petraea), in order to identify genes differentially expressed between the quiescent and active stage of bud development. Different transcriptomic techniques combining the construction of suppression subtractive hybridization (SSH) libraries and the monitoring of gene expression using macroarray and real-time reverse transcriptase polymerase chain reaction (RT-PCR) were performed to dissect bud burst, with a special emphasis on the onset of the process. We generated 801 expressed sequence tags (ESTs) derived from six developmental stages of bud burst. Macroarray experiment revealed a total of 233 unique transcripts exhibiting differential expression during the process, and a putative function was assigned to 65% of them. Cell rescue/defense-, metabolism-, protein synthesis-, cell cycle- and transcription-related transcripts were among the most regulated genes. Macroarray and real-time RT-PCR showed that several genes exhibited contrasted expressions between quiescent and swelling buds, such as a putative homologue of the transcription factor DAG2 (Dof Affecting Germination 2), previously reported to be involved in the control of seed germination in Arabidopsis thaliana. These differentially expressed genes constitute relevant candidates for signaling pathway of bud burst in trees.
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Affiliation(s)
- Jérémy Derory
- UMR Biodiversité Gènes et Ecosystèmes, INRA, F-33612 Cestas cedex, France
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González-Martínez SC, Krutovsky KV, Neale DB. Forest-tree population genomics and adaptive evolution. THE NEW PHYTOLOGIST 2006; 170:227-38. [PMID: 16608450 DOI: 10.1111/j.1469-8137.2006.01686.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Forest trees have gained much attention in recent years as nonclassical model eukaryotes for population, evolutionary and ecological genomic studies. Because of low domestication, large open-pollinated native populations, and high levels of both genetic and phenotypic variation, they are ideal organisms to unveil the molecular basis of population adaptive divergence in nature. Population genomics, in its broad-sense definition, is an emerging discipline that combines genome-wide sampling with traditional population genetic approaches to understanding evolution. Here we briefly review traditional methods of studying adaptive genetic variation in forest trees, and describe a new, integrated population genomics approach. First, alleles (haplotypes) at candidate genes for adaptive traits and their effects on phenotypes need to be characterized via sequencing and association mapping. At this stage, functional genomics can assist in understanding gene action and regulation by providing detailed transcriptional profiles. Second, frequencies of alleles in native populations for causative single-nucleotide polymorphisms are estimated to identify patterns of adaptive variation across heterogeneous environments. Population genomics, through deciphering allelic effects on phenotypes and identifying patterns of adaptive variation at the landscape level, will in the future constitute a useful tool, if cost-effective, to design conservation strategies for forest trees.
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Casasoli M, Derory J, Morera-Dutrey C, Brendel O, Porth I, Guehl JM, Villani F, Kremer A. Comparison of quantitative trait loci for adaptive traits between oak and chestnut based on an expressed sequence tag consensus map. Genetics 2006; 172:533-46. [PMID: 16204213 PMCID: PMC1456181 DOI: 10.1534/genetics.105.048439] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Accepted: 09/21/2005] [Indexed: 11/18/2022] Open
Abstract
A comparative genetic and QTL mapping was performed between Quercus robur L. and Castanea sativa Mill., two major forest tree species belonging to the Fagaceae family. Oak EST-derived markers (STSs) were used to align the 12 linkage groups of the two species. Fifty-one and 45 STSs were mapped in oak and chestnut, respectively. These STSs, added to SSR markers previously mapped in both species, provided a total number of 55 orthologous molecular markers for comparative mapping within the Fagaceae family. Homeologous genomic regions identified between oak and chestnut allowed us to compare QTL positions for three important adaptive traits. Colocation of the QTL controlling the timing of bud burst was significant between the two species. However, conservation of QTL for height growth was not supported by statistical tests. No QTL for carbon isotope discrimination was conserved between the two species. Putative candidate genes for bud burst can be identified on the basis of colocations between EST-derived markers and QTL.
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Affiliation(s)
- Manuela Casasoli
- INRA, UMR Biodiversité Gènes et Ecosystèmes, 33612 Cestas Cedex, France
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Gailing O, Kremer A, Steiner W, Hattemer HH, Finkeldey R. Results on quantitative trait loci for flushing date in oaks can be transferred to different segregating progenies. PLANT BIOLOGY (STUTTGART, GERMANY) 2005; 7:516-25. [PMID: 16163617 DOI: 10.1055/s-2005-865841] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Flushing date (bud burst) is one of the most important traits for the adaptation to different environments and climates in the temperate zone. Because of their wide geographic distribution, Quercus robur L. and Q. petraea (Matt.) Liebl. are suitable as model plants to study the genetic basis of bud burst. QTLs (Quantitative Trait Loci) with comparatively large effects have been mapped in a former study in a Q. robur x Q. robur full-sib family (French cross). In the present study, we performed a Bulked Segregant Analysis (BSA) in the F (1) progeny comprising 144 seedlings derived from a cross between a single Q. robur tree as common seed parent and five different pollen donors both from Q. robur and Q. petraea (Q. robur x Q. spp., Diekholzen crosses). In addition, markers linked to two bud burst QTLs with comparably strong effect in the above-mentioned full-sib family (French cross) were tested for their association with bud burst in the Q. robur x Q. spp. (Diekholzen) progeny. Using three microsatellite markers as anchor points, we could map QTLs on linkage group 7 and on linkage group 2, together explaining 16.2 % of the total phenotypic variance (PVE) in 1999 and 38.1 % in 2003. Out of 10 markers that segregated in both mapping progenies, four markers including the two microsatellite markers, showed a significant effect on bud burst in both materials. At microsatellite loci ssrQpZAG1/5 (linkage group 7) and ssrQpZAG119 (linkage group 2) alleles associated with early (allele 166 bp in ssrQpZAG1/5) and late bud burst (allele 57 bp in ssrQpZAG119) in the Q. robur x Q. robur full-sib family (French cross) showed a highly significant association with the same polarity of the effect in the Q. robur x Q. spp. (Diekholzen) progeny. The usefulness of these markers for marker-assisted selection in full-sib and half-sib families is discussed.
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Affiliation(s)
- O Gailing
- Institute of Forest Genetics and Forest Tree Breeding, Georg August University Göttingen, Germany.
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