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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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Romero B, Scotti I, Fady B, Ganteaume A. Fire frequency, as well as stress response and developmental gene control serotiny level variation in a widespread pioneer Mediterranean conifer, Pinus halepensis. Ecol Evol 2023; 13:e9919. [PMID: 36960240 PMCID: PMC10030233 DOI: 10.1002/ece3.9919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 02/21/2023] [Accepted: 03/05/2023] [Indexed: 03/24/2023] Open
Abstract
Many plants undergo adaptation to fire. Yet, as global change is increasing fire frequency worldwide, our understanding of the genetics of adaptation to fire is still limited. We studied the genetic basis of serotiny (the ability to disseminate seeds exclusively after fire) in the widespread, pioneer Mediterranean conifer Pinus halepensis Mill., by linking individual variation in serotiny presence and level to fire frequency and to genetic polymorphism in natural populations. After filtering steps, 885 single nucleotide polymorphisms (SNPs) out of 8000 SNPs used for genotyping were implemented to perform an in situ association study between genotypes and serotiny presence and level. To identify serotiny‐associated loci, we performed random forest analyses of the effect of SNPs on serotiny levels, while controlling for tree size, frequency of wildfires, and background environmental parameters. Serotiny showed a bimodal distribution, with serotinous trees more frequent in populations exposed to fire in their recent history. Twenty‐two SNPs found in genes involved in stress tolerance were associated with the presence‐absence of serotiny while 37 found in genes controlling for flowering were associated with continuous serotiny variation. This study shows the high potential of P. halepensis to adapt to changing fire regimes, benefiting from a large and flexible genetic basis of trait variation.
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Pelletier E, de Lafontaine G. Jack pine of all trades: Deciphering intraspecific variability of a key adaptive trait at the rear edge of a widespread fire-embracing North American conifer. AMERICAN JOURNAL OF BOTANY 2023; 110:e16111. [PMID: 36462149 DOI: 10.1002/ajb2.16111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
PREMISE Understanding mechanisms fostering long-term persistence of marginal populations should provide key insights about species resilience facing climate change. Cone serotiny is a key adaptive trait in Pinus banksiana (jack pine), which shows phenotypic variation according to the fire regime. Compared to range-core populations within the fire-prone boreal forest, low and variable serotiny in rear-edge populations suggest local adaptation to uncommon and unpredictable wildfire regime. We assessed environmental/physiological factors that might modulate intraspecific variation in cone serotiny. METHODS We experimentally subjected closed cones to incrementing temperatures, then tested seed germination to determine whether and how various ecological factors (cone age, branch height, tree size, tree age) are related to cone dehiscence and seed viability in jack pines from rear-edge and range-core populations in eastern Canada. RESULTS Cones from rear-edge populations dehisce at a lower opening temperature, which increases with cone age. Cones from range-core stands open at a more constant, yet higher temperature. Cones from rear-edge stands take between 13 and 27 years to reach the level of serotiny achieved at the range core. At the rear edge, seed viability is steady (51%), whereas it decreases from 70% to 30% in 20 years at the range core. CONCLUSIONS We inferred the mechanisms of a bet-hedging strategy in rear-edge populations, which ensures steady recruitment during fire-free intervals and successful postfire regeneration. This capacity to cope with infrequent and unpredictable fire regime should increase the resilience of jack pine populations as global changes alter fire dynamics of the boreal forest.
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Affiliation(s)
- Emmanuelle Pelletier
- Canada Research Chair in Integrative Biology of the Northern Flora, Département de biologie, chimie et géographie, Centre for Northern Studies, Centre for Forest Research, Université du Québec à Rimouski, Rimouski, Québec, Canada
| | - Guillaume de Lafontaine
- Canada Research Chair in Integrative Biology of the Northern Flora, Département de biologie, chimie et géographie, Centre for Northern Studies, Centre for Forest Research, Université du Québec à Rimouski, Rimouski, Québec, Canada
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Aurelle D, Thomas S, Albert C, Bally M, Bondeau A, Boudouresque C, Cahill AE, Carlotti F, Chenuil A, Cramer W, Davi H, De Jode A, Ereskovsky A, Farnet A, Fernandez C, Gauquelin T, Mirleau P, Monnet A, Prévosto B, Rossi V, Sartoretto S, Van Wambeke F, Fady B. Biodiversity, climate change, and adaptation in the Mediterranean. Ecosphere 2022. [DOI: 10.1002/ecs2.3915] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Didier Aurelle
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO Marseille France
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS Sorbonne Université, EPHE Paris France
| | - Séverine Thomas
- Aix Marseille Université, Labex‐OT‐Med Aix‐en‐Provence France
| | - Cécile Albert
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | - Marc Bally
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO Marseille France
| | - Alberte Bondeau
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | | | | | - François Carlotti
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO Marseille France
| | - Anne Chenuil
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | - Wolfgang Cramer
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | - Hendrik Davi
- INRAE, Ecologie des Forêts Méditerranéennes (URFM) Avignon France
| | - Aurélien De Jode
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
- Department of Marine Sciences‐Tjärnö University of Gothenburg, Tjärnö Marine Laboratory Gothenburg Sweden
| | - Alexander Ereskovsky
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
- Saint‐Petersburg State University St. Petersburg Russia
| | - Anne‐Marie Farnet
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | | | - Thierry Gauquelin
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | - Pascal Mirleau
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | | | | | - Vincent Rossi
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO Marseille France
| | | | - France Van Wambeke
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO Marseille France
| | - Bruno Fady
- INRAE, Ecologie des Forêts Méditerranéennes (URFM) Avignon France
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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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Hurel A, de Miguel M, Dutech C, Desprez‐Loustau M, Plomion C, Rodríguez‐Quilón I, Cyrille A, Guzman T, Alía R, González‐Martínez SC, Budde KB. Genetic basis of growth, spring phenology, and susceptibility to biotic stressors in maritime pine. Evol Appl 2021; 14:2750-2772. [PMID: 34950227 PMCID: PMC8674897 DOI: 10.1111/eva.13309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 10/03/2021] [Indexed: 11/30/2022] Open
Abstract
Forest ecosystems are increasingly challenged by extreme events, for example, drought, storms, pest attacks, and fungal pathogen outbreaks, causing severe ecological and economic losses. Understanding the genetic basis of adaptive traits in tree species is of key importance to preserve forest ecosystems, as genetic variation in a trait (i.e., heritability) determines its potential for human-mediated or evolutionary change. Maritime pine (Pinus pinaster Aiton), a conifer widely distributed in southwestern Europe and northwestern Africa, grows under contrasted environmental conditions promoting local adaptation. Genetic variation at adaptive phenotypes, including height, spring phenology, and susceptibility to two fungal pathogens (Diplodia sapinea and Armillaria ostoyae) and an insect pest (Thaumetopoea pityocampa), was assessed in a range-wide clonal common garden of maritime pine. Broad-sense heritability was significant for height (0.219), spring phenology (0.165-0.310), and pathogen susceptibility (necrosis length caused by D. sapinea, 0.152; and by A. ostoyae, 0.021, measured on inoculated, excised branches under controlled conditions), but not for pine processionary moth incidence in the common garden. The correlations of trait variation among populations revealed contrasting trends for pathogen susceptibility to D. sapinea and A. ostoyae with respect to height. Taller trees showed longer necrosis length caused by D. sapinea while shorter trees were more affected by A. ostoyae. Moreover, maritime pine populations from areas with high summer temperatures and frequent droughts were less susceptible to D. sapinea but more susceptible to A. ostoyae. Finally, an association study using 4227 genome-wide SNPs revealed several loci significantly associated with each trait (range of 3-26), including a possibly disease-induced translation initiation factor, eIF-5, associated with needle discoloration caused by D. sapinea. This study provides important insights to develop genetic conservation and breeding strategies integrating species responses to biotic stressors.
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Affiliation(s)
- Agathe Hurel
- BIOGECO, INRAEUniversity of BordeauxCestasFrance
| | - Marina de Miguel
- BIOGECO, INRAEUniversity of BordeauxCestasFrance
- EGFV, INRAEUniversity of BordeauxVillenave‐d'OrnonFrance
| | - Cyril Dutech
- BIOGECO, INRAEUniversity of BordeauxCestasFrance
| | | | | | | | | | | | | | | | - Katharina B. Budde
- BIOGECO, INRAEUniversity of BordeauxCestasFrance
- Büsgen‐InstituteGeorg‐August University GöttingenGöttingenGermany
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7
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Pérez-Izquierdo L, Zabal-Aguirre M, Verdú M, Buée M, Rincón A. Ectomycorrhizal fungal diversity decreases in Mediterranean pine forests adapted to recurrent fires. Mol Ecol 2020; 29:2463-2476. [PMID: 32500559 DOI: 10.1111/mec.15493] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 01/02/2023]
Abstract
Fire is a major disturbance linked to the evolutionary history and climate of Mediterranean ecosystems, where the vegetation has evolved fire-adaptive traits (e.g., serotiny in pines). In Mediterranean forests, mutualistic feedbacks between trees and ectomycorrhizal (ECM) fungi, essential for ecosystem dynamics, might be shaped by recurrent fires. We tested how the structure and function of ECM fungal communities of Pinus pinaster and Pinus halepensis vary among populations subjected to high and low fire recurrence in Mediterranean ecosystems, and analysed the relative contribution of environmental (climate, soil properties) and tree-mediated (serotiny) factors. For both pines, local and regional ECM fungal diversity were lower in areas of high than low fire recurrence, although certain fungal species were favoured in the former. A general decline of ECM root-tip enzymatic activity for P. pinaster was associated with high fire recurrence, but not for P. halepensis. Fire recurrence and fire-related factors such as climate, soil properties or tree phenotype explained these results. In addition to the main influence of climate, the tree fire-adaptive trait serotiny recovered a great portion of the variation in structure and function of ECM fungal communities associated with fire recurrence. Edaphic conditions (especially pH, tightly linked to bedrock type) were an important driver shaping ECM fungal communities, but mainly at the local scale and probably independently of the fire recurrence. Our results show that ECM fungal community shifts are associated with fire recurrence in fire-prone dry Mediterranean forests, and reveal complex feedbacks among trees, mutualistic fungi and the surrounding environment in these ecosystems.
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Affiliation(s)
| | | | | | - Marc Buée
- INRA, UMR1136 INRA Nancy - Université de Lorraine, Interactions Arbres-Microorganismes Labex ARBRE, Champenoux, France
| | - Ana Rincón
- Instituto de Ciencias Agrarias, ICA-CSIC, Madrid, Spain
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8
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Looking for Local Adaptation: Convergent Microevolution in Aleppo Pine ( Pinus halepensis). Genes (Basel) 2019; 10:genes10090673. [PMID: 31487909 PMCID: PMC6771008 DOI: 10.3390/genes10090673] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 08/29/2019] [Accepted: 09/03/2019] [Indexed: 01/15/2023] Open
Abstract
Finding outlier loci underlying local adaptation is challenging and is best approached by suitable sampling design and rigorous method selection. In this study, we aimed to detect outlier loci (single nucleotide polymorphisms, SNPs) at the local scale by using Aleppo pine (Pinus halepensis), a drought resistant conifer that has colonized many habitats in the Mediterranean Basin, as the model species. We used a nested sampling approach that considered replicated altitudinal gradients for three contrasting sites. We genotyped samples at 294 SNPs located in genomic regions selected to maximize outlier detection. We then applied three different statistical methodologies-Two Bayesian outlier methods and one latent factor principal component method-To identify outlier loci. No SNP was an outlier for all three methods, while eight SNPs were detected by at least two methods and 17 were detected only by one method. From the intersection of outlier SNPs, only one presented an allelic frequency pattern associated with the elevational gradient across the three sites. In a context of multiple populations under similar selective pressures, our results underline the need for careful examination of outliers detected in genomic scans before considering them as candidates for convergent adaptation.
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9
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Simpson KJ, Olofsson JK, Ripley BS, Osborne CP. Frequent fires prime plant developmental responses to burning. Proc Biol Sci 2019; 286:20191315. [PMID: 31431130 DOI: 10.1098/rspb.2019.1315] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Coping with temporal variation in fire requires plants to have plasticity in traits that promote persistence, but how plastic responses to current conditions are affected by past fire exposure remains unknown. We investigate phenotypic divergence between populations of four resprouting grasses exposed to differing experimental fire regimes (annually burnt or unburnt for greater than 35 years) and test whether divergence persists after plants are grown in a common environment for 1 year. Traits relating to flowering and biomass allocation were measured before plants were experimentally burnt, and their regrowth was tracked. Genetic differentiation between populations was investigated for a subset of individuals. Historic fire frequency influenced traits relating to flowering and below-ground investment. Previously burnt plants produced more inflorescences and invested proportionally more biomass below ground, suggesting a greater capacity for recruitment and resprouting than unburnt individuals. Tiller-scale regrowth rate did not differ between treatments, but prior fire exposure enhanced total regrown biomass in two species. We found no consistent genetic differences between populations suggesting trait differences arose from developmental plasticity. Grass development is influenced by prior fire exposure, independent of current environmental conditions. This priming response to fire, resulting in adaptive trait changes, may produce communities more resistant to future fire regime changes.
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Affiliation(s)
- Kimberley J Simpson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Jill K Olofsson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Brad S Ripley
- Department of Botany, Rhodes University, PO Box 94, Grahamstown 6140, South Africa
| | - Colin P Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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10
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Robledo‐Arnuncio JJ, Unger GM. Measuring viability selection from prospective cohort mortality studies: A case study in maritime pine. Evol Appl 2019; 12:863-877. [PMID: 31080501 PMCID: PMC6503825 DOI: 10.1111/eva.12729] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 10/05/2018] [Accepted: 10/15/2018] [Indexed: 11/27/2022] Open
Abstract
By changing the genetic background available for selection at subsequent life stages, stage-specific selection can define adaptive potential across the life cycle. We propose and evaluate here a neutrality test and a Bayesian method to infer stage-specific viability selection coefficients using sequential random genotypic samples drawn from a longitudinal cohort mortality study, within a generation. The approach is suitable for investigating selective mortality in large natural or experimental cohorts of any organism in which individual tagging and tracking are unfeasible. Numerical simulation results indicate that the method can discriminate loci under strong viability selection, and provided samples are large, yield accurate estimates of the corresponding selection coefficients. Genotypic frequency changes are largely driven by sampling noise under weak selection, however, compromising inference in that case. We apply the proposed methods to analyze viability selection operating at early recruitment stages in a natural maritime pine (Pinus pinaster Ait.) population. We measured temporal genotypic frequency changes at 384 candidate-gene SNP loci among seedlings sampled from the time of emergence in autumn until the summer of the following year, a period with high elimination rates. We detected five loci undergoing allele frequency changes larger than expected from stochastic mortality and sampling, with putative functions that could influence survival at early seedling stages. Our results illustrate how new statistical and sampling schemes can be used to conduct genomic scans of contemporary selection on specific life stages.
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Affiliation(s)
| | - Gregor M. Unger
- Department of Forest Ecology & GeneticsINIA‐CIFORMadridSpain
- Escuela Internacional de DoctoradoUniversidad Rey Juan CarlosMóstolesSpain
- Present address:
Department of Forest GeneticsFederal Research and Training Centre for ForestsNatural Hazards and LandscapeViennaAustria
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11
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The Resistance of Scots Pine (Pinus sylvestris L.) Half-sib Families to Heterobasidion annosum. FORESTS 2019. [DOI: 10.3390/f10030287] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This study observed the genotypic variation among Scots pine (Pinus sylvestris L.) half-sib families’ susceptibility to Heterobasidion annosum. Scots pine susceptibility was tested in 12 half-sib families by inoculating them with four different H. annosum strains. At two, six, and ten months after the inoculations, the susceptibility indicators (incidence rate, pathogen spread, and mortality rate) were compared and the total phenolic compounds (TPC) in the inoculated and control groups determined using the Folin–Ciocalteu method. Among half-sib families, significant differences were found for seedling mortality (range: 1.3%–21.2%); however, the differences in incidence rate (range: 54%–77%) and pathogen spread (range: 24–53 mm) were not significant. The incidence rate among half-sib families correlated positively and significantly (r = 0.72, p < 0.05) with the mortality rate, while the pathogen spread correlated negatively with mortality, although the correlation was not significant (r = −0.29, p > 0.05). The TPC comparison with susceptibility indicators showed that the half-sib families with lower susceptibility were characterized by the ability to increase TPC after inoculation compared to the control group. This tendency was most apparent in stems and roots six and two months after inoculation, respectively. Correlation analyses revealed that higher TPC in stems six months after inoculation determined a lower incidence rate (r = −0.32, p < 0.05), while higher Change in concentration of total phenolic compounds (TPCΔ) indicated a lower pathogen spread (r = −0.60, p < 0.05). The lowest incidence of the pathogen was determined in half-sib families with the highest TPCΔ in the roots two months after inoculation. The lower susceptibility of Scots pine half-sib families is based on a combination of enhanced constitutive and inducible phenolic defense mechanisms. The data may facilitate the selection of Scots pine half-sib families with low susceptibility for breeding programs and forest management strategies.
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12
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Lamont BB, He T, Yan Z. Evolutionary history of fire‐stimulated resprouting, flowering, seed release and germination. Biol Rev Camb Philos Soc 2018; 94:903-928. [DOI: 10.1111/brv.12483] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/23/2018] [Accepted: 11/01/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Byron B. Lamont
- School of Molecular and Life Sciences Curtin University PO Box U1987, Perth, WA 6845 Australia
| | - Tianhua He
- School of Molecular and Life Sciences Curtin University PO Box U1987, Perth, WA 6845 Australia
| | - Zhaogui Yan
- College of Horticulture and Forestry Sciences Huazhong Agricultural University Wuhan 430070 China
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Abstract
The keystone species concept is used in ecology to describe individual species with disproportionately large effects on their communities. We extend this idea to the level of genes with disproportionately large effects on ecological processes. Such 'keystone genes' (KGs) would underlie traits involved in species interactions or causing critical biotic and/or abiotic changes that influence emergent community and ecosystem properties. We propose a general framework for how KGs could be identified, while keeping KGs under the umbrella of 'ecologically important genes' (EIGs) that also include categories such as 'foundation genes', 'ecosystem engineering genes', and more. Although likely rare, KGs and other EIGs could dominate certain ecological processes; thus, their discovery and study are relevant for understanding eco-evolutionary dynamics.
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Ruiz Daniels R, Taylor RS, Serra-Varela MJ, Vendramin GG, González-Martínez SC, Grivet D. Inferring selection in instances of long-range colonization: The Aleppo pine (Pinus halepensis) in the Mediterranean Basin. Mol Ecol 2018; 27:3331-3345. [PMID: 29972881 DOI: 10.1111/mec.14786] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 05/31/2018] [Accepted: 06/14/2018] [Indexed: 01/03/2023]
Abstract
Teasing apart the effects of natural selection and demography on current allele frequencies is challenging, due to both processes leaving a similar molecular footprint. In particular, when attempting to identify selection in species that have undergone a recent range expansion, the increase in genetic drift at the edges of range expansions ("allele surfing") can be a confounding factor. To address this potential issue, we first assess the long-range colonization history of the Aleppo pine across the Mediterranean Basin, using molecular markers. We then look for single nucleotide polymorphisms (SNPs) involved in local adaptation using: (a) environmental correlation methods (bayenv2), focusing on bioclimatic variables important for the species' adaptation (i.e., temperature, precipitation and water availability); and (b) FST -related methods (pcadapt). To assess the rate of false positives caused by the allele surfing effect, these results are compared with results from simulated SNP data that mimics the species' past range expansions and the effect of genetic drift, but with no selection. We find that the Aleppo pine shows a previously unsuspected complex genetic structure across its range, as well as evidence of selection acting on SNPs involved with the response to bioclimatic variables such as drought. This study uses an original approach to disentangle the confounding effects of drift and selection in range margin populations. It also contributes to the increased evidence that plant populations are able to adapt to new environments despite the expected accumulation of deleterious mutations that takes place during long-range colonizations.
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Affiliation(s)
- Rose Ruiz Daniels
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Madrid, Spain
| | | | - María Jesús Serra-Varela
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Madrid, Spain
- Department of Plant Production and Forest Resources, University of Valladolid, Palencia, Spain
- Sustainable Forest Management Research Institute, INIA, University of Valladolid, Palencia, Spain
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino, FI, Italy
| | - Santiago C González-Martínez
- Sustainable Forest Management Research Institute, INIA, University of Valladolid, Palencia, Spain
- BIOGECO, INRA, University of Bordeaux, Cestas, France
| | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Madrid, Spain
- Sustainable Forest Management Research Institute, INIA, University of Valladolid, Palencia, Spain
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15
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Heer K, Behringer D, Piermattei A, Bässler C, Brandl R, Fady B, Jehl H, Liepelt S, Lorch S, Piotti A, Vendramin G, Weller M, Ziegenhagen B, Büntgen U, Opgenoorth L. Linking dendroecology and association genetics in natural populations: Stress responses archived in tree rings associate with SNP genotypes in silver fir (Abies albaMill.). Mol Ecol 2018; 27:1428-1438. [DOI: 10.1111/mec.14538] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 02/08/2018] [Indexed: 01/07/2023]
Affiliation(s)
- K. Heer
- Faculty of Biology, Conservation Biology; Philipps-University Marburg; Marburg Germany
- Department of Ecology; Faculty of Biology; Philipps-University Marburg; Marburg Germany
| | - D. Behringer
- Faculty of Biology, Conservation Biology; Philipps-University Marburg; Marburg Germany
| | - A. Piermattei
- Department of Geography; University of Cambridge; Cambridge UK
- Department of Agricultural, Food and Environmental Sciences; Marche Polytechnic University; Ancona Italy
- Dendro Science; Swiss Federal Research Institute WSL; Birmensdorf Switzerland
| | - C. Bässler
- Bavarian Forest National Park; Grafenau Germany
| | - R. Brandl
- Department of Ecology; Faculty of Biology; Philipps-University Marburg; Marburg Germany
| | - B. Fady
- INRA; UR Ecologie des Forêts Méditerranéennes; Avignon France
| | - H. Jehl
- Bavarian Forest National Park; Grafenau Germany
| | - S. Liepelt
- Faculty of Biology, Conservation Biology; Philipps-University Marburg; Marburg Germany
| | - S. Lorch
- Department of Ecology; Faculty of Biology; Philipps-University Marburg; Marburg Germany
| | - A. Piotti
- National Research Council; Institute of Biosciences and Bioresources; Firenze Italy
| | - G.G. Vendramin
- National Research Council; Institute of Biosciences and Bioresources; Firenze Italy
| | - M. Weller
- Department of Ecology; Faculty of Biology; Philipps-University Marburg; Marburg Germany
| | - B. Ziegenhagen
- Faculty of Biology, Conservation Biology; Philipps-University Marburg; Marburg Germany
| | - U. Büntgen
- Department of Geography; University of Cambridge; Cambridge UK
- Dendro Science; Swiss Federal Research Institute WSL; Birmensdorf Switzerland
- CzechGlobe, Global Change Research Institute CAS and Masaryk University; Brno Czech Republic
| | - L. Opgenoorth
- Department of Ecology; Faculty of Biology; Philipps-University Marburg; Marburg Germany
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16
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Ganthaler A, Stöggl W, Mayr S, Kranner I, Schüler S, Wischnitzki E, Sehr EM, Fluch S, Trujillo-Moya C. Association genetics of phenolic needle compounds in Norway spruce with variable susceptibility to needle bladder rust. PLANT MOLECULAR BIOLOGY 2017; 94:229-251. [PMID: 28190131 PMCID: PMC5443855 DOI: 10.1007/s11103-017-0589-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 01/24/2017] [Indexed: 05/15/2023]
Abstract
KEY MESSAGE Accumulation of phenolic needle metabolites in Norway spruce is regulated by many genes with small and additive effects and is correlated with the susceptibility against fungal attack. Norway spruce accumulates high foliar concentrations of secondary phenolic metabolites, with important functions for pathogen defence responses. However, the molecular genetic basis underlying the quantitative variation of phenolic compounds and their role in enhanced resistance of spruce to infection by needle bladder rust are unknown. To address these questions, a set of 1035 genome-wide single nucleotide polymorphisms (SNPs) was associated to the quantitative variation of four simple phenylpropanoids, eight stilbenes, nine flavonoids, six related arithmetic parameters and the susceptibility to infection by Chrysomyxa rhododendri in an unstructured natural population of Norway spruce. Thirty-one significant genetic associations for the flavonoids gallocatechin, kaempferol 3-glucoside and quercetin 3-glucoside and the stilbenes resveratrol, piceatannol, astringin and isorhapontin were discovered, explaining 22-59% of phenotypic variation, and indicating a regulation of phenolic accumulation by many genes with small and additive effects. The phenolics profile differed between trees with high and low susceptibility to the fungus, underlining the importance of phenolic compounds in the defence mechanisms of Norway spruce to C. rhododendri. Results highlight the utility of association studies in non-model tree species and may enable marker-assisted selection of Norway spruce adapted to severe pathogen attack.
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Affiliation(s)
- Andrea Ganthaler
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, 6020, Innsbruck, Austria.
- alpS - Centre for Climate Change Adaptation, Grabenweg 68, 6020, Innsbruck, Austria.
| | - Wolfgang Stöggl
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, 6020, Innsbruck, Austria
| | - Stefan Mayr
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, 6020, Innsbruck, Austria
| | - Ilse Kranner
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, 6020, Innsbruck, Austria
| | - Silvio Schüler
- Department of Forest Genetics, Federal Research and Training Centre for Forests, Natural Hazards and Landscapes (BFW), Seckendorff-Gudent-Weg 8, 1131, Vienna, Austria
| | - Elisabeth Wischnitzki
- Health and Environment Department, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430, Tulln, Austria
| | - Eva Maria Sehr
- Health and Environment Department, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430, Tulln, Austria
| | - Silvia Fluch
- Health and Environment Department, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430, Tulln, Austria
| | - Carlos Trujillo-Moya
- Department of Forest Genetics, Federal Research and Training Centre for Forests, Natural Hazards and Landscapes (BFW), Seckendorff-Gudent-Weg 8, 1131, Vienna, Austria
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17
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Lind BM, Friedline CJ, Wegrzyn JL, Maloney PE, Vogler DR, Neale DB, Eckert AJ. Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin, USA. Mol Ecol 2017; 26:3168-3185. [PMID: 28316116 DOI: 10.1111/mec.14106] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 03/03/2017] [Accepted: 03/06/2017] [Indexed: 12/18/2022]
Abstract
Patterns of local adaptation at fine spatial scales are central to understanding how evolution proceeds, and are essential to the effective management of economically and ecologically important forest tree species. Here, we employ single and multilocus analyses of genetic data (n = 116 231 SNPs) to describe signatures of fine-scale adaptation within eight whitebark pine (Pinus albicaulis Engelm.) populations across the local extent of the environmentally heterogeneous Lake Tahoe Basin, USA. We show that despite highly shared genetic variation (FST = 0.0069), there is strong evidence for adaptation to the rain shadow experienced across the eastern Sierra Nevada. Specifically, we build upon evidence from a common garden study and find that allele frequencies of loci associated with four phenotypes (mean = 236 SNPs), 18 environmental variables (mean = 99 SNPs), and those detected through genetic differentiation (n = 110 SNPs) exhibit significantly higher signals of selection (covariance of allele frequencies) than could be expected to arise, given the data. We also provide evidence that this covariance tracks environmental measures related to soil water availability through subtle allele frequency shifts across populations. Our results replicate empirical support for theoretical expectations of local adaptation for populations exhibiting strong gene flow and high selective pressures and suggest that ongoing adaptation of many P. albicaulis populations within the Lake Tahoe Basin will not be constrained by the lack of genetic variation. Even so, some populations exhibit low levels of heritability for the traits presumed to be related to fitness. These instances could be used to prioritize management to maintain adaptive potential. Overall, we suggest that established practices regarding whitebark pine conservation be maintained, with the additional context of fine-scale adaptation.
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Affiliation(s)
- Brandon M Lind
- Integrative Life Sciences Program, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | | | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Patricia E Maloney
- Department of Plant Pathology and Tahoe Environmental Research Center, University of California, Davis, CA, 95616, USA
| | - Detlev R Vogler
- USDA, Forest Service, Pacific Southwest Research Station, Institute of Forest Genetics, 2480 Carson Road, Placerville, CA, 95667, USA
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
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18
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He T, Lamont BB. Baptism by fire: the pivotal role of ancient conflagrations in evolution of the Earth's flora. Natl Sci Rev 2017. [DOI: 10.1093/nsr/nwx041] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Fire became a defining feature of the Earth's processes as soon as land plants evolved 420 million years ago and has played a major role in shaping the composition and physiognomy of many ecosystems ever since. However, there remains a general lack of appreciation of the place of fire in the origin, evolution, ecology and conservation of the Earth's biodiversity. We review the literature on the presence of fire throughout the Earth's history following the evolution of land plants and examine the evidence for the origin and evolution of adaptive functional traits, biomes and major plant groups in relation to fire. We show that: (1) fire activities have fluctuated throughout geological time due to variations in climate, and more importantly in atmospheric oxygen, as these affected fuel levels and flammability; (2) fire promoted the early evolution and spread of major terrestrial plant groups; (3) fire has shaped the floristics, structure and function of major global biomes; and (4) fire has initiated and maintained the evolution of a wide array of fire-adapted functional traits since the evolution of land plants. We conclude that fire has been a fundamental agent of natural selection on terrestrial plants throughout the history of life on the Earth's land surface. We suggest that a paradigm shift is required to reassess ecological and evolutionary theories that exclude a role for fire, and also there is a need to review fire-suppression policies on ecosystem management and biodiversity conservation in global fire-prone regions.
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Affiliation(s)
- Tianhua He
- Department of Environment and Agriculture, Curtin University, Perth, WA 6845, Australia
| | - Byron B Lamont
- Department of Environment and Agriculture, Curtin University, Perth, WA 6845, Australia
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19
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Budde KB, González-Martínez SC, Navascués M, Burgarella C, Mosca E, Lorenzo Z, Zabal-Aguirre M, Vendramin GG, Verdú M, Pausas JG, Heuertz M. Increased fire frequency promotes stronger spatial genetic structure and natural selection at regional and local scales in Pinus halepensis Mill. ANNALS OF BOTANY 2017; 119:1061-1072. [PMID: 28159988 PMCID: PMC5604561 DOI: 10.1093/aob/mcw286] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/13/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND AND AIMS The recurrence of wildfires is predicted to increase due to global climate change, resulting in severe impacts on biodiversity and ecosystem functioning. Recurrent fires can drive plant adaptation and reduce genetic diversity; however, the underlying population genetic processes have not been studied in detail. In this study, the neutral and adaptive evolutionary effects of contrasting fire regimes were examined in the keystone tree species Pinus halepensis Mill. (Aleppo pine), a fire-adapted conifer. The genetic diversity, demographic history and spatial genetic structure were assessed at local (within-population) and regional scales for populations exposed to different crown fire frequencies. METHODS Eight natural P. halepensis stands were sampled in the east of the Iberian Peninsula, five of them in a region exposed to frequent crown fires (HiFi) and three of them in an adjacent region with a low frequency of crown fires (LoFi). Samples were genotyped at nine neutral simple sequence repeats (SSRs) and at 251 single nucleotide polymorphisms (SNPs) from coding regions, some of them potentially important for fire adaptation. KEY RESULTS Fire regime had no effects on genetic diversity or demographic history. Three high-differentiation outlier SNPs were identified between HiFi and LoFi stands, suggesting fire-related selection at the regional scale. At the local scale, fine-scale spatial genetic structure (SGS) was overall weak as expected for a wind-pollinated and wind-dispersed tree species. HiFi stands displayed a stronger SGS than LoFi stands at SNPs, which probably reflected the simultaneous post-fire recruitment of co-dispersed related seeds. SNPs with exceptionally strong SGS, a proxy for microenvironmental selection, were only reliably identified under the HiFi regime. CONCLUSIONS An increasing fire frequency as predicted due to global change can promote increased SGS with stronger family structures and alter natural selection in P. halepensis and in plants with similar life history traits.
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Affiliation(s)
- Katharina B. Budde
- INIA Forest Research Centre, Department of Forest Ecology and Genetics, Carretera A Coruña km 7·5, 28040 Madrid, Spain
- INRA, Université de Bordeaux, UMR 1202 BIOGECO, 33610 Cestas, France
- For correspondence. E-mail or
| | - Santiago C. González-Martínez
- INIA Forest Research Centre, Department of Forest Ecology and Genetics, Carretera A Coruña km 7·5, 28040 Madrid, Spain
- INRA, Université de Bordeaux, UMR 1202 BIOGECO, 33610 Cestas, France
| | | | - Concetta Burgarella
- INRA, UMR 1334 AGAP, 34060 Montpellier, France
- Present address: IRD, UMR DIADE, BP 64501, Montpellier, France
| | - Elena Mosca
- Faculty of Science and Technology, Free University of Bolzano, piazza Università 1, 39100 Bolzano, Italy
| | - Zaida Lorenzo
- INIA Forest Research Centre, Department of Forest Ecology and Genetics, Carretera A Coruña km 7·5, 28040 Madrid, Spain
| | - Mario Zabal-Aguirre
- INIA Forest Research Centre, Department of Forest Ecology and Genetics, Carretera A Coruña km 7·5, 28040 Madrid, Spain
| | - Giovanni G. Vendramin
- National Research Council, Institute of Biosciences and Bioresources, Via Madonna del Piano 10, 50019 Sesto Fiorentino (Florence), Italy
| | - Miguel Verdú
- Centro de Investigaciones sobre Desertificación (CIDE-CSIC), 46113 Moncada (Valencia), Spain
| | - Juli G. Pausas
- Centro de Investigaciones sobre Desertificación (CIDE-CSIC), 46113 Moncada (Valencia), Spain
| | - Myriam Heuertz
- INIA Forest Research Centre, Department of Forest Ecology and Genetics, Carretera A Coruña km 7·5, 28040 Madrid, Spain
- INRA, Université de Bordeaux, UMR 1202 BIOGECO, 33610 Cestas, France
- For correspondence. E-mail or
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20
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Rodríguez-Quilón I, Santos-del-Blanco L, Grivet D, Jaramillo-Correa JP, Majada J, Vendramin GG, Alía R, González-Martínez SC. Local effects drive heterozygosity-fitness correlations in an outcrossing long-lived tree. Proc Biol Sci 2017; 282:20152230. [PMID: 26631567 DOI: 10.1098/rspb.2015.2230] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Heterozygosity-fitness correlations (HFCs) have been used to understand the complex interactions between inbreeding, genetic diversity and evolution. Although frequently reported for decades, evidence for HFCs was often based on underpowered studies or inappropriate methods, and hence their underlying mechanisms are still under debate. Here, we used 6100 genome-wide single nucleotide polymorphisms (SNPs) to test for general and local effect HFCs in maritime pine (Pinus pinaster Ait.), an iconic Mediterranean forest tree. Survival was used as a fitness proxy, and HFCs were assessed at a four-site common garden under contrasting environmental conditions (total of 16 288 trees). We found no significant correlations between genome-wide heterozygosity and fitness at any location, despite variation in inbreeding explaining a substantial proportion of the total variance for survival. However, four SNPs (including two non-synonymous mutations) were involved in significant associations with survival, in particular in the common gardens with higher environmental stress, as shown by a novel heterozygosity-fitness association test at the species-wide level. Fitness effects of SNPs involved in significant HFCs were stable across maritime pine gene pools naturally growing in distinct environments. These results led us to dismiss the general effect hypothesis and suggested a significant role of heterozygosity in specific candidate genes for increasing fitness in maritime pine. Our study highlights the importance of considering the species evolutionary and demographic history and different spatial scales and testing environments when assessing and interpreting HFCs.
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Affiliation(s)
- Isabel Rodríguez-Quilón
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera A Coruña km 7.5, Madrid 28040, Spain
| | - Luis Santos-del-Blanco
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne 1015, Switzerland
| | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera A Coruña km 7.5, Madrid 28040, Spain
| | - Juan Pablo Jaramillo-Correa
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera A Coruña km 7.5, Madrid 28040, Spain Department of Evolutionary Ecology, Institute of Ecology, Universidad Nacional Autónoma de México, AP 70-275, México D.F., Mexico
| | - Juan Majada
- CETEMAS-SERIDA, Sección Forestal, Finca Experimental La Mata, Grado 33820, Spain
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (Florence) 50019, Italy
| | - Ricardo Alía
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera A Coruña km 7.5, Madrid 28040, Spain Sustainable Forest Management Research Institute, University of Valladolid-INIA, Palencia 34071, Spain
| | - Santiago C González-Martínez
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera A Coruña km 7.5, Madrid 28040, Spain INRA, UMR 1202 Biodiversité Gènes Ecosystèmes (Biogeco), Cestas 33610, France Université de Bordeaux, UMR 1202 Biodiversité Gènes Ecosystèmes (Biogeco), Talence 33170, France
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21
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Lucas-Borja ME, Ahrazem O, Candel-Pérez D, Moya D, Fonseca T, Hernández Tecles E, De Las Heras J, Gómez-Gómez L. Evaluation of fire recurrence effect on genetic diversity in maritime pine (Pinus pinaster Ait.) stands using Inter-Simple Sequence Repeat profiles. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 572:1322-1328. [PMID: 26822471 DOI: 10.1016/j.scitotenv.2016.01.105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/17/2016] [Accepted: 01/17/2016] [Indexed: 06/05/2023]
Abstract
The management of maritime pine in fire-prone habitats is a challenging task and fine-scale population genetic analyses are necessary to check if different fire recurrences affect genetic variability. The objective of this study was to assess the effect of fire recurrence on maritime pine genetic diversity using inter-simple sequence repeat markers (ISSR). Three maritime pine (Pinus pinaster Ait.) populations from Northern Portugal were chosen to characterize the genetic variability among populations. In relation to fire recurrence, Seirós population was affected by fire both in 1990 and 2005 whereas Vila Seca-2 population was affected by fire just in 2005. The Vila Seca-1 population has been never affected by fire. Our results showed the highest Nei's genetic diversity (He=0.320), Shannon information index (I=0.474) and polymorphic loci (PPL=87.79%) among samples from twice burned populations (Seirós site). Thus, fire regime plays an important role affecting genetic diversity in the short-term, although not generating maritime pine genetic erosion.
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Affiliation(s)
- M E Lucas-Borja
- Department of Agricultural Technology and Science and Genetics, ETSIAM, University of Castilla-La Mancha, Campus Universitario s/n, Albacete E-02071, Spain
| | - O Ahrazem
- Department of Agricultural Technology and Science and Genetics, Faculty of Pharmacy, Institute of Botany, University of Castilla-La Mancha, Campus Universitario s/n, Albacete, E-02071, Spain
| | - D Candel-Pérez
- Department of Agricultural Technology and Science and Genetics, ETSIAM, University of Castilla-La Mancha, Campus Universitario s/n, Albacete E-02071, Spain.
| | - D Moya
- Department of Vegetal Production, ETSIAM, University of Castilla-La Mancha, Campus Universitario s/n, Albacete E-02071, Spain
| | - T Fonseca
- Department of Forestry Sciences and Landscape Architecture, University of Trás-os-Montes e Alto Douro, 5001-801, Vila Real, Portugal
| | - E Hernández Tecles
- Department of Vegetal Production, ETSIAM, University of Castilla-La Mancha, Campus Universitario s/n, Albacete E-02071, Spain
| | - J De Las Heras
- Department of Vegetal Production, ETSIAM, University of Castilla-La Mancha, Campus Universitario s/n, Albacete E-02071, Spain
| | - L Gómez-Gómez
- Department of Agricultural Technology and Science and Genetics, Faculty of Pharmacy, Institute of Botany, University of Castilla-La Mancha, Campus Universitario s/n, Albacete, E-02071, Spain
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22
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Bartholomé J, Bink MCAM, van Heerwaarden J, Chancerel E, Boury C, Lesur I, Isik F, Bouffier L, Plomion C. Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness. PLoS One 2016; 11:e0165323. [PMID: 27806077 PMCID: PMC5091878 DOI: 10.1371/journal.pone.0165323] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/10/2016] [Indexed: 01/26/2023] Open
Abstract
Background Increasing our understanding of the genetic architecture of complex traits, through analyses of genotype-phenotype associations and of the genes/polymorphisms accounting for trait variation, is crucial, to improve the integration of molecular markers into forest tree breeding. In this study, two full-sib families and one breeding population of maritime pine were used to identify quantitative trait loci (QTLs) for height growth and stem straightness, through linkage analysis (LA) and linkage disequilibrium (LD) mapping approaches. Results The populations used for LA consisted of two unrelated three-generation full-sib families (n = 197 and n = 477). These populations were assessed for height growth or stem straightness and genotyped for 248 and 217 markers, respectively. The population used for LD mapping consisted of 661 founders of the first and second generations of the breeding program. This population was phenotyped for the same traits and genotyped for 2,498 single-nucleotide polymorphism (SNP) markers corresponding to 1,652 gene loci. The gene-based reference genetic map of maritime pine was used to localize and compare the QTLs detected by the two approaches, for both traits. LA identified three QTLs for stem straightness and two QTLs for height growth. The LD study yielded seven significant associations (P ≤ 0.001): four for stem straightness and three for height growth. No colocalisation was found between QTLs identified by LA and SNPs detected by LD mapping for the same trait. Conclusions This study provides the first comparison of LA and LD mapping approaches in maritime pine, highlighting the complementary nature of these two approaches for deciphering the genetic architecture of two mandatory traits of the breeding program.
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Affiliation(s)
| | - Marco CAM Bink
- Biometris, Wageningen University and Research Centre, NL-6700 AC, Wageningen, Netherlands
| | - Joost van Heerwaarden
- Biometris, Wageningen University and Research Centre, NL-6700 AC, Wageningen, Netherlands
| | | | | | - Isabelle Lesur
- BIOGECO, INRA, Univ. Bordeaux, 33610, Cestas, France
- HelixVenture, Mérignac, France
| | - Fikret Isik
- North Carolina State University, Department of Forestry and Environmental Resources, Raleigh, NC, United States of America
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23
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Rodríguez-Quilón I, Santos-Del-Blanco L, Serra-Varela MJ, Koskela J, González-Martínez SC, Alía R. Capturing neutral and adaptive genetic diversity for conservation in a highly structured tree species. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2016; 26:2254-2266. [PMID: 27755736 DOI: 10.1002/eap.1361] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 03/26/2016] [Accepted: 04/12/2016] [Indexed: 06/06/2023]
Abstract
Preserving intraspecific genetic diversity is essential for long-term forest sustainability in a climate change scenario. Despite that, genetic information is largely neglected in conservation planning, and how conservation units should be defined is still heatedly debated. Here, we use maritime pine (Pinus pinaster Ait.), an outcrossing long-lived tree with a highly fragmented distribution in the Mediterranean biodiversity hotspot, to prove the importance of accounting for genetic variation, of both neutral molecular markers and quantitative traits, to define useful conservation units. Six gene pools associated to distinct evolutionary histories were identified within the species using 12 microsatellites and 266 single nucleotide polymorphisms (SNPs). In addition, height and survival standing variation, their genetic control, and plasticity were assessed in a multisite clonal common garden experiment (16 544 trees). We found high levels of quantitative genetic differentiation within previously defined neutral gene pools. Subsequent cluster analysis and post hoc trait distribution comparisons allowed us to define 10 genetically homogeneous population groups with high evolutionary potential. They constitute the minimum number of units to be represented in a maritime pine dynamic conservation program. Our results uphold that the identification of conservation units below the species level should account for key neutral and adaptive components of genetic diversity, especially in species with strong population structure and complex evolutionary histories. The environmental zonation approach currently used by the pan-European genetic conservation strategy for forest trees would be largely improved by gradually integrating molecular and quantitative trait information, as data become available.
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Affiliation(s)
- Isabel Rodríguez-Quilón
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Carretera A Coruña km 7.5, Madrid, 28040, Spain.
| | - Luis Santos-Del-Blanco
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
- Sustainable Forest Management Research Institute, University of Valladolid-INIA, Palencia, 34071, Spain
| | - María Jesús Serra-Varela
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Carretera A Coruña km 7.5, Madrid, 28040, Spain
- Sustainable Forest Management Research Institute, University of Valladolid-INIA, Palencia, 34071, Spain
| | - Jarkko Koskela
- Bioversity International, Via dei Tre Denari 472/a, Maccarese, 00057, Italy
| | - Santiago C González-Martínez
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Carretera A Coruña km 7.5, Madrid, 28040, Spain
- Sustainable Forest Management Research Institute, University of Valladolid-INIA, Palencia, 34071, Spain
- BIOGECO, INRA, University of Bordeaux, Cestas, 33610, France
| | - Ricardo Alía
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Carretera A Coruña km 7.5, Madrid, 28040, Spain
- Sustainable Forest Management Research Institute, University of Valladolid-INIA, Palencia, 34071, Spain
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24
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Clark LV, Dzyubenko E, Dzyubenko N, Bagmet L, Sabitov A, Chebukin P, Johnson DA, Kjeldsen JB, Petersen KK, Jørgensen U, Yoo JH, Heo K, Yu CY, Zhao H, Jin X, Peng J, Yamada T, Sacks EJ. Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia. ANNALS OF BOTANY 2016; 118:941-955. [PMID: 27451985 PMCID: PMC5055818 DOI: 10.1093/aob/mcw137] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 05/24/2016] [Indexed: 05/08/2023]
Abstract
Background and aims Miscanthus is a genus of perennial C4 grasses native to East Asia. It includes the emerging ligno-cellulosic biomass crop M. ×giganteus, a hybrid between M. sinensis and M. sacchariflorus. Biomass yield and cold tolerance are of particular interest in Miscanthus, given that this crop is more temperate adapted than its C4 relatives maize, sorghum and sugarcane. Methods A plant exploration was conducted in eastern Russia, at the northern extreme of the native range for Miscanthus, with collections including 174 clonal germplasm accessions (160 M. sacchariflorus and 14 M. sinensis) from 47 sites. Accessions were genotyped by restriction site-associated DNA sequencing (RAD-seq) and plastid microsatellites. Key Results Miscanthus sinensis was found in maritime climates near Vladivostok (43·6°N) and on southern Sakhalin Island (46·6°N). Miscanthus sacchariflorus was found inland at latitudes as high as 49·3°N, where M. sinensis was absent. Most M. sacchariflorus accessions were diploid, but approx. 2 % were tetraploids. Molecular markers revealed little population structure (Jost's D < 0·007 among diploid groups) but high genetic diversity (expected heterozygosity = 0·14) within the collection of Russian M. sacchariflorus. Genome-wide association (GWA) analysis for traits measured at the collection sites revealed three M. sacchariflorus single nucleotide polymorphisms (SNPs) significantly associated with the number of stems per unit area, one with height and one with basal stem diameter; three were near or within previously described sorghum quantitative trait loci for related traits. Conclusions This new Miscanthus germplasm collection from eastern Russia will be useful for breeding Miscanthus and sugarcane cultivars with improved adaptation to cold. Moreover, a strategy is proposed to facilitate the rapid utilization of new germplasm collections: by implementing low-cost SNP genotyping to conduct GWA studies of phenotypic data obtained at collection sites, plant breeders can be provided with actionable information on which accessions have desirable traits and alleles.
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Affiliation(s)
- Lindsay V. Clark
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, Urbana, IL 61802, USA
| | - Elena Dzyubenko
- Vavilov All-Russian Institute of Plant Genetic Resources, 42–44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Nikolay Dzyubenko
- Vavilov All-Russian Institute of Plant Genetic Resources, 42–44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Larisa Bagmet
- Vavilov All-Russian Institute of Plant Genetic Resources, 42–44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Andrey Sabitov
- Vavilov All-Russian Institute of Plant Genetic Resources, 42–44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Pavel Chebukin
- Vavilov All-Russian Institute of Plant Genetic Resources, 42–44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Douglas A. Johnson
- USDA-ARS Forage and Range Research Lab, Utah State University, Logan, UT 84322-6300, USA
| | | | - Karen Koefoed Petersen
- Department of Food Science, Aarhus University, Kirstinebjergvej 10, DK-5792 Årslev, Denmark
| | - Uffe Jørgensen
- Department of Agroecology, Aarhus University, Blichers Allé 20, DK-8830 Tjele, Denmark
| | - Ji Hye Yoo
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Kweon Heo
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Chang Yeon Yu
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Hua Zhao
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xiaoli Jin
- Agronomy Department, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Junhua Peng
- Science and Technology Center, China Seed Group Co. Ltd, Wuhan, Hubei 430040, China
| | - Toshihiko Yamada
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Erik J. Sacks
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, Urbana, IL 61802, USA
- *For correspondence. E-mail
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25
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Castellanos MC, González-Martínez SC, Pausas JG. Field heritability of a plant adaptation to fire in heterogeneous landscapes. Mol Ecol 2015; 24:5633-42. [DOI: 10.1111/mec.13421] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 10/05/2015] [Accepted: 10/09/2015] [Indexed: 12/21/2022]
Affiliation(s)
- M. C. Castellanos
- Consejo Superior de Investigaciones Científicas; Centro de Investigaciones sobre Desertificación (CIDE-CSIC-UV-GV); 46113 Moncada Valencia Spain
| | | | - J. G. Pausas
- Consejo Superior de Investigaciones Científicas; Centro de Investigaciones sobre Desertificación (CIDE-CSIC-UV-GV); 46113 Moncada Valencia Spain
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26
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Plomion C, Bartholomé J, Lesur I, Boury C, Rodríguez-Quilón I, Lagraulet H, Ehrenmann F, Bouffier L, Gion JM, Grivet D, de Miguel M, de María N, Cervera MT, Bagnoli F, Isik F, Vendramin GG, González-Martínez SC. High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster). Mol Ecol Resour 2015; 16:574-87. [PMID: 26358548 DOI: 10.1111/1755-0998.12464] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 08/28/2015] [Accepted: 09/03/2015] [Indexed: 12/18/2022]
Abstract
Maritime pine provides essential ecosystem services in the south-western Mediterranean basin, where it covers around 4 million ha. Its scattered distribution over a range of environmental conditions makes it an ideal forest tree species for studies of local adaptation and evolutionary responses to climatic change. Highly multiplexed single nucleotide polymorphism (SNP) genotyping arrays are increasingly used to study genetic variation in living organisms and for practical applications in plant and animal breeding and genetic resource conservation. We developed a 9k Illumina Infinium SNP array and genotyped maritime pine trees from (i) a three-generation inbred (F2) pedigree, (ii) the French breeding population and (iii) natural populations from Portugal and the French Atlantic coast. A large proportion of the exploitable SNPs (2052/8410, i.e. 24.4%) segregated in the mapping population and could be mapped, providing the densest ever gene-based linkage map for this species. Based on 5016 SNPs, natural and breeding populations from the French gene pool exhibited similar level of genetic diversity. Population genetics and structure analyses based on 3981 SNP markers common to the Portuguese and French gene pools revealed high levels of differentiation, leading to the identification of a set of highly differentiated SNPs that could be used for seed provenance certification. Finally, we discuss how the validated SNPs could facilitate the identification of ecologically and economically relevant genes in this species, improving our understanding of the demography and selective forces shaping its natural genetic diversity, and providing support for new breeding strategies.
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Affiliation(s)
- C Plomion
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - J Bartholomé
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - I Lesur
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,HelixVenture, F-33700, Mérignac, France
| | - C Boury
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | | | - H Lagraulet
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - F Ehrenmann
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - L Bouffier
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - J M Gion
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,UMR AGAP, CIRAD, F-33612, Cestas, France
| | - D Grivet
- Forest Research Centre, INIA, E-28040, Madrid, Spain
| | - M de Miguel
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - N de María
- Forest Research Centre, INIA, E-28040, Madrid, Spain
| | - M T Cervera
- Forest Research Centre, INIA, E-28040, Madrid, Spain
| | - F Bagnoli
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (FI), Italy
| | - F Isik
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
| | - G G Vendramin
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (FI), Italy
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27
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Cabezas JA, González-Martínez SC, Collada C, Guevara MA, Boury C, de María N, Eveno E, Aranda I, Garnier-Géré PH, Brach J, Alía R, Plomion C, Cervera MT. Nucleotide polymorphisms in a pine ortholog of the Arabidopsis degrading enzyme cellulase KORRIGAN are associated with early growth performance in Pinus pinaster. TREE PHYSIOLOGY 2015; 35:1000-1006. [PMID: 26093373 DOI: 10.1093/treephys/tpv050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/24/2015] [Indexed: 06/04/2023]
Abstract
We have carried out a candidate-gene-based association genetic study in Pinus pinaster Aiton and evaluated the predictive performance for genetic merit gain of the most significantly associated genes and single nucleotide polymorphisms (SNPs). We used a second generation 384-SNP array enriched with candidate genes for growth and wood properties to genotype mother trees collected in 20 natural populations covering most of the European distribution of the species. Phenotypic data for total height, polycyclism, root-collar diameter and biomass were obtained from a replicated provenance-progeny trial located in two sites with contrasting environments (Atlantic vs Mediterranean climate). General linear models identified strong associations between growth traits (total height and polycyclism) and four SNPs from the korrigan candidate gene, after multiple testing corrections using false discovery rate. The combined genomic breeding value predictions assessed for the four associated korrigan SNPs by ridge regression-best linear unbiased prediction (RR-BLUP) and cross-validation accounted for up to 8 and 15% of the phenotypic variance for height and polycyclic growth, respectively, and did not improve adding SNPs from other growth-related candidate genes. For root-collar diameter and total biomass, they accounted for 1.6 and 1.1% of the phenotypic variance, respectively, but increased to 15 and 4.1% when other SNPs from lp3.1, lp3.3 and cad were included in RR-BLUP models. These results point towards a desirable integration of candidate-gene studies as a means to pre-select relevant markers, and aid genomic selection in maritime pine breeding programs.
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Affiliation(s)
- José Antonio Cabezas
- Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain
| | - Santiago C González-Martínez
- Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France
| | - Carmen Collada
- Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain Departamento de Biotecnología, ETSIM, Ciudad Universitaria s/n 28040 Madrid, Spain
| | - María Angeles Guevara
- Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain
| | - Christophe Boury
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France
| | - Nuria de María
- Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain
| | - Emmanuelle Eveno
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France
| | - Ismael Aranda
- Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain
| | - Pauline H Garnier-Géré
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France
| | - Jean Brach
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France
| | - Ricardo Alía
- Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain
| | - Christophe Plomion
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France
| | - María Teresa Cervera
- Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain
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28
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Pausas JG. Evolutionary fire ecology: lessons learned from pines. TRENDS IN PLANT SCIENCE 2015; 20:318-324. [PMID: 25814325 DOI: 10.1016/j.tplants.2015.03.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/25/2015] [Accepted: 03/01/2015] [Indexed: 05/09/2023]
Abstract
Macroevolutionary studies of the genus Pinus provide the oldest current evidence of fire as an evolutionary pressure on plants and date back to ca. 125 million years ago (Ma). Microevolutionary studies show that fire traits are variable within and among populations, especially among those subject to different fire regimes. In addition, there is increasing evidence of an inherited genetic basis to variability in fire traits. Added together, pines provide compelling evidence that fire can exert an evolutionary pressure on plants and, thus, shape biodiversity. In addition, evolutionary fire ecology is providing insights to improve the management of pine forests under changing conditions. The lessons learned from pines may guide research on the evolutionary ecology of other taxa.
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Affiliation(s)
- Juli G Pausas
- CIDE-CSIC, Ctra. Naquera Km 4.5 (IVIA), Montcada, Valencia, 46113 Spain.
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29
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Ogura T, Busch W. From phenotypes to causal sequences: using genome wide association studies to dissect the sequence basis for variation of plant development. CURRENT OPINION IN PLANT BIOLOGY 2015; 23:98-108. [PMID: 25449733 DOI: 10.1016/j.pbi.2014.11.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 11/04/2014] [Accepted: 11/05/2014] [Indexed: 05/20/2023]
Abstract
Tremendous natural variation of growth and development exists within species. Uncovering the molecular mechanisms that tune growth and development promises to shed light on a broad set of biological issues including genotype to phenotype relations, regulatory mechanisms of biological processes and evolutionary questions. Recent progress in sequencing and data processing capabilities has enabled Genome Wide Association Studies (GWASs) to identify DNA sequence polymorphisms that underlie the variation of biological traits. In the last years, GWASs have proven powerful in revealing the complex genetic bases of many phenotypes in various plant species. Here we highlight successful recent GWASs that uncovered mechanistic and sequence bases of trait variation related to plant growth and development and discuss important considerations for conducting successful GWASs.
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Affiliation(s)
- Takehiko Ogura
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Wolfgang Busch
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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30
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Molecular proxies for climate maladaptation in a long-lived tree (Pinus pinaster Aiton, Pinaceae). Genetics 2014; 199:793-807. [PMID: 25549630 DOI: 10.1534/genetics.114.173252] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Understanding adaptive genetic responses to climate change is a main challenge for preserving biological diversity. Successful predictive models for climate-driven range shifts of species depend on the integration of information on adaptation, including that derived from genomic studies. Long-lived forest trees can experience substantial environmental change across generations, which results in a much more prominent adaptation lag than in annual species. Here, we show that candidate-gene SNPs (single nucleotide polymorphisms) can be used as predictors of maladaptation to climate in maritime pine (Pinus pinaster Aiton), an outcrossing long-lived keystone tree. A set of 18 SNPs potentially associated with climate, 5 of them involving amino acid-changing variants, were retained after performing logistic regression, latent factor mixed models, and Bayesian analyses of SNP-climate correlations. These relationships identified temperature as an important adaptive driver in maritime pine and highlighted that selective forces are operating differentially in geographically discrete gene pools. The frequency of the locally advantageous alleles at these selected loci was strongly correlated with survival in a common garden under extreme (hot and dry) climate conditions, which suggests that candidate-gene SNPs can be used to forecast the likely destiny of natural forest ecosystems under climate change scenarios. Differential levels of forest decline are anticipated for distinct maritime pine gene pools. Geographically defined molecular proxies for climate adaptation will thus critically enhance the predictive power of range-shift models and help establish mitigation measures for long-lived keystone forest trees in the face of impending climate change.
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31
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Ramírez-Valiente JA, Robledo-Arnuncio JJ. Adaptive consequences of human-mediated introgression for indigenous tree species: the case of a relict Pinus pinaster population. TREE PHYSIOLOGY 2014; 34:1376-1387. [PMID: 25466514 DOI: 10.1093/treephys/tpu097] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Human-induced gene movement via afforestation and restoration programs is a widespread phenomenon throughout the world. However, its effects on the genetic composition of native populations have received relatively little attention, particularly in forest trees. Here, we examine to what extent gene flow from allochthonous plantations of Pinus pinaster Aiton impacts offspring performance in a neighboring relict natural population and discuss the potential consequences for the long-term genetic composition of the latter. Specifically, we conducted a greenhouse experiment involving two contrasting watering treatments to test for differences in a set of functional traits and mortality rates between P. pinaster progenies from three different parental origins: (i) local native parents, (ii) exotic parents and (iii) intercrosses between local mothers and exotic fathers (intraspecific hybrids). Our results showed differences among crosses in cumulative mortality over time: seedlings of exotic parents exhibited the lowest mortality rates and seedlings of local origin the highest, while intraspecific hybrids exhibited an intermediate response. Linear regressions showed that seedlings with higher water-use efficiency (WUE, δ(13)C) were more likely to survive under drought stress, consistent with previous findings suggesting that WUE has an important role under dry conditions in this species. However, differences in mortality among crosses were only partially explained by WUE. Other non-measured traits and factors such as inbreeding depression in the relict population are more likely to explain the lower performance of native progenies. Overall, our results indicated that intraspecific hybrids and exotic individuals are more likely to survive under stressful conditions than local native individuals, at least during the first year of development. Since summer drought is the most important demographic and selective filter affecting tree establishment in Mediterranean ecosystems, a potential early selective advantage of exotic and hybrid genotypes would enhance initial steps of introgression of non-native genes into the study relict population of P. pinaster.
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Affiliation(s)
- José Alberto Ramírez-Valiente
- Department of Forest Ecology and Genetics, INIA-CIFOR, Carretera de La Coruña km 7.5, E-28040 Madrid, Spain Present address: Department of Ecology, Evolution and Behavior, University of Minnesota, 1987 Upper Buford Circle, Saint Paul, MN 55108, USA
| | - Juan José Robledo-Arnuncio
- Department of Forest Ecology and Genetics, INIA-CIFOR, Carretera de La Coruña km 7.5, E-28040 Madrid, Spain
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32
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Hernández-Serrano A, Verdú M, Santos-Del-Blanco L, Climent J, González-Martínez SC, Pausas JG. Heritability and quantitative genetic divergence of serotiny, a fire-persistence plant trait. ANNALS OF BOTANY 2014; 114:571-7. [PMID: 25008363 PMCID: PMC4204669 DOI: 10.1093/aob/mcu142] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 05/19/2014] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Although it is well known that fire acts as a selective pressure shaping plant phenotypes, there are no quantitative estimates of the heritability of any trait related to plant persistence under recurrent fires, such as serotiny. In this study, the heritability of serotiny in Pinus halepensis is calculated, and an evaluation is made as to whether fire has left a selection signature on the level of serotiny among populations by comparing the genetic divergence of serotiny with the expected divergence of neutral molecular markers (QST-FST comparison). METHODS A common garden of P. halepensis was used, located in inland Spain and composed of 145 open-pollinated families from 29 provenances covering the entire natural range of P. halepensis in the Iberian Peninsula and Balearic Islands. Narrow-sense heritability (h(2)) and quantitative genetic differentiation among populations for serotiny (QST) were estimated by means of an 'animal model' fitted by Bayesian inference. In order to determine whether genetic differentiation for serotiny is the result of differential natural selection, QST estimates for serotiny were compared with FST estimates obtained from allozyme data. Finally, a test was made of whether levels of serotiny in the different provenances were related to different fire regimes, using summer rainfall as a proxy for fire regime in each provenance. KEY RESULTS Serotiny showed a significant narrow-sense heritability (h(2)) of 0·20 (credible interval 0·09-0·40). Quantitative genetic differentiation among provenances for serotiny (QST = 0·44) was significantly higher than expected under a neutral process (FST = 0·12), suggesting adaptive differentiation. A significant negative relationship was found between the serotiny level of trees in the common garden and summer rainfall of their provenance sites. CONCLUSIONS Serotiny is a heritable trait in P. halepensis, and selection acts on it, giving rise to contrasting serotiny levels among populations depending on the fire regime, and supporting the role of fire in generating genetic divergence for adaptive traits.
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Affiliation(s)
- Ana Hernández-Serrano
- CIDE-CSIC, Ctra. Moncada - Nàquera Km. 4·5 (IVIA campus), 46113 Moncada, Valencia, Spain
| | - Miguel Verdú
- CIDE-CSIC, Ctra. Moncada - Nàquera Km. 4·5 (IVIA campus), 46113 Moncada, Valencia, Spain
| | - Luís Santos-Del-Blanco
- INIA-Forest Research Centre, Ctra. A Coruña Km 7·5, 28040 Madrid, Spain Sustainable Forest Management Research Institute, INIA-University of Valladolid, Palencia, Spain Department of Ecology and Evolution, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - José Climent
- INIA-Forest Research Centre, Ctra. A Coruña Km 7·5, 28040 Madrid, Spain Sustainable Forest Management Research Institute, INIA-University of Valladolid, Palencia, Spain
| | - Santiago C González-Martínez
- INIA-Forest Research Centre, Ctra. A Coruña Km 7·5, 28040 Madrid, Spain Department of Ecology and Evolution, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - Juli G Pausas
- CIDE-CSIC, Ctra. Moncada - Nàquera Km. 4·5 (IVIA campus), 46113 Moncada, Valencia, Spain
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de Miguel M, Cabezas JA, de María N, Sánchez-Gómez D, Guevara MÁ, Vélez MD, Sáez-Laguna E, Díaz LM, Mancha JA, Barbero MC, Collada C, Díaz-Sala C, Aranda I, Cervera MT. Genetic control of functional traits related to photosynthesis and water use efficiency in Pinus pinaster Ait. drought response: integration of genome annotation, allele association and QTL detection for candidate gene identification. BMC Genomics 2014; 15:464. [PMID: 24919981 PMCID: PMC4144121 DOI: 10.1186/1471-2164-15-464] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 06/05/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Understanding molecular mechanisms that control photosynthesis and water use efficiency in response to drought is crucial for plant species from dry areas. This study aimed to identify QTL for these traits in a Mediterranean conifer and tested their stability under drought. RESULTS High density linkage maps for Pinus pinaster were used in the detection of QTL for photosynthesis and water use efficiency at three water irrigation regimes. A total of 28 significant and 27 suggestive QTL were found. QTL detected for photochemical traits accounted for the higher percentage of phenotypic variance. Functional annotation of genes within the QTL suggested 58 candidate genes for the analyzed traits. Allele association analysis in selected candidate genes showed three SNPs located in a MYB transcription factor that were significantly associated with efficiency of energy capture by open PSII reaction centers and specific leaf area. CONCLUSIONS The integration of QTL mapping of functional traits, genome annotation and allele association yielded several candidate genes involved with molecular control of photosynthesis and water use efficiency in response to drought in a conifer species. The results obtained highlight the importance of maintaining the integrity of the photochemical machinery in P. pinaster drought response.
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Affiliation(s)
- Marina de Miguel
- />Departamento de Ecología y Genética Forestal, INIA-CIFOR., Ctra, de La Coruña Km 7.5, 28040 Madrid, Spain
- />Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, Madrid, Spain
| | - José-Antonio Cabezas
- />Departamento de Ecología y Genética Forestal, INIA-CIFOR., Ctra, de La Coruña Km 7.5, 28040 Madrid, Spain
- />Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, Madrid, Spain
| | - Nuria de María
- />Departamento de Ecología y Genética Forestal, INIA-CIFOR., Ctra, de La Coruña Km 7.5, 28040 Madrid, Spain
- />Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, Madrid, Spain
| | - David Sánchez-Gómez
- />Departamento de Ecología y Genética Forestal, INIA-CIFOR., Ctra, de La Coruña Km 7.5, 28040 Madrid, Spain
| | - María-Ángeles Guevara
- />Departamento de Ecología y Genética Forestal, INIA-CIFOR., Ctra, de La Coruña Km 7.5, 28040 Madrid, Spain
- />Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, Madrid, Spain
| | - María-Dolores Vélez
- />Departamento de Ecología y Genética Forestal, INIA-CIFOR., Ctra, de La Coruña Km 7.5, 28040 Madrid, Spain
- />Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, Madrid, Spain
| | - Enrique Sáez-Laguna
- />Departamento de Ecología y Genética Forestal, INIA-CIFOR., Ctra, de La Coruña Km 7.5, 28040 Madrid, Spain
- />Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, Madrid, Spain
| | - Luis-Manuel Díaz
- />Departamento de Ecología y Genética Forestal, INIA-CIFOR., Ctra, de La Coruña Km 7.5, 28040 Madrid, Spain
- />Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, Madrid, Spain
| | - Jose-Antonio Mancha
- />Departamento de Ecología y Genética Forestal, INIA-CIFOR., Ctra, de La Coruña Km 7.5, 28040 Madrid, Spain
| | - María-Carmen Barbero
- />Departamento de Ecología y Genética Forestal, INIA-CIFOR., Ctra, de La Coruña Km 7.5, 28040 Madrid, Spain
- />Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, Madrid, Spain
| | - Carmen Collada
- />Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, Madrid, Spain
- />ETSIM, Departamento de Biotecnología, Ciudad Universitaria, s/n, 28040 Madrid, Spain
| | - Carmen Díaz-Sala
- />Departamento de Ciencias de la Vida, Universidad de Alcalá, Ctra. de Barcelona Km 33.6, 28871 Alcalá de Henares, Madrid, Spain
| | - Ismael Aranda
- />Departamento de Ecología y Genética Forestal, INIA-CIFOR., Ctra, de La Coruña Km 7.5, 28040 Madrid, Spain
| | - María-Teresa Cervera
- />Departamento de Ecología y Genética Forestal, INIA-CIFOR., Ctra, de La Coruña Km 7.5, 28040 Madrid, Spain
- />Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, Madrid, Spain
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Pinosio S, González-Martínez SC, Bagnoli F, Cattonaro F, Grivet D, Marroni F, Lorenzo Z, Pausas JG, Verdú M, Vendramin GG. First insights into the transcriptome and development of new genomic tools of a widespread circum-Mediterranean tree species, Pinus halepensis Mill. Mol Ecol Resour 2014; 14:846-56. [PMID: 24450970 DOI: 10.1111/1755-0998.12232] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 01/15/2014] [Accepted: 01/17/2014] [Indexed: 11/30/2022]
Abstract
Aleppo pine (Pinus halepensis Mill.) is a relevant conifer species for studying adaptive responses to drought and fire regimes in the Mediterranean region. In this study, we performed Illumina next-generation sequencing of two phenotypically divergent Aleppo pine accessions with the aims of (i) characterizing the transcriptome through Illumina RNA-Seq on trees phenotypically divergent for adaptive traits linked to fire adaptation and drought, (ii) performing a functional annotation of the assembled transcriptome, (iii) identifying genes with accelerated evolutionary rates, (iv) studying the expression levels of the annotated genes and (v) developing gene-based markers for population genomic and association genetic studies. The assembled transcriptome consisted of 48,629 contigs and covered about 54.6 Mbp. The comparison of Aleppo pine transcripts to Picea sitchensis protein-coding sequences resulted in the detection of 34,014 SNPs across species, with a Ka /Ks average value of 0.216, suggesting that the majority of the assembled genes are under negative selection. Several genes were differentially expressed across the two pine accessions with contrasted phenotypes, including a glutathione-s-transferase, a cellulose synthase and a cobra-like protein. A large number of new markers (3334 amplifiable SSRs and 28,236 SNPs) have been identified which should facilitate future population genomics and association genetics in this species. A 384-SNP Oligo Pool Assay for genotyping with the Illumina VeraCode technology has been designed which showed an high overall SNP conversion rate (76.6%). Our results showed that Illumina next-generation sequencing is a valuable technology to obtain an extensive overview on whole transcriptomes of nonmodel species with large genomes.
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Affiliation(s)
- S Pinosio
- Institute of Biosciences and Bioresources, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy; IGA Technology Services s.r.l., Via J. Linussio, 51, 33100, Udine, Italy
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Moreira B, Castellanos MC, Pausas JG. Genetic component of flammability variation in a Mediterranean shrub. Mol Ecol 2014; 23:1213-23. [DOI: 10.1111/mec.12665] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 12/29/2013] [Accepted: 01/08/2014] [Indexed: 02/02/2023]
Affiliation(s)
- B. Moreira
- CIDE-CSIC; Ctra. Náquera Km. 4.5 46113 Montcada Valencia Spain
| | | | - J. G. Pausas
- CIDE-CSIC; Ctra. Náquera Km. 4.5 46113 Montcada Valencia Spain
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