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Izaguirre-Toriz V, Aguirre-Liguori JA, Latorre-Cárdenas MC, Arima EY, González-Rodríguez A. Local adaptation of Pinus leiophylla under climate and land use change models in the Avocado Belt of Michoacán. Mol Ecol 2024; 33:e17424. [PMID: 38813851 DOI: 10.1111/mec.17424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/01/2024] [Accepted: 05/17/2024] [Indexed: 05/31/2024]
Abstract
Climate change and land use change are two main drivers of global biodiversity decline, decreasing the genetic diversity that populations harbour and altering patterns of local adaptation. Landscape genomics allows measuring the effect of these anthropogenic disturbances on the adaptation of populations. However, both factors have rarely been considered simultaneously. Based on a set of 3660 SNPs from which 130 were identified as outliers by a genome-environment association analysis (LFMM), we modelled the spatial turnover of allele frequencies in 19 localities of Pinus leiophylla across the Avocado Belt in Michoacán state, Mexico. Then, we evaluated the effect of climate change and land use change scenarios, in addition to evaluating assisted gene flow strategies and connectivity metrics across the landscape to identify priority conservation areas for the species. We found that localities in the centre-east of the Avocado Belt would be more vulnerable to climate change, while localities in the western area are more threatened by land conversion to avocado orchards. Assisted gene flow actions could aid in mitigating both threats. Connectivity patterns among forest patches will also be modified by future habitat loss, with central and eastern parts of the Avocado Belt maintaining the highest connectivity. These results suggest that areas with the highest priority for conservation are in the eastern part of the Avocado Belt, including the Monarch Butterfly Biosphere Reserve. This work is useful as a framework that incorporates distinct layers of information to provide a more robust representation of the response of tree populations to anthropogenic disturbances.
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Affiliation(s)
- Vanessa Izaguirre-Toriz
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México (Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio D, 1° Piso, Circuito de Posgrados, Ciudad Universitaria), Coyoacán, Mexico
| | - Jonás A Aguirre-Liguori
- Departamento de Ecología Tropical, Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - María Camila Latorre-Cárdenas
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, Mexico
| | - Eugenio Y Arima
- Department of Geography and the Environment, University of Texas at Austin, Austin, Texas, USA
| | - Antonio González-Rodríguez
- Laboratorio Nacional de Innovación Ecotecnológica Para la Sustentabilidad (LANIES), Instituto de Investigaciones en Ecosistemas y Sustentabilidad, UNAM Campus Morelia, Morelia, Mexico
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Archambeau J, Benito Garzón M, de Miguel M, Brachi B, Barraquand F, González-Martínez SC. Reduced within-population quantitative genetic variation is associated with climate harshness in maritime pine. Heredity (Edinb) 2023; 131:68-78. [PMID: 37221230 PMCID: PMC10313832 DOI: 10.1038/s41437-023-00622-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 05/25/2023] Open
Abstract
How evolutionary forces interact to maintain genetic variation within populations has been a matter of extensive theoretical debates. While mutation and exogenous gene flow increase genetic variation, stabilizing selection and genetic drift are expected to deplete it. To date, levels of genetic variation observed in natural populations are hard to predict without accounting for other processes, such as balancing selection in heterogeneous environments. We aimed to empirically test three hypotheses: (i) admixed populations have higher quantitative genetic variation due to introgression from other gene pools, (ii) quantitative genetic variation is lower in populations from harsher environments (i.e., experiencing stronger selection), and (iii) quantitative genetic variation is higher in populations from heterogeneous environments. Using growth, phenological and functional trait data from three clonal common gardens and 33 populations (522 clones) of maritime pine (Pinus pinaster Aiton), we estimated the association between the population-specific total genetic variances (i.e., among-clone variances) for these traits and ten population-specific indices related to admixture levels (estimated based on 5165 SNPs), environmental temporal and spatial heterogeneity and climate harshness. Populations experiencing colder winters showed consistently lower genetic variation for early height growth (a fitness-related trait in forest trees) in the three common gardens. Within-population quantitative genetic variation was not associated with environmental heterogeneity or population admixture for any trait. Our results provide empirical support for the potential role of natural selection in reducing genetic variation for early height growth within populations, which indirectly gives insight into the adaptive potential of populations to changing environments.
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Affiliation(s)
- Juliette Archambeau
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France.
- UK Centre for Ecology & Hydrology, Bush Estate, Penicuik, UK.
| | | | - Marina de Miguel
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
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3
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Feng S, Wan W, Li Y, Wang D, Ren G, Ma T, Ru D. Transcriptome-based analyses of adaptive divergence between two closely related spruce species on the Qinghai-Tibet plateau and adjacent regions. Mol Ecol 2023; 32:476-491. [PMID: 36320185 DOI: 10.1111/mec.16758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 10/07/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022]
Abstract
Speciation among populations connected by gene flow is driven by adaptation to different environments, but underlying gene-environment associations remain largely unknown. Here, 162 individuals from 32 populations were sampled to obtain 191,648 independent single nucleotide polymorphisms (SNPs) across the genomes of two closely related spruce species, Picea asperata and Picea crassifolia, which occur on the Qinghai-Tibet Plateau and in surrounding regions. Using the SNP data set, genotype-environment associations and demographic modelling were used to examine local adaptation and genetic divergence between these two species. While morphologically similar, the two Picea species were genetically differentiated in multiple analyses. These species diverged despite continuous gene flow, and their initial divergence was dated back to the late Quaternary. The effective population sizes of both species have expanded since their divergence, as confirmed by niche distribution simulations. A total of 6365 genes were associated with the tested environmental variables; of these, 41 were positively selected in P. asperata and were mainly associated with temperature, while 83 were positively selected in P. crassifolia and were primarily associated with precipitation. These results deepen our understanding of the adaptive divergence and demographic histories of these two spruce species and highlight the importance of genomic data in deciphering the environmental selection underlying Quaternary interspecific divergence.
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Affiliation(s)
- Shuo Feng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Wei Wan
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Yang Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - DongLei Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Guangpeng Ren
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Tao Ma
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Dafu Ru
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
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4
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Lombardi E, Shestakova TA, Santini F, Resco de Dios V, Voltas J. Harnessing tree-ring phenotypes to disentangle gene by environment interactions and their climate dependencies in a circum-Mediterranean pine. ANNALS OF BOTANY 2022; 130:509-523. [PMID: 35797146 PMCID: PMC9510947 DOI: 10.1093/aob/mcac092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS Understanding the genetic basis of adaptation and plasticity in trees constitutes a knowledge gap. We linked dendrochronology and genomics [single nucleotide polymorphisms (SNPs)] for a widespread conifer (Pinus halepensis Mill.) to characterize intraspecific growth differences elicited by climate. METHODS The analysis comprised 20-year tree-ring series of 130 trees structured in 23 populations evaluated in a common garden. We tested for genotype by environment interactions (G × E) of indexed ring width (RWI) and early- to latewood ratios (ELI) using factorial regression, which describes G × E as differential gene sensitivity to climate. KEY RESULTS The species' annual growth was positively influenced by winter temperature and spring moisture and negatively influenced by previous autumn precipitation and warm springs. Four and five climate factors explained 10 % (RWI) and 16 % (ELI) of population-specific interannual variability, respectively, with populations from drought-prone areas and with uneven precipitation experiencing larger growth reductions during dry vegetative periods. Furthermore, four and two SNPs explained 14 % (RWI) and 10 % (ELI) of interannual variability among trees, respectively. Two SNPs played a putative role in adaptation to climate: one identified from transcriptome sequencing of P. halepensis and another involved in response regulation to environmental stressors. CONCLUSIONS We highlight how tree-ring phenotypes, obtained from a common garden experiment, combined with a candidate-gene approach allow the quantification of genetic and environmental effects determining adaptation for a conifer with a large and complex genome.
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Affiliation(s)
| | | | - Filippo Santini
- Joint Research Unit CTFC – AGROTECNIO – CERCA, Av. Alcalde Rovira Roure 191, Lleida E-25198, Spain
- Departament of Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, Lleida E-25198, Spain
| | - Víctor Resco de Dios
- Joint Research Unit CTFC – AGROTECNIO – CERCA, Av. Alcalde Rovira Roure 191, Lleida E-25198, Spain
- Departament of Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, Lleida E-25198, Spain
| | - Jordi Voltas
- Joint Research Unit CTFC – AGROTECNIO – CERCA, Av. Alcalde Rovira Roure 191, Lleida E-25198, Spain
- Departament of Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, Lleida E-25198, Spain
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5
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Lecoy J, Sachin Ranade S, Rosario García-Gil M. Analysis of the ASR and LP3 homologous gene families reveal positive selection acting on LP3-3 gene. Gene 2022; 850:146935. [DOI: 10.1016/j.gene.2022.146935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/20/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022]
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6
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Archambeau J, Garzón MB, Barraquand F, Miguel MD, Plomion C, González-Martínez SC. Combining climatic and genomic data improves range-wide tree height growth prediction in a forest tree. Am Nat 2022; 200:E141-E159. [DOI: 10.1086/720619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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7
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Pinto-Carrasco D, Delgado L, Sánchez Agudo JA, Rico E, Martínez-Ortega MM. Phylogeography and ecological differentiation of strictly Mediterranean taxa: the case of the Iberian endemic Odontites recordonii. AMERICAN JOURNAL OF BOTANY 2022; 109:166-183. [PMID: 34668187 DOI: 10.1002/ajb2.1787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Ecological drivers for genetic differentiation in Mediterranean climates are still underexplored. We have used the strictly Mediterranean endemic Odontites recordonii as a model species to address this question. This species is one of the three Iberian representatives of the O. vernus group, which are morphologically similar. Thus, it was additionally necessary to clarify their phylogenetic relationships. METHODS We used amplified fragment length polymorphisms to reveal phylogenetic relationships within O. vernus group, and to reconstruct the phylogeographic patterns within O. recordonii. Additionally, ecological niche models were generated to detect refugia along the Quaternary climatic oscillations. And finally, alleles under natural selection were identified, and correlations between allele presences and environmental variables were calculated in order to shed light on the ecological drivers promoting differentiation. RESULTS The three species from the O. vernus group were recovered as distinct species. Three genetic groups were found within O. recordonii and a putative refugium was detected for each one. Eighty-one alleles could be under diversifying selection, and 58 alleles showed significant correlations with environmental variables, especially with temperature and precipitation seasonality and summer drought. CONCLUSIONS The three Iberian species of the O. vernus group are reciprocal monophyletic taxa. The three genetic groups of O. recordonii could have been restricted to narrow refugia during the Quaternary and displayed present distributions in accordance with bioclimatic conditions. Temperature and precipitation seasonality and the intensity of summer drought are definitory climatic parameters of Mediterranean-type climates, and they could have acted as drivers of genetic differentiation on O. recordonii.
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Affiliation(s)
- Daniel Pinto-Carrasco
- Departamento de Botánica y Fisiología Vegetal, Universidad de Salamanca, Av. Licenciado Méndez Nieto s/n, E-37007, Salamanca, Spain
- Biobanco de ADN vegetal, Universidad de Salamanca, C/Espejo s/n, E-37007, Salamanca, Spain
| | - Luis Delgado
- Departamento de Botánica y Fisiología Vegetal, Universidad de Salamanca, Av. Licenciado Méndez Nieto s/n, E-37007, Salamanca, Spain
| | - José A Sánchez Agudo
- Departamento de Botánica y Fisiología Vegetal, Universidad de Salamanca, Av. Licenciado Méndez Nieto s/n, E-37007, Salamanca, Spain
| | - Enrique Rico
- Departamento de Botánica y Fisiología Vegetal, Universidad de Salamanca, Av. Licenciado Méndez Nieto s/n, E-37007, Salamanca, Spain
| | - M Montserrat Martínez-Ortega
- Departamento de Botánica y Fisiología Vegetal, Universidad de Salamanca, Av. Licenciado Méndez Nieto s/n, E-37007, Salamanca, Spain
- Biobanco de ADN vegetal, Universidad de Salamanca, C/Espejo s/n, E-37007, Salamanca, Spain
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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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9
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Olsson S, Lorenzo Z, Zabal-Aguirre M, Piotti A, Vendramin GG, González-Martínez SC, Grivet D. Evolutionary history of the mediterranean Pinus halepensis-brutia species complex using gene-resequencing and transcriptomic approaches. PLANT MOLECULAR BIOLOGY 2021; 106:367-380. [PMID: 33934278 DOI: 10.1007/s11103-021-01155-7] [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: 12/14/2020] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
Complementary gene-resequencing and transcriptomic approaches reveal contrasted evolutionary histories in a species complex. Pinus halepensis and Pinus brutia are closely related species that can intercross, but occupy different geographical ranges and bioclimates. To study the evolution of this species complex and to provide genomic resources for further research, we produce and analyze two new complementary sets of genetic resources: (i) a set of 172 re-sequenced genomic target loci analyzed in 45 individuals, and (ii) a set of 11 transcriptome assemblies. These two datasets provide insights congruent with previous studies: P. brutia displays high level of genetic diversity and no genetic sub-structure, while P. halepensis shows three main genetic clusters, the western Mediterranean and North African clusters displaying much lower genetic diversity than the eastern Mediterranean cluster, the latter cluster having similar genetic diversity to P. brutia. In addition, these datasets provide new insights on the timing of the species-complex history: the two species would have split at the end of the tertiary, and the changing climatic conditions of the Mediterranean region at the end of the Tertiary-beginning of the Quaternary, together with the distinct species tolerance to harsh climatic conditions would have resulted in different geographic distributions, demographic histories and genetic patterns of the two pines. The multiple glacial-interglacial cycles during the Quaternary would have led to the expansion of P. brutia in the Middle East, while P. halepensis would have been through bottlenecks. The last glaciations, from 0.6 Mya on, would have affected further the Western genetic pool of P. halepensis.
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Affiliation(s)
- Sanna Olsson
- Department of Forest Ecology & Genetics, Forest Research Centre, INIA-CSIC, Carretera de la Coruña km 7.5, 28040, Madrid, Spain.
| | - Zaida Lorenzo
- Department of Forest Ecology & Genetics, Forest Research Centre, INIA-CSIC, Carretera de la Coruña km 7.5, 28040, Madrid, Spain
| | - Mario Zabal-Aguirre
- Department of Forest Ecology & Genetics, Forest Research Centre, INIA-CSIC, Carretera de la Coruña km 7.5, 28040, Madrid, Spain
| | - Andrea Piotti
- Institute of Biosciences and Bioresources, Division of Florence, National Research Council, 50019, Sesto Fiorentino, Florence, Italy
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, Division of Florence, National Research Council, 50019, Sesto Fiorentino, Florence, Italy
| | - Santiago C González-Martínez
- UMR BIOGECO, INRAE, University of Bordeaux, 33610, Cestas, France
- Sustainable Forest Management Research Institute, INIA - University of Valladolid, Avda. Madrid 44, 34004, Palencia, Spain
| | - Delphine Grivet
- Department of Forest Ecology & Genetics, Forest Research Centre, INIA-CSIC, Carretera de la Coruña km 7.5, 28040, Madrid, Spain.
- Sustainable Forest Management Research Institute, INIA - University of Valladolid, Avda. Madrid 44, 34004, Palencia, Spain.
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López-Hinojosa M, de María N, Guevara MA, Vélez MD, Cabezas JA, Díaz LM, Mancha JA, Pizarro A, Manjarrez LF, Collada C, Díaz-Sala C, Cervera Goy MT. Rootstock effects on scion gene expression in maritime pine. Sci Rep 2021; 11:11582. [PMID: 34078936 PMCID: PMC8173007 DOI: 10.1038/s41598-021-90672-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 05/04/2021] [Indexed: 12/04/2022] Open
Abstract
Pines are the dominant conifers in Mediterranean forests. As long-lived sessile organisms that seasonally have to cope with drought periods, they have developed a variety of adaptive responses. However, during last decades, highly intense and long-lasting drought events could have contributed to decay and mortality of the most susceptible trees. Among conifer species, Pinus pinaster Ait. shows remarkable ability to adapt to different environments. Previous molecular analysis of a full-sib family designed to study drought response led us to find active transcriptional activity of stress-responding genes even without water deprivation in tolerant genotypes. To improve our knowledge about communication between above- and below-ground organs of maritime pine, we have analyzed four graft-type constructions using two siblings as rootstocks and their progenitors, Gal 1056 and Oria 6, as scions. Transcriptomic profiles of needles from both scions were modified by the rootstock they were grafted on. However, the most significant differential gene expression was observed in drought-sensitive Gal 1056, while in drought-tolerant Oria 6, differential gene expression was very much lower. Furthermore, both scions grafted onto drought-tolerant rootstocks showed activation of genes involved in tolerance to abiotic stress, and is most remarkable in Oria 6 grafts where higher accumulation of transcripts involved in phytohormone action, transcriptional regulation, photosynthesis and signaling has been found. Additionally, processes, such as those related to secondary metabolism, were mainly associated with the scion genotype. This study provides pioneering information about rootstock effects on scion gene expression in conifers.
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Affiliation(s)
- M López-Hinojosa
- Departamento de Ecología y Genética Forestal, Centro de Investigación Forestal (CIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain.,Unidad Mixta de Genómica y Ecofisiología Forestal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (INIA/UPM), Madrid, Spain
| | - N de María
- Departamento de Ecología y Genética Forestal, Centro de Investigación Forestal (CIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain.,Unidad Mixta de Genómica y Ecofisiología Forestal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (INIA/UPM), Madrid, Spain
| | - M A Guevara
- Departamento de Ecología y Genética Forestal, Centro de Investigación Forestal (CIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain.,Unidad Mixta de Genómica y Ecofisiología Forestal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (INIA/UPM), Madrid, Spain
| | - M D Vélez
- Departamento de Ecología y Genética Forestal, Centro de Investigación Forestal (CIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain.,Unidad Mixta de Genómica y Ecofisiología Forestal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (INIA/UPM), Madrid, Spain
| | - J A Cabezas
- Departamento de Ecología y Genética Forestal, Centro de Investigación Forestal (CIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain.,Unidad Mixta de Genómica y Ecofisiología Forestal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (INIA/UPM), Madrid, Spain
| | - L M Díaz
- Departamento de Ecología y Genética Forestal, Centro de Investigación Forestal (CIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain.,Unidad Mixta de Genómica y Ecofisiología Forestal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (INIA/UPM), Madrid, Spain
| | - J A Mancha
- Departamento de Ecología y Genética Forestal, Centro de Investigación Forestal (CIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain.,Unidad Mixta de Genómica y Ecofisiología Forestal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (INIA/UPM), Madrid, Spain
| | - A Pizarro
- Departamento de Ciencias de la Vida, Universidad de Alcalá (UAH), Alcalá de Henares, Spain
| | - L F Manjarrez
- Departamento de Ecología y Genética Forestal, Centro de Investigación Forestal (CIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain.,Unidad Mixta de Genómica y Ecofisiología Forestal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (INIA/UPM), Madrid, Spain
| | - C Collada
- Unidad Mixta de Genómica y Ecofisiología Forestal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (INIA/UPM), Madrid, Spain.,Departamento de Sistemas y Recursos Naturales, E.T.S.I. Montes, Forestal y Medio Natural, Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - C Díaz-Sala
- Departamento de Ciencias de la Vida, Universidad de Alcalá (UAH), Alcalá de Henares, Spain
| | - M T Cervera Goy
- Departamento de Ecología y Genética Forestal, Centro de Investigación Forestal (CIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain. .,Unidad Mixta de Genómica y Ecofisiología Forestal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (INIA/UPM), Madrid, Spain.
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Chien WM, Chang CT, Chiang YC, Hwang SY. Ecological Factors Generally Not Altitude Related Played Main Roles in Driving Potential Adaptive Evolution at Elevational Range Margin Populations of Taiwan Incense Cedar ( Calocedrus formosana). Front Genet 2020; 11:580630. [PMID: 33262787 PMCID: PMC7686793 DOI: 10.3389/fgene.2020.580630] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/21/2020] [Indexed: 12/05/2022] Open
Abstract
Population diversification can be shaped by a combination of environmental factors as well as geographic isolation interacting with gene flow. We surveyed genetic variation of 243 samples from 12 populations of Calocedrus formosana using amplified fragment length polymorphism (AFLP) and scored a total of 437 AFLP fragments using 11 selective amplification primer pairs. The AFLP variation was used to assess the role of gene flow on the pattern of genetic diversity and to test environments in driving population adaptive evolution. This study found the relatively lower level of genetic diversity and the higher level of population differentiation in C. formosana compared with those estimated in previous studies of conifers including Cunninghamia konishii, Keteleeria davidiana var. formosana, and Taiwania cryptomerioides occurring in Taiwan. BAYESCAN detected 26 FST outlier loci that were found to be associated strongly with various environmental variables using multiple univariate logistic regression, latent factor mixed model, and Bayesian logistic regression. We found several environmentally dependent adaptive loci with high frequencies in low- or high-elevation populations, suggesting their involvement in local adaptation. Ecological factors, including relative humidity and sunshine hours, that are generally not altitude related could have been the most important selective drivers for population divergent evolution in C. formosana. The present study provides fundamental information in relation to adaptive evolution and can be useful for assisted migration program of C. formosana in the future conservation of this species.
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Affiliation(s)
- Wei-Ming Chien
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chung-Te Chang
- Department of Life Science, Tunghai University, Taichung, Taiwan
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Shih-Ying Hwang
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
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12
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Vázquez-González C, Zas R, Erbilgin N, Ferrenberg S, Rozas V, Sampedro L. Resin ducts as resistance traits in conifers: linking dendrochronology and resin-based defences. TREE PHYSIOLOGY 2020; 40:1313-1326. [PMID: 32478382 DOI: 10.1093/treephys/tpaa064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 05/26/2020] [Indexed: 05/20/2023]
Abstract
Conifers have evolved different chemical and anatomical defences against a wide range of antagonists. Resin ducts produce, store and translocate oleoresin, a complex terpenoid mixture that acts as both a physical and a chemical defence. Although resin duct characteristics (e.g., number, density, area) have been positively related to biotic resistance in several conifer species, the literature reporting this association remains inconclusive. Axial resin ducts recorded in annual growth rings are an archive of annual defensive investment in trees. This whole-life record of defence investment can be analysed using standard dendrochronological procedures, which allows us to assess interannual variability and the effect of understudied drivers of phenotypic variation on resin-based defences. Understanding the sources of phenotypic variation in defences, such as genetic differentiation and environmental plasticity, is essential for assessing the adaptive potential of forest tree populations to resist pests under climate change. Here, we reviewed the evidence supporting the importance of resin ducts in conifer resistance, and summarized current knowledge about the sources of variation in resin duct production. We propose a standardized methodology to measure resin duct production by means of dendrochronological procedures. This approach will illuminate the roles of resin ducts in tree defence across species, while helping to fill pivotal knowledge gaps in plant defence theory, and leading to a robust understanding of the patterns of variation in resin-based defences throughout the tree's lifespan.
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Affiliation(s)
- Carla Vázquez-González
- Misión Biológica de Galicia, National Spanish Research Council (MBG-CSIC), Carballeira 8, Salcedo, Pontevedra 3614, Spain
| | - Rafael Zas
- Misión Biológica de Galicia, National Spanish Research Council (MBG-CSIC), Carballeira 8, Salcedo, Pontevedra 3614, Spain
| | - Nadir Erbilgin
- Department of Renewable Resources, University of Alberta, Edmonton, T6G 2H1 Alberta, Canada
| | - Scott Ferrenberg
- Department of Biology, New Mexico State University, 1305 Frenger St., Las Cruces, 88001, NM, USA
| | - Vicente Rozas
- iuFOR-EiFAB, Campus Duques de Soria, Universidad de Valladolid, Soria 42004, Spain
- Laboratorio de Dendrocronología y Cambio Global, Facultad de Ciencias Forestales y Recursos Naturales, Universidad Austral de Chile, Valdivia 5090000, Chile
| | - Luis Sampedro
- Misión Biológica de Galicia, National Spanish Research Council (MBG-CSIC), Carballeira 8, Salcedo, Pontevedra 3614, Spain
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13
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de María N, Guevara MÁ, Perdiguero P, Vélez MD, Cabezas JA, López‐Hinojosa M, Li Z, Díaz LM, Pizarro A, Mancha JA, Sterck L, Sánchez‐Gómez D, Miguel C, Collada C, Díaz‐Sala MC, Cervera MT. Molecular study of drought response in the Mediterranean conifer Pinus pinaster Ait.: Differential transcriptomic profiling reveals constitutive water deficit-independent drought tolerance mechanisms. Ecol Evol 2020; 10:9788-9807. [PMID: 33005345 PMCID: PMC7520194 DOI: 10.1002/ece3.6613] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/19/2020] [Accepted: 06/29/2020] [Indexed: 12/27/2022] Open
Abstract
Adaptation of long-living forest trees to respond to environmental changes is essential to secure their performance under adverse conditions. Water deficit is one of the most significant stress factors determining tree growth and survival. Maritime pine (Pinus pinaster Ait.), the main source of softwood in southwestern Europe, is subjected to recurrent drought periods which, according to climate change predictions for the years to come, will progressively increase in the Mediterranean region. The mechanisms regulating pine adaptive responses to environment are still largely unknown. The aim of this work was to go a step further in understanding the molecular mechanisms underlying maritime pine response to water stress and drought tolerance at the whole plant level. A global transcriptomic profiling of roots, stems, and needles was conducted to analyze the performance of siblings showing contrasted responses to water deficit from an ad hoc designed full-sib family. Although P. pinaster is considered a recalcitrant species for vegetative propagation in adult phase, the analysis was conducted using vegetatively propagated trees exposed to two treatments: well-watered and moderate water stress. The comparative analyses led us to identify organ-specific genes, constitutively expressed as well as differentially expressed when comparing control versus water stress conditions, in drought-sensitive and drought-tolerant genotypes. Different response strategies can point out, with tolerant individuals being pre-adapted for coping with drought by constitutively expressing stress-related genes that are detected only in latter stages on sensitive individuals subjected to drought.
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Affiliation(s)
- Nuria de María
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
| | - María Ángeles Guevara
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
| | - Pedro Perdiguero
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Centro de Investigación en Sanidad Animal (CISA‐INIA)MadridSpain
- Departamento de Cultivos HerbáceosCentro de Investigación Agroforestal de AlbaladejitoCuencaSpain
| | - María Dolores Vélez
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
| | - José Antonio Cabezas
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
| | - Miriam López‐Hinojosa
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
| | - Zhen Li
- Ghent University Department of Plant Biotechnology and BioinformaticsGhentBelgium
- VIB‐UGent Center for Plant Systems BiologyGhentBelgium
- Bioinformatics Institute GhentGhent UniversityGhentBelgium
| | - Luís Manuel Díaz
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
| | - Alberto Pizarro
- Departamento de Ciencias de la VidaUniversidad de AlcaláAlcalá de HenaresSpain
| | - José Antonio Mancha
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
| | - Lieven Sterck
- Ghent University Department of Plant Biotechnology and BioinformaticsGhentBelgium
- VIB‐UGent Center for Plant Systems BiologyGhentBelgium
- Bioinformatics Institute GhentGhent UniversityGhentBelgium
| | - David Sánchez‐Gómez
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
- Departamento de Cultivos HerbáceosCentro de Investigación Agroforestal de AlbaladejitoCuencaSpain
| | - Célia Miguel
- BioISI‐Biosystems & Integrative Sciences InstituteFaculdade de CiênciasUniversidade de LisboaLisboaPortugal
- Instituto de Biologia Experimental e Tecnológica (iBET)OeirasPortugal
| | - Carmen Collada
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
- Grupo de investigación Sistemas Naturales e Historia ForestalUPMMadridSpain
| | | | - María Teresa Cervera
- Departamento de Ecología y Genética ForestalCentro de Investigación Forestal (CIFOR)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
- Unidad Mixta de Genómica y Ecofisiología ForestalInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Universidad Politécnica de Madrid (UPM)MadridSpain
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14
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Estravis-Barcala M, Mattera MG, Soliani C, Bellora N, Opgenoorth L, Heer K, Arana MV. Molecular bases of responses to abiotic stress in trees. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3765-3779. [PMID: 31768543 PMCID: PMC7316969 DOI: 10.1093/jxb/erz532] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/25/2019] [Indexed: 05/05/2023]
Abstract
Trees are constantly exposed to climate fluctuations, which vary with both time and geographic location. Environmental changes that are outside of the physiological favorable range usually negatively affect plant performance and trigger responses to abiotic stress. Long-living trees in particular have evolved a wide spectrum of molecular mechanisms to coordinate growth and development under stressful conditions, thus minimizing fitness costs. The ongoing development of techniques directed at quantifying abiotic stress has significantly increased our knowledge of physiological responses in woody plants. However, it is only within recent years that advances in next-generation sequencing and biochemical approaches have enabled us to begin to understand the complexity of the molecular systems that underlie these responses. Here, we review recent progress in our understanding of the molecular bases of drought and temperature stresses in trees, with a focus on functional, transcriptomic, epigenetic, and population genomic studies. In addition, we highlight topics that will contribute to progress in our understanding of the plastic and adaptive responses of woody plants to drought and temperature in a context of global climate change.
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Affiliation(s)
- Maximiliano Estravis-Barcala
- Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales, (Consejo Nacional de Investigaciones Científicas y Técnicas- Universidad Nacional del Comahue), San Carlos de Bariloche, Rio Negro, Argentina
| | - María Gabriela Mattera
- Instituto de Investigaciones Forestales y Agropecuarias Bariloche (Instituto Nacional de Tecnología Agropecuaria - Consejo Nacional de Investigaciones Científicas y Técnicas), San Carlos de Bariloche, Rio Negro, Argentina
| | - Carolina Soliani
- Instituto de Investigaciones Forestales y Agropecuarias Bariloche (Instituto Nacional de Tecnología Agropecuaria - Consejo Nacional de Investigaciones Científicas y Técnicas), San Carlos de Bariloche, Rio Negro, Argentina
| | - Nicolás Bellora
- Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales, (Consejo Nacional de Investigaciones Científicas y Técnicas- Universidad Nacional del Comahue), San Carlos de Bariloche, Rio Negro, Argentina
| | - Lars Opgenoorth
- Department of Ecology, Philipps University Marburg, Marburg, Germany
- Swiss Federal Research Institute WSL, BirmensdorfSwitzerland
| | - Katrin Heer
- Department of Conservation Biology, Philipps University Marburg, Marburg Germany
| | - María Verónica Arana
- Instituto de Investigaciones Forestales y Agropecuarias Bariloche (Instituto Nacional de Tecnología Agropecuaria - Consejo Nacional de Investigaciones Científicas y Técnicas), San Carlos de Bariloche, Rio Negro, Argentina
- Correspondence:
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15
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López‐Goldar X, Zas R, Sampedro L. Resource availability drives microevolutionary patterns of plant defences. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13610] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Xosé López‐Goldar
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
- Misión Biológica de Galicia Consejo Superior de Investigaciones Científicas Pontevedra Spain
| | - Rafael Zas
- Misión Biológica de Galicia Consejo Superior de Investigaciones Científicas Pontevedra Spain
| | - Luis Sampedro
- Misión Biológica de Galicia Consejo Superior de Investigaciones Científicas Pontevedra Spain
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16
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Geographical Gradients of Genetic Diversity and Differentiation among the Southernmost Marginal Populations of Abies sachalinensis Revealed by EST-SSR Polymorphism. FORESTS 2020. [DOI: 10.3390/f11020233] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Research Highlights: We detected the longitudinal gradients of genetic diversity parameters, such as the number of alleles, effective number of alleles, heterozygosity, and inbreeding coefficient, and found that these might be attributable to climatic conditions, such as temperature and snow depth. Background and Objectives: Genetic diversity among local populations of a plant species at its distributional margin has long been of interest in ecological genetics. Populations at the distribution center grow well in favorable conditions, but those at the range margins are exposed to unfavorable environments, and the environmental conditions at establishment sites might reflect the genetic diversity of local populations. This is known as the central-marginal hypothesis in which marginal populations show lower genetic variation and higher differentiation than in central populations. In addition, genetic variation in a local population is influenced by phylogenetic constraints and the population history of selection under environmental constraints. In this study, we investigated this hypothesis in relation to Abies sachalinensis, a major conifer species in Hokkaido. Materials and Methods: A total of 1189 trees from 25 natural populations were analyzed using 19 EST-SSR loci. Results: The eastern populations, namely, those in the species distribution center, showed greater genetic diversity than did the western peripheral populations. Another important finding is that the southwestern marginal populations were genetically differentiated from the other populations. Conclusions: These differences might be due to genetic drift in the small and isolated populations at the range margin. Therefore, our results indicated that the central-marginal hypothesis held true for the southernmost A. sachalinensis populations in Hokkaido.
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17
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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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18
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Li YS, Shih KM, Chang CT, Chung JD, Hwang SY. Testing the Effect of Mountain Ranges as a Physical Barrier to Current Gene Flow and Environmentally Dependent Adaptive Divergence in Cunninghamia konishii (Cupressaceae). Front Genet 2019; 10:742. [PMID: 31447888 PMCID: PMC6697026 DOI: 10.3389/fgene.2019.00742] [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: 02/01/2019] [Accepted: 07/15/2019] [Indexed: 11/29/2022] Open
Abstract
Populations can be genetically isolated by differences in their ecology or environment that hampered efficient migration, or they may be isolated solely by geographic distance. Moreover, mountain ranges across a species’ distribution area might have acted as barriers to gene flow. Genetic variation was quantified using amplified fragment length polymorphism (AFLP) and 13 selective amplification primer combinations used generated a total of 482 fragments. Here, we tested the barrier effects of mountains on gene flow and environmentally dependent local adaptation of Cunninghamia konishii occur in Taiwan. A pattern of genetic isolation by distance was not found and variation partitioning revealed that environment explained a relatively larger proportion of genetic variation than geography. The effect of mountains as barriers to genetic exchange, despite low population differentiation indicating a high rate of gene flow, was found within the distribution range of C. konishii. Twelve AFLP loci were identified as potential selective outliers using genome-scan methods (BAYESCAN and DFDIST) and strongly associated with environmental variables using regression approaches (LFMM, Samβada, and rstanarm) demonstrating adaptive divergence underlying local adaptation. Annual mean temperature, annual precipitation, and slope could be the most important environmental factors causally associated with adaptive genetic variation in C. konishii. The study revealed the existence of physical barriers to current gene flow and environmentally dependent adaptive divergence, and a significant proportion of the rate of gene flow may represent a reflection of demographic history.
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Affiliation(s)
- Yi-Shao Li
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Kai-Ming Shih
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chung-Te Chang
- Department of Life Science, Tunghai University, Taichung, Taiwan
| | - Jeng-Der Chung
- Division of Silviculture, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Shih-Ying Hwang
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
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19
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Wachowiak W, Zaborowska J, Łabiszak B, Perry A, Zucca GM, González-Martínez SC, Cavers S. Molecular signatures of divergence and selection in closely related pine taxa. TREE GENETICS & GENOMES 2018; 14:83. [PMID: 30930708 PMCID: PMC6404648 DOI: 10.1007/s11295-018-1296-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/01/2018] [Accepted: 10/10/2018] [Indexed: 06/09/2023]
Abstract
Efforts to detect loci under selection in plants have mostly focussed on single species. However, assuming that intraspecific divergence may lead to speciation, comparisons of genetic variation within and among recently diverged taxa can help to locate such genes. In this study, coalescent and outlier detection methods were used to assess nucleotide polymorphism and divergence at 79 nuclear gene fragments (1212 SNPs) in 16 populations (153 individuals) of the closely related, but phenotypically and ecologically distinct, pine taxa Pinus mugo, P. uliginosa and P. uncinata across their European distributions. Simultaneously, mitochondrial DNA markers, which are maternally inherited in pines and distributed by seeds at short geographic distance, were used to assess genetic relationships of the focal populations and taxa. The majority of nuclear loci showed homogenous patterns of variation between the taxa due to a high number of shared SNPs and haplotypes, similar levels of polymorphism, and low net divergence. However, against this common genetic background and an overall low population structure within taxa at mitochondrial markers, we identified several genes showing signatures of selection, accompanied by significant intra- and interspecific divergence. Our results indicate that loci involved in species divergence may be involved in intraspecific local adaptation.
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Affiliation(s)
- Witold Wachowiak
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB UK
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Julia Zaborowska
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Bartosz Łabiszak
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Annika Perry
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB UK
| | - Giovanni M. Zucca
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB UK
| | | | - Stephen Cavers
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB UK
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20
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Li YS, Chang CT, Wang CN, Thomas P, Chung JD, Hwang SY. The Contribution of Neutral and Environmentally Dependent Processes in Driving Population and Lineage Divergence in Taiwania ( Taiwania cryptomerioides). FRONTIERS IN PLANT SCIENCE 2018; 9:1148. [PMID: 30135693 PMCID: PMC6092574 DOI: 10.3389/fpls.2018.01148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
The question of what determines divergence both between and within species has been the central topic in evolutionary biology. Neutral drift and environmentally dependent divergence are predicted to play roles in driving population and lineage divergence. However, neutral drift may preclude adaptation if the rate of gene flow between populations is high. Here, we sampled populations of three Taiwania (Taiwania cryptomerioides) lineages occurring in Taiwan, the mainland of China (Yunnan-Myanmar border), and northern Vietnam, and tested the relative strength of neutral drift and divergent selection in shaping divergence of those populations and lineages. We quantified genetic and epigenetic variation, respectively, using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP). Analysis of 1413 AFLP and 462 MSAP loci using frequency-based genome scan methods and generalized linear models (GLMs) found no potential selective outliers when only Taiwanese populations were examined, suggesting that neutral drift was the predominant evolutionary process driving differentiation between those populations. However, environmentally associated divergence was found when lineages were compared. Thirty-two potential selective outliers were identified based on genome scans and their associations with environmental variables were tested with GLMs, generalized linear mixed effect models (GLMMs), and model selection with a model averaging approach. Ten loci (six AFLP and four MSAP) were found to be strongly associated with environmental variables, particularly monthly temperature variation and normalized difference vegetation index (NDVI) using model selection and a model averaging approach. Because only a small portion of genetic and epigenetic loci were found to be potential selective outliers, neutral evolutionary process might also have played crucial roles in driving lineage divergence, particularly between geographically and genetically isolated island and mainland Asia lineages. Nevertheless, the vast amount of neutral drift causing genetic and epigenetic variations might have the potential for adaptation to future climate changes. These could be important for the survival of Taiwania in different geographic areas.
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Affiliation(s)
- Yi-Shao Li
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chung-Te Chang
- Department of Geography, National Taiwan University, Taipei, Taiwan
| | - Chun-Neng Wang
- Institute of Ecology and Evolution, National Taiwan University, Taipei, Taiwan
| | - Philip Thomas
- International Conifer Conservation Programme of the Royal Botanic Garden, Edinburgh, United Kingdom
| | - Jeng-Der Chung
- Division of Silviculture, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Shih-Ying Hwang
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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21
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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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22
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Abstract
Conifers are the dominant plant species throughout the high latitude boreal forests as well as some lower latitude temperate forests of North America, Europe, and Asia. As such, they play an integral economic and ecological role across much of the world. This study focused on the characterization of needle transcriptomes from four ecologically important and understudied North American white pines within the Pinus subgenus Strobus. The populations of many Strobus species are challenged by native and introduced pathogens, native insects, and abiotic factors. RNA from the needles of western white pine (Pinus monticola), limber pine (Pinus flexilis), whitebark pine (Pinus albicaulis), and sugar pine (Pinus lambertiana) was sampled, Illumina short read sequenced, and de novo assembled. The assembled transcripts and their subsequent structural and functional annotations were processed through custom pipelines to contend with the challenges of non-model organism transcriptome validation. Orthologous gene family analysis of over 58,000 translated transcripts, implemented through Tribe-MCL, estimated the shared and unique gene space among the four species. This revealed 2025 conserved gene families, of which 408 were aligned to estimate levels of divergence and reveal patterns of selection. Specific candidate genes previously associated with drought tolerance and white pine blister rust resistance in conifers were investigated.
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23
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Shih KM, Chang CT, Chung JD, Chiang YC, Hwang SY. Adaptive Genetic Divergence Despite Significant Isolation-by-Distance in Populations of Taiwan Cow-Tail Fir ( Keteleeria davidiana var. formosana). FRONTIERS IN PLANT SCIENCE 2018; 9:92. [PMID: 29449860 PMCID: PMC5799944 DOI: 10.3389/fpls.2018.00092] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/17/2018] [Indexed: 05/05/2023]
Abstract
Double digest restriction site-associated DNA sequencing (ddRADseq) is a tool for delivering genome-wide single nucleotide polymorphism (SNP) markers for non-model organisms useful in resolving fine-scale population structure and detecting signatures of selection. This study performs population genetic analysis, based on ddRADseq data, of a coniferous species, Keteleeria davidiana var. formosana, disjunctly distributed in northern and southern Taiwan, for investigation of population adaptive divergence in response to environmental heterogeneity. A total of 13,914 SNPs were detected and used to assess genetic diversity, FST outlier detection, population genetic structure, and individual assignments of five populations (62 individuals) of K. davidiana var. formosana. Principal component analysis (PCA), individual assignments, and the neighbor-joining tree were successful in differentiating individuals between northern and southern populations of K. davidiana var. formosana, but apparent gene flow between the southern DW30 population and northern populations was also revealed. Fifteen of 23 highly differentiated SNPs identified were found to be strongly associated with environmental variables, suggesting isolation-by-environment (IBE). However, multiple matrix regression with randomization analysis revealed strong IBE as well as significant isolation-by-distance. Environmental impacts on divergence were found between populations of the North and South regions and also between the two southern neighboring populations. BLASTN annotation of the sequences flanking outlier SNPs gave significant hits for three of 23 markers that might have biological relevance to mitochondrial homeostasis involved in the survival of locally adapted lineages. Species delimitation between K. davidiana var. formosana and its ancestor, K. davidiana, was also examined (72 individuals). This study has produced highly informative population genomic data for the understanding of population attributes, such as diversity, connectivity, and adaptive divergence associated with large- and small-scale environmental heterogeneity in K. davidiana var. formosana.
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Affiliation(s)
- Kai-Ming Shih
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chung-Te Chang
- Department of Geography, National Taiwan University, Taipei, Taiwan
| | - Jeng-Der Chung
- Division of Silviculture, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Shih-Ying Hwang
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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24
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Grivet D, Avia K, Vaattovaara A, Eckert AJ, Neale DB, Savolainen O, González-Martínez SC. High rate of adaptive evolution in two widespread European pines. Mol Ecol 2017; 26:6857-6870. [PMID: 29110402 DOI: 10.1111/mec.14402] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 09/14/2017] [Accepted: 09/25/2017] [Indexed: 12/18/2022]
Abstract
Comparing related organisms with differing ecological requirements and evolutionary histories can shed light on the mechanisms and drivers underlying genetic adaptation. Here, by examining a common set of hundreds of loci, we compare patterns of nucleotide diversity and molecular adaptation of two European conifers (Scots pine and maritime pine) living in contrasted environments and characterized by distinct population genetic structure (low and clinal in Scots pine, high and ecotypic in maritime pine) and demographic histories. We found higher nucleotide diversity in Scots pine than in maritime pine, whereas rates of new adaptive substitutions (ωa ), as estimated from the distribution of fitness effects, were similar across species and among the highest found in plants. Sample size and population genetic structure did not appear to have resulted in significant bias in estimates of ωa . Moreover, population contraction-expansion dynamics for each species did not affect differentially the rate of adaptive substitution in these two pines. Several methodological and biological factors may underlie the unusually high rate of adaptive evolution of Scots pine and maritime pine. By providing two new case studies with contrasting evolutionary histories, we contribute to disentangling the multiple factors potentially affecting adaptive evolution in natural plant populations.
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Affiliation(s)
- Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Madrid, Spain.,Sustainable Forest Management Research Institute, INIA - University of Valladolid, Palencia, Spain
| | - Komlan Avia
- Department of Ecology and Genetics and Biocenter Oulu, University of Oulu, Oulu, Finland.,Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, Roscoff, France.,UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique Roscoff, Roscoff, France
| | - Aleksia Vaattovaara
- Department of Ecology and Genetics and Biocenter Oulu, University of Oulu, Oulu, Finland.,Division of Plant Biology, Department of Biosciences, Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland
| | - Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA, USA
| | - David B Neale
- Department of Plant Sciences, University of California at Davis, Davis, CA, USA
| | - Outi Savolainen
- Department of Ecology and Genetics and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Santiago C González-Martínez
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Madrid, Spain.,Sustainable Forest Management Research Institute, INIA - University of Valladolid, Palencia, Spain.,BIOGECO, INRA, Univ. Bordeaux, Cestas, France
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25
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Grant OM, O'Reilly C. Impact of genetic variation and long-term limited water availability on the ecophysiology of young Sitka spruce (Picea sitchensis (Bong.) Carr.). TREE PHYSIOLOGY 2017; 37:536-549. [PMID: 27677274 DOI: 10.1093/treephys/tpw093] [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: 03/07/2016] [Accepted: 08/29/2016] [Indexed: 06/06/2023]
Abstract
Future limited water availability may reduce the potential of tree improvement to increase timber yields. We investigated ecophysiological variation between full-sibling families of Sitka spruce (Picea sitchensis (Bong.) Carr.) growing under contrasting water availability conditions: control (optimal) water availability and limited water availability. One-year-old seedlings of nine improved families plus an unimproved seed lot were grown in pots in a greenhouse and the two water availability treatments imposed via drip irrigation. Whole-plant water use varied between families. Stomatal conductance and the light-saturated quantum yield of photosystem II at times differed between families, but not consistently. Certain families showed considerably greater increases in electron transport rate with increasing photosynthetically active radiation. Limited water availability resulted in reduced branch water potential, leaf stomatal conductance and transpiration per unit leaf area, and increased whole-plant water-use efficiency, in all genetic material. The responses of plant water use and leaf carbon isotope composition to water limitation, were, however, initially influenced by variation in vigour between families-with conservative growth in some material slowing the decline in substrate moisture content. As the duration of water deficit extended, these variables showed a more uniform response across families. Between-family variation in physiological mechanisms of drought tolerance was not detected. Thus, for Sitka spruce, assessing juvenile material may not allow selection to prevent reductions in productivity associated with long-term sub-optimal growing conditions, but screening for conservative growth (within families as well as between families) may be beneficial where survival of relatively short-term water limitation is the primary concern.
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Affiliation(s)
- Olga M Grant
- School of Agriculture and Food Science, University College Dublin, UCD Forestry, Belfield, Dublin 4, Ireland
- Present address: Room 239, Engineering Building, University College Dublin, Belfield, Dublin 4, Ireland
| | - Conor O'Reilly
- School of Agriculture and Food Science, University College Dublin, UCD Forestry, Belfield, Dublin 4, Ireland
- Present address: Room 239, Engineering Building, University College Dublin, Belfield, Dublin 4, Ireland
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26
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Steane DA, Mclean EH, Potts BM, Prober SM, Stock WD, Stylianou VM, Vaillancourt RE, Byrne M. Evidence for adaptation and acclimation in a widespread eucalypt of semi-arid Australia. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw051] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Dorothy A. Steane
- School of Biological Sciences and ARC Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Queensland, 4556, Australia
- CSIRO Land and Water, Private Bag 5, Wembley 6913, Western Australia
| | - Elizabeth H. Mclean
- CSIRO Land and Water, Private Bag 5, Wembley 6913, Western Australia
- Science and Conservation Division, Department of Parks and Wildlife, Locked Bag 104, Bentley Delivery Centre, WA 6983, Australia
| | - Brad M. Potts
- School of Biological Sciences and ARC Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Suzanne M. Prober
- CSIRO Land and Water, Private Bag 5, Wembley 6913, Western Australia
| | - William D. Stock
- Centre for Ecosystem Management, School of Science, Edith Cowan University, Joondalup, 6027, Western Australia
| | - Vanessa M. Stylianou
- Centre for Ecosystem Management, School of Science, Edith Cowan University, Joondalup, 6027, Western Australia
| | - René E. Vaillancourt
- School of Biological Sciences and ARC Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Margaret Byrne
- Science and Conservation Division, Department of Parks and Wildlife, Locked Bag 104, Bentley Delivery Centre, WA 6983, Australia
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27
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Steane DA, Potts BM, McLean EH, Collins L, Holland BR, Prober SM, Stock WD, Vaillancourt RE, Byrne M. Genomic Scans across Three Eucalypts Suggest that Adaptation to Aridity is a Genome-Wide Phenomenon. Genome Biol Evol 2017; 9:253-265. [PMID: 28391293 PMCID: PMC5381606 DOI: 10.1093/gbe/evw290] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2016] [Indexed: 01/01/2023] Open
Abstract
Widespread species spanning strong environmental (e.g., climatic) gradients frequently display morphological and physiological adaptations to local conditions. Some adaptations are common to different species that occupy similar environments. However, the genomic architecture underlying such convergent traits may not be the same between species. Using genomic data from previous studies of three widespread eucalypt species that grow along rainfall gradients in southern Australia, our probabilistic approach provides evidence that adaptation to aridity is a genome-wide phenomenon, likely to involve multiple and diverse genes, gene families and regulatory regions that affect a multitude of complex genetic and biochemical processes.
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Affiliation(s)
- Dorothy A. Steane
- School of Biological Sciences and ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
- CSIRO Land and Water, Wembley, Western Australia, Australia
| | - Brad M. Potts
- School of Biological Sciences and ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
| | - Elizabeth H. McLean
- CSIRO Land and Water, Wembley, Western Australia, Australia
- Science and Conservation Division, Department of Parks and Wildlife, Bentley Delivery Centre, Western Australia, Australia
| | - Lesley Collins
- Faculty of Health Science, Universal College of Learning, Palmerston North, New Zealand
| | - Barbara R. Holland
- School of Physical Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | | | - William D. Stock
- Centre for Ecosystem Management, School of Natural Sciences, Edith Cowan University, Perth, Western Australia, Australia
| | - René E. Vaillancourt
- School of Biological Sciences and ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
| | - Margaret Byrne
- Science and Conservation Division, Department of Parks and Wildlife, Bentley Delivery Centre, Western Australia, Australia
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28
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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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29
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Yang J, Miao CY, Mao RL, Li Y. Landscape Population Genomics of Forsythia ( Forsythia suspensa) Reveal That Ecological Habitats Determine the Adaptive Evolution of Species. FRONTIERS IN PLANT SCIENCE 2017; 8:481. [PMID: 28424728 PMCID: PMC5380681 DOI: 10.3389/fpls.2017.00481] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/20/2017] [Indexed: 05/06/2023]
Abstract
Understanding the genetic mechanisms of adaptation to environmental variables is a key concern in molecular ecology and evolutionary biology. Determining the adaptive evolutionary direction and evaluating the adaptation status of species can improve our understanding of these mechanisms. In this study, we sampled 20 populations of Forsythia suspensa to infer the relationship between environmental variables and adaptive genetic variations. Population structure analysis revealed that four genetic groups of F. suspensa exist resulting from divergent selection driven by seven environmental variables. A total of 26 outlier loci were identified by both BayeScan and FDIST2, 23 of which were environment-associated loci (EAL). Environmental association analysis revealed that the environmental variables related to the ecological habitats of F. suspensa are associated with high numbers of EAL. Results of EAL characterization in F. suspensa are consistent with the hypothesis that ecological habitats determine the adaptive evolution of this species. Moreover, a model of species adaptation to environmental variables was proposed in this study. The adaptation model was used to further evaluate the adaptation status of F. suspensa to environmental variables. This study will be useful to help us in understanding the adaptive evolution of species in regions lacking strong selection pressure.
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30
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Nadeau S, Meirmans PG, Aitken SN, Ritland K, Isabel N. The challenge of separating signatures of local adaptation from those of isolation by distance and colonization history: The case of two white pines. Ecol Evol 2016; 6:8649-8664. [PMID: 28035257 PMCID: PMC5192886 DOI: 10.1002/ece3.2550] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/25/2016] [Accepted: 09/06/2016] [Indexed: 01/13/2023] Open
Abstract
Accurately detecting signatures of local adaptation using genetic‐environment associations (GEAs) requires controlling for neutral patterns of population structure to reduce the risk of false positives. However, a high degree of collinearity between climatic gradients and neutral population structure can greatly reduce power, and the performance of GEA methods in such case is rarely evaluated in empirical studies. In this study, we attempted to disentangle the effects of local adaptation and isolation by environment (IBE) from those of isolation by distance (IBD) and isolation by colonization from glacial refugia (IBC) using range‐wide samples in two white pine species. For this, SNPs from 168 genes, including 52 candidate genes for growth and phenology, were genotyped in 133 and 61 populations of Pinus strobus and P. monticola, respectively. For P. strobus and using all 153 SNPs, climate (IBE) did not significantly explained among‐population variation when controlling for IBD and IBC in redundancy analyses (RDAs). However, 26 SNPs were significantly associated with climate in single‐locus GEA analyses (Bayenv2 and LFMM), suggesting that local adaptation took place in the presence of high gene flow. For P. monticola, we found no evidence of IBE using RDAs and weaker signatures of local adaptation using GEA and FST outlier tests, consistent with adaptation via phenotypic plasticity. In both species, the majority of the explained among‐population variation (69 to 96%) could not be partitioned between the effects of IBE, IBD, and IBC. GEA methods can account differently for this confounded variation, and this could explain the small overlap of SNPs detected between Bayenv2 and LFMM. Our study illustrates the inherent difficulty of taking into account neutral structure in natural populations and the importance of sampling designs that maximize climatic variation, while minimizing collinearity between climatic gradients and neutral structure.
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Affiliation(s)
- Simon Nadeau
- Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre Québec QC Canada; Department of Forest and Conservation Sciences The University of British Columbia Vancouver BC Canada
| | - Patrick G Meirmans
- Institute for Biodiversity and Ecosystem Dynamics University of Amsterdam Amsterdam The Netherlands
| | - Sally N Aitken
- Department of Forest and Conservation Sciences The University of British Columbia Vancouver BC Canada
| | - Kermit Ritland
- Department of Forest and Conservation Sciences The University of British Columbia Vancouver BC Canada
| | - Nathalie Isabel
- Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre Québec QC Canada
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31
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Lu P, Parker WC, Colombo SJ, Man R. Restructuring tree provenance test data to conform to reciprocal transplant experiments for detecting local adaptation. J Appl Ecol 2016. [DOI: 10.1111/1365-2664.12647] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pengxin Lu
- Ontario Forest Research Institute; Ontario Ministry of Natural Resources and Forestry; 1235 Queen Street East Sault Ste. Marie ON P6A 2E5 Canada
| | - William C. Parker
- Ontario Forest Research Institute; Ontario Ministry of Natural Resources and Forestry; 1235 Queen Street East Sault Ste. Marie ON P6A 2E5 Canada
| | - Stephen J. Colombo
- Ontario Forest Research Institute; Ontario Ministry of Natural Resources and Forestry; 1235 Queen Street East Sault Ste. Marie ON P6A 2E5 Canada
| | - Rongzhou Man
- Ontario Forest Research Institute; Ontario Ministry of Natural Resources and Forestry; 1235 Queen Street East Sault Ste. Marie ON P6A 2E5 Canada
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32
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Bailey SF, Bataillon T. Can the experimental evolution programme help us elucidate the genetic basis of adaptation in nature? Mol Ecol 2016; 25:203-18. [PMID: 26346808 PMCID: PMC5019151 DOI: 10.1111/mec.13378] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 08/26/2015] [Accepted: 09/04/2015] [Indexed: 02/04/2023]
Abstract
There have been a variety of approaches taken to try to characterize and identify the genetic basis of adaptation in nature, spanning theoretical models, experimental evolution studies and direct tests of natural populations. Theoretical models can provide formalized and detailed hypotheses regarding evolutionary processes and patterns, from which experimental evolution studies can then provide important proofs of concepts and characterize what is biologically reasonable. Genetic and genomic data from natural populations then allow for the identification of the particular factors that have and continue to play an important role in shaping adaptive evolution in the natural world. Further to this, experimental evolution studies allow for tests of theories that may be difficult or impossible to test in natural populations for logistical and methodological reasons and can even generate new insights, suggesting further refinement of existing theories. However, as experimental evolution studies often take place in a very particular set of controlled conditions--that is simple environments, a small range of usually asexual species, relatively short timescales--the question remains as to how applicable these experimental results are to natural populations. In this review, we discuss important insights coming from experimental evolution, focusing on four key topics tied to the evolutionary genetics of adaptation, and within those topics, we discuss the extent to which the experimental work compliments and informs natural population studies. We finish by making suggestions for future work in particular a need for natural population genomic time series data, as well as the necessity for studies that combine both experimental evolution and natural population approaches.
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Affiliation(s)
- Susan F. Bailey
- Bioinformatics Research CentreAarhus UniversityC.F. Møllers Allé 8DK‐8000Aarhus CDenmark
| | - Thomas Bataillon
- Bioinformatics Research CentreAarhus UniversityC.F. Møllers Allé 8DK‐8000Aarhus CDenmark
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33
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Voltas J, Lucabaugh D, Chambel MR, Ferrio JP. Intraspecific variation in the use of water sources by the circum-Mediterranean conifer Pinus halepensis. THE NEW PHYTOLOGIST 2015; 208:1031-41. [PMID: 26193768 DOI: 10.1111/nph.13569] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 06/13/2015] [Indexed: 05/13/2023]
Abstract
The relevance of interspecific variation in the use of plant water sources has been recognized in drought-prone environments. By contrast, the characterization of intraspecific differences in water uptake patterns remains elusive, although preferential access to particular soil layers may be an important adaptive response for species along aridity gradients. Stable water isotopes were analysed in soil and xylem samples of 56 populations of the drought-avoidant conifer Pinus halepensis grown in a common garden test. We found that most populations reverted to deep soil layers as the main plant water source during seasonal summer droughts. More specifically, we detected a clear geographical differentiation among populations in water uptake patterns even under relatively mild drought conditions (early autumn), with populations originating from more arid regions taking up more water from deep soil layers. However, the preferential access to deep soil water was largely independent of aboveground growth. Our findings highlight the high plasticity and adaptive relevance of the differential access to soil water pools among Aleppo pine populations. The observed ecotypic patterns point to the adaptive relevance of resource investment in deep roots as a strategy towards securing a source of water in dry environments for P. halepensis.
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Affiliation(s)
- Jordi Voltas
- Department of Crop and Forest Sciences - AGROTECNIO Center, University of Lleida, Rovira Roure 191, Lleida, E-25198, Spain
| | - Devon Lucabaugh
- Department of Crop and Forest Sciences - AGROTECNIO Center, University of Lleida, Rovira Roure 191, Lleida, E-25198, Spain
| | | | - Juan Pedro Ferrio
- Department of Crop and Forest Sciences - AGROTECNIO Center, University of Lleida, Rovira Roure 191, Lleida, E-25198, Spain
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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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35
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Mayol M, Riba M, González-Martínez SC, Bagnoli F, de Beaulieu JL, Berganzo E, Burgarella C, Dubreuil M, Krajmerová D, Paule L, Romšáková I, Vettori C, Vincenot L, Vendramin GG. Adapting through glacial cycles: insights from a long-lived tree (Taxus baccata). THE NEW PHYTOLOGIST 2015; 208:973-986. [PMID: 26096330 DOI: 10.1111/nph.13496] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/30/2015] [Indexed: 06/04/2023]
Abstract
Despite the large body of research devoted to understanding the role of Quaternary glacial cycles in the genetic divergence of European trees, the differential contribution of geographic isolation and/or environmental adaptation in creating population genetic divergence remains unexplored. In this study, we used a long-lived tree (Taxus baccata) as a model species to investigate the impact of Quaternary climatic changes on genetic diversity via neutral (isolation-by-distance) and selective (isolation-by-adaptation) processes. We applied approximate Bayesian computation to genetic data to infer its demographic history, and combined this information with past and present climatic data to assess the role of environment and geography in the observed patterns of genetic structure. We found evidence that yew colonized Europe from the East, and that European samples diverged into two groups (Western, Eastern) at the beginning of the Quaternary glaciations, c. 2.2 Myr before present. Apart from the expected effects of geographical isolation during glacials, we discovered a significant role of environmental adaptation during interglacials at the origin of genetic divergence between both groups. This process may be common in other organisms, providing new research lines to explore the effect of Quaternary climatic factors on present-day patterns of genetic diversity.
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Affiliation(s)
| | - Miquel Riba
- CREAF, Cerdanyola del Vallès, 08193, Spain
- Univ Autonòma Barcelona, Cerdanyola del Vallès, 08193, Spain
| | | | - Francesca Bagnoli
- Plant Protection Institute, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino (FI), Italy
| | | | | | - Concetta Burgarella
- Université Montpellier 2, CNRS UMR, Institut de Sciences de l'Evolution de Montpellier, Montpellier, 5554, France
| | | | - Diana Krajmerová
- Faculty of Forestry, Technical University, SK-96053, Zvolen, Slovakia
| | - Ladislav Paule
- Faculty of Forestry, Technical University, SK-96053, Zvolen, Slovakia
| | - Ivana Romšáková
- Faculty of Forestry, Technical University, SK-96053, Zvolen, Slovakia
| | - Cristina Vettori
- Institute of Biosciences and Bioresources, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino (FI), Italy
| | | | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino (FI), Italy
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36
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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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37
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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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38
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Rellstab C, Gugerli F, Eckert AJ, Hancock AM, Holderegger R. A practical guide to environmental association analysis in landscape genomics. Mol Ecol 2015; 24:4348-70. [DOI: 10.1111/mec.13322] [Citation(s) in RCA: 441] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 07/10/2015] [Accepted: 07/13/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Christian Rellstab
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Felix Gugerli
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Andrew J. Eckert
- Department of Biology; Virginia Commonwealth University; Richmond VA 23284 USA
| | - Angela M. Hancock
- Faculty of Molecular Biology; Max F. Perutz Laboratories and University of Vienna; Oskar-Morgenstern-Platz 1 1090 Vienna Austria
| | - Rolf Holderegger
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 8903 Birmensdorf Switzerland
- ETH Zürich; Institute of Integrative Biology; Universitätstrasse 16 8092 Zürich Switzerland
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39
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Nadeau S, Godbout J, Lamothe M, Gros-Louis MC, Isabel N, Ritland K. Contrasting patterns of genetic diversity across the ranges of Pinus monticola and P. strobus: a comparison between eastern and western North American postglacial colonization histories. AMERICAN JOURNAL OF BOTANY 2015; 102:1342-1355. [PMID: 26290557 DOI: 10.3732/ajb.1500160] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 07/09/2015] [Indexed: 06/04/2023]
Abstract
UNLABELLED • Premises of the study: Understanding the influence of recent glacial and postglacial periods on species' distributions is key for predicting the effects of future environmental changes. We investigated the influence of two physiographic landscapes on population structure and postglacial colonization of two white pine species of contrasting habitats: P. monticola, which occurs in the highly mountainous region of western North America, and P. strobus, which occurs in a much less mountainous area in eastern North America.• METHODS To characterize the patterns of genetic diversity and population structure across the ranges of both species, 158 and 153 single nucleotide polymorphism (SNP) markers derived from expressed genes were genotyped on range-wide samples of 61 P. monticola and 133 P. strobus populations, respectively.• KEY RESULTS In P. monticola, a steep latitudinal decrease in genetic diversity likely resulted from postglacial colonization involving rare long-distance dispersal (LDD) events. In contrast, no geographic patterns of diversity were detected in P. strobus, suggesting recolonization via a gradually advancing front or frequent LDD events. For each species, structure analyses identified two distinct southern and northern genetic groups that likely originated from two different glacial lineages. At a finer scale, and for the two species, smaller subgroups were detected that could be remnants of cryptic refugia.• CONCLUSION During postglacial colonization, the western and eastern North American landscapes had different impacts on genetic signatures in P. monticola compared with P. strobus. We discuss the importance of our findings for conservation programs and predictions of species' response to climate change.
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Affiliation(s)
- Simon Nadeau
- The University of British Columbia, Department of Forest and Conservation Sciences, Forest Science Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380 Stn., Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - Julie Godbout
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380 Stn., Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380 Stn., Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - Marie-Claude Gros-Louis
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380 Stn., Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380 Stn., Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - Kermit Ritland
- The University of British Columbia, Department of Forest and Conservation Sciences, Forest Science Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
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40
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Mosaic genetic differentiation along environmental and geographic gradients indicate divergent selection in a white pine species complex. Evol Ecol 2015. [DOI: 10.1007/s10682-015-9785-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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41
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Hamlin JAP, Arnold ML. Neutral and Selective Processes Drive Population Differentiation for Iris hexagona. J Hered 2015; 106:628-36. [PMID: 26163584 DOI: 10.1093/jhered/esv045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/11/2015] [Indexed: 11/15/2022] Open
Abstract
Gene flow among widespread populations can be reduced by geographical distance or by divergent selection resulting from local adaptation. In this study, we tested for the divergence of phenotypes and genotypes among 8 populations of Iris hexagona. Using a genotyping-by-sequencing approach, we generated a panel of 750 single nucleotide polymorphisms (SNPs) and used population genetic analyses to determine what may affect patterns of divergence across I. hexagona populations. Specifically, genetic differentiation was compared between populations at neutral and nonneutral SNPs and detected significant differences between the 2 types of markers. We then asked whether loci with the strongest degree of population genetic differentiation were also the loci with the strongest association to morphology or climate differences, allowing us to test if pollinators or climate drive population differentiation or some combination of both. We found 2 markers that were associated with morphology and 1 marker associated with 2 of the environmental variables, which were also identified in the outlier analysis. We then show that the SNPs putatively under selection were positively correlated with both geographic distance and phenotypic distance, albeit weakly to phenotypic distance. Moreover, neutral SNPs were only correlated with geographic distance and thus isolation-by-distance was observed for neutral SNPs. Our data suggest that both deterministic and neutral processes have contributed to the evolutionary trajectory of I. hexagona populations.
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Affiliation(s)
- Jennafer A P Hamlin
- From the Department of Genetics, University of Georgia, 120 East Green St., Davison Life Sciences Building, Athens, GA (Arnold) and the Department of Biology, Indiana University, Bloomington, IN 47405, USA (Hamlin).
| | - Michael L Arnold
- From the Department of Genetics, University of Georgia, 120 East Green St., Davison Life Sciences Building, Athens, GA (Arnold) and the Department of Biology, Indiana University, Bloomington, IN 47405, USA (Hamlin)
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42
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Zenni RD, Hoban SM. Loci under selection during multiple range expansions of an invasive plant are mostly population specific, but patterns are associated with climate. Mol Ecol 2015; 24:3360-71. [DOI: 10.1111/mec.13234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 05/05/2015] [Accepted: 05/06/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Rafael D. Zenni
- Department of Ecology; University of Brasília; Campus Universitário Darcy Ribeiro Brasília CEP 70910-900 Brazil
| | - Sean M. Hoban
- National Institute for Mathematical and Biological Synthesis; University of Tennessee; Suite 110A Knoxville TN USA
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De Kort H, Vandepitte K, Mergeay J, Mijnsbrugge KV, Honnay O. The population genomic signature of environmental selection in the widespread insect-pollinated tree species Frangula alnus at different geographical scales. Heredity (Edinb) 2015; 115:415-25. [PMID: 25944466 DOI: 10.1038/hdy.2015.41] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 02/20/2015] [Accepted: 03/20/2015] [Indexed: 01/17/2023] Open
Abstract
The evaluation of the molecular signatures of selection in species lacking an available closely related reference genome remains challenging, yet it may provide valuable fundamental insights into the capacity of populations to respond to environmental cues. We screened 25 native populations of the tree species Frangula alnus subsp. alnus (Rhamnaceae), covering three different geographical scales, for 183 annotated single-nucleotide polymorphisms (SNPs). Standard population genomic outlier screens were combined with individual-based and multivariate landscape genomic approaches to examine the strength of selection relative to neutral processes in shaping genomic variation, and to identify the main environmental agents driving selection. Our results demonstrate a more distinct signature of selection with increasing geographical distance, as indicated by the proportion of SNPs (i) showing exceptional patterns of genetic diversity and differentiation (outliers) and (ii) associated with climate. Both temperature and precipitation have an important role as selective agents in shaping adaptive genomic differentiation in F. alnus subsp. alnus, although their relative importance differed among spatial scales. At the 'intermediate' and 'regional' scales, where limited genetic clustering and high population diversity were observed, some indications of natural selection may suggest a major role for gene flow in safeguarding adaptability. High genetic diversity at loci under selection in particular, indicated considerable adaptive potential, which may nevertheless be compromised by the combined effects of climate change and habitat fragmentation.
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Affiliation(s)
- H De Kort
- Biology Department, University of Leuven, Plant Conservation and Population Biology, Kasteelpark Arenberg 31, Heverlee, Belgium
| | - K Vandepitte
- Biology Department, University of Leuven, Plant Conservation and Population Biology, Kasteelpark Arenberg 31, Heverlee, Belgium
| | - J Mergeay
- Department of Genetic Diversity, Research Institute for Nature and Forest, Gaverstraat 4, Geraardsbergen, Belgium
| | - K V Mijnsbrugge
- Department of Genetic Diversity, Research Institute for Nature and Forest, Gaverstraat 4, Geraardsbergen, Belgium.,Department of Nature Conservation, Agency for Nature and Forest, Koning Albert II laan 20, Brussels, Belgium
| | - O Honnay
- Biology Department, University of Leuven, Plant Conservation and Population Biology, Kasteelpark Arenberg 31, Heverlee, Belgium
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Salces-Ortiz J, González C, Martínez M, Mayoral T, Calvo JH, Serrano MM. Looking for adaptive footprints in the HSP90AA1 ovine gene. BMC Evol Biol 2015; 15:7. [PMID: 25648535 PMCID: PMC4351680 DOI: 10.1186/s12862-015-0280-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/05/2015] [Indexed: 11/10/2022] Open
Abstract
Background Climatic factors play an important role in determining species distributions and phenotypic variation of populations over geographic space. Since domestic sheep is managed under low intensive systems animals could have retained some genome adaptive footprints. The gene encoding the Hsp90α has been extensively studied in sheep and some polymorphisms located at its promoter have been associates with differences in the transcription rate of the gene depending on climatic conditions. In this work the relationships among the distribution and frequencies of 11 polymorphisms of the ovine HSP90AA1 gene promoter in 31 sheep breeds and the climatic and geographic variables prevailing in their regions of origin have been studied. Also the promoter sequence has been characterized in 9 species of the Caprinae subfamily. Results Correlations among several climatic variables and allele frequencies of the polymorphisms of the HSP90AA1 gene promoter linked with differences in the transcription activity of the gene under heat stress conditions have been assessed. A group of breeds reared in semi dry climates have high frequencies of the insertion allele of the g.667-668insC associated with the heat stress response. Other group of breeds native to semi arid conditions showed very low frequencies of this same allele. However, in some cases, this previous correlation has not been achieved, revealing the high levels of gene flow among populations occurred following domestication. The Bayesian Test of Beaumont and Balding identified two outlier loci, the g.522A > G and g.703_704del(2)A candidates to balancing and directional selection, respectively. Polymorphisms detected in O. aries are also present in several species of the Caprinae subfamily being C. hircus, O. musimon and O. moschatus those sharing the highest number of them with O. aries. Conclusions Despite domestication, sheep breeds showed some genetic footprints related to climatic variables. Adaptation of breeds to heat climates can suppose a selective advantage to cope with global warming caused by climatic change. Polymorphisms of the HSP90AA1 gene detected in the Ovis aries species are also present in wild species from the Caprinae subfamily, indicating a great antiquity of these mutations and its importance in the adaptation of species to past climatic conditions existing in its native environments. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0280-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Carmen González
- INIA, Carretera de La Coruña Km. 7,5. 280040, Madrid, Spain.
| | - Marta Martínez
- Laboratorio Central de Veterinaria, MAGRAMA, Ctra. M-106 km1.4 28110, Madrid, Spain.
| | - Tomás Mayoral
- Laboratorio Central de Veterinaria, MAGRAMA, Ctra. M-106 km1.4 28110, Madrid, Spain.
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Micro- and macro-geographic scale effect on the molecular imprint of selection and adaptation in Norway spruce. PLoS One 2014; 9:e115499. [PMID: 25551624 PMCID: PMC4281139 DOI: 10.1371/journal.pone.0115499] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 11/19/2014] [Indexed: 11/19/2022] Open
Abstract
Forest tree species of temperate and boreal regions have undergone a long history of demographic changes and evolutionary adaptations. The main objective of this study was to detect signals of selection in Norway spruce (Picea abies [L.] Karst), at different sampling-scales and to investigate, accounting for population structure, the effect of environment on species genetic diversity. A total of 384 single nucleotide polymorphisms (SNPs) representing 290 genes were genotyped at two geographic scales: across 12 populations distributed along two altitudinal-transects in the Alps (micro-geographic scale), and across 27 populations belonging to the range of Norway spruce in central and south-east Europe (macro-geographic scale). At the macrogeographic scale, principal component analysis combined with Bayesian clustering revealed three major clusters, corresponding to the main areas of southern spruce occurrence, i.e. the Alps, Carpathians, and Hercynia. The populations along the altitudinal transects were not differentiated. To assess the role of selection in structuring genetic variation, we applied a Bayesian and coalescent-based FST-outlier method and tested for correlations between allele frequencies and climatic variables using regression analyses. At the macro-geographic scale, the FST-outlier methods detected together 11 FST-outliers. Six outliers were detected when the same analyses were carried out taking into account the genetic structure. Regression analyses with population structure correction resulted in the identification of two (micro-geographic scale) and 38 SNPs (macro-geographic scale) significantly correlated with temperature and/or precipitation. Six of these loci overlapped with FST-outliers, among them two loci encoding an enzyme involved in riboflavin biosynthesis and a sucrose synthase. The results of this study indicate a strong relationship between genetic and environmental variation at both geographic scales. It also suggests that an integrative approach combining different outlier detection methods and population sampling at different geographic scales is useful to identify loci potentially involved in adaptation.
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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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Elvira-Recuenco M, Iturritxa E, Majada J, Alia R, Raposo R. Adaptive potential of maritime pine (Pinus pinaster) populations to the emerging pitch canker pathogen, Fusarium circinatum. PLoS One 2014; 9:e114971. [PMID: 25500822 PMCID: PMC4263721 DOI: 10.1371/journal.pone.0114971] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 11/17/2014] [Indexed: 11/30/2022] Open
Abstract
There is a concern on how emerging pests and diseases will affect the distribution range and adaptability of their host species, especially due to different conditions derived from climate change and growing globalization. Fusarium circinatum, which causes pitch canker disease in Pinus species, is an exotic pathogen of recent introduction in Spain that threatens its maritime pine (P. pinaster) stands. To predict the impact this disease will have on the species, we examine host resistance traits and their genetic architecture. Resistance phenotyping was done in a clonal provenance/progeny trial, using three-year-old cuttings artificially inoculated with the pathogen and maintained under controlled environmental conditions. A total number of 670 ramets were assessed, distributed in 10 populations, with a total of 47 families, 2 to 5 half-sibs per family, and 3-7 ramets per clone. High genetic variation was found at the three hierarchical levels studied: population, family and clone, being both additive and non-additive effects important. Narrow-sense and broad-sense heritability estimates were relatively high, with respective values of 0.43-0.58 and 0.51-0.8, depending on the resistance traits measured (lesion length, lesion length rate, time to wilting, and survival). These values suggest the species' high capacity of evolutionary response to the F. circinatum pathogen. A population originated in Northern Spain was the most resistant, while another from Morocco was the most susceptible. The total number of plants that did not show lesion development or presented a small lesion (length<30 mm) was 224 out of 670, indicating a high proportion of resistant trees in the offspring within the analyzed populations. We found large differences among populations and considerable genetic variation within populations, which should allow, through natural or artificial selection, the successful adaptation of maritime pine to pitch canker disease.
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Affiliation(s)
- Margarita Elvira-Recuenco
- Silviculture and Forest Management Department, Forest Research Center (CIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Eugenia Iturritxa
- Instituto Vasco de Investigación y Desarrollo Agrario (NEIKER), Granja Modelo-Arkaute, Vitoria-Gasteiz, Spain
| | - Juan Majada
- Forest and Wood Technology Research Center (CETEMAS), Finca Experimental La Mata, Principado de Asturias, Spain
| | - Ricardo Alia
- Forest Ecology and Genetics Department, Forest Research Center (CIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
- Sustainable Forest Management Research Institute, Palencia, Spain
| | - Rosa Raposo
- Silviculture and Forest Management Department, Forest Research Center (CIFOR), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
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Torre S, Tattini M, Brunetti C, Fineschi S, Fini A, Ferrini F, Sebastiani F. RNA-seq analysis of Quercus pubescens Leaves: de novo transcriptome assembly, annotation and functional markers development. PLoS One 2014; 9:e112487. [PMID: 25393112 PMCID: PMC4231058 DOI: 10.1371/journal.pone.0112487] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 10/15/2014] [Indexed: 12/21/2022] Open
Abstract
Quercus pubescens Willd., a species distributed from Spain to southwest Asia, ranks high for drought tolerance among European oaks. Q. pubescens performs a role of outstanding significance in most Mediterranean forest ecosystems, but few mechanistic studies have been conducted to explore its response to environmental constrains, due to the lack of genomic resources. In our study, we performed a deep transcriptomic sequencing in Q. pubescens leaves, including de novo assembly, functional annotation and the identification of new molecular markers. Our results are a pre-requisite for undertaking molecular functional studies, and may give support in population and association genetic studies. 254,265,700 clean reads were generated by the Illumina HiSeq 2000 platform, with an average length of 98 bp. De novo assembly, using CLC Genomics, produced 96,006 contigs, having a mean length of 618 bp. Sequence similarity analyses against seven public databases (Uniprot, NR, RefSeq and KOGs at NCBI, Pfam, InterPro and KEGG) resulted in 83,065 transcripts annotated with gene descriptions, conserved protein domains, or gene ontology terms. These annotations and local BLAST allowed identify genes specifically associated with mechanisms of drought avoidance. Finally, 14,202 microsatellite markers and 18,425 single nucleotide polymorphisms (SNPs) were, in silico, discovered in assembled and annotated sequences. We completed a successful global analysis of the Q. pubescens leaf transcriptome using RNA-seq. The assembled and annotated sequences together with newly discovered molecular markers provide genomic information for functional genomic studies in Q. pubescens, with special emphasis to response mechanisms to severe constrain of the Mediterranean climate. Our tools enable comparative genomics studies on other Quercus species taking advantage of large intra-specific ecophysiological differences.
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Affiliation(s)
- Sara Torre
- Institute for Plant Protection, Department of Biology, Agricultural and Food Sciences, The National Research Council of Italy (CNR), Sesto Fiorentino, Italy
| | - Massimiliano Tattini
- Institute for Plant Protection, Department of Biology, Agricultural and Food Sciences, The National Research Council of Italy (CNR), Sesto Fiorentino, Italy
| | - Cecilia Brunetti
- Institute for Plant Protection, Department of Biology, Agricultural and Food Sciences, The National Research Council of Italy (CNR), Sesto Fiorentino, Italy
- Department of Agri-Food and Environmental Sciences, University of Florence, Sesto Fiorentino, Italy
| | - Silvia Fineschi
- Institute for Plant Protection, Department of Biology, Agricultural and Food Sciences, The National Research Council of Italy (CNR), Sesto Fiorentino, Italy
| | - Alessio Fini
- Department of Agri-Food and Environmental Sciences, University of Florence, Sesto Fiorentino, Italy
| | - Francesco Ferrini
- Department of Agri-Food and Environmental Sciences, University of Florence, Sesto Fiorentino, Italy
| | - Federico Sebastiani
- Institute for Biosciences and BioResources, Department of Biology, Agricultural and Food Sciences, The National Research Council of Italy (CNR), Sesto Fiorentino, Italy
- * E-mail:
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Zhou Y, Zhang L, Liu J, Wu G, Savolainen O. Climatic adaptation and ecological divergence between two closely related pine species in Southeast China. Mol Ecol 2014; 23:3504-22. [PMID: 24935279 DOI: 10.1111/mec.12830] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 05/09/2014] [Accepted: 05/21/2014] [Indexed: 02/04/2023]
Abstract
Climate is one of the most important drivers for adaptive evolution in forest trees. Climatic selection contributes greatly to local adaptation and intraspecific differentiation, but this kind of selection could also have promoted interspecific divergence through ecological speciation. To test this hypothesis, we examined intra- and interspecific genetic variation at 25 climate-related candidate genes and 12 reference loci in two closely related pine species, Pinus massoniana Lamb. and Pinus hwangshanensis Hisa, using population genetic and landscape genetic approaches. These two species occur in Southeast China but have contrasting ecological preferences in terms of several environmental variables, notably altitude, although hybrids form where their distributions overlap. One or more robust tests detected signals of recent and/or ancient selection at two-thirds (17) of the 25 candidate genes, at varying evolutionary timescales, but only three of the 12 reference loci. The signals of recent selection were species specific, but signals of ancient selection were mostly shared by the two species likely because of the shared evolutionary history. FST outlier analysis identified six SNPs in five climate-related candidate genes under divergent selection between the two species. In addition, a total of 24 candidate SNPs representing nine candidate genes showed significant correlation with altitudinal divergence in the two species based on the covariance matrix of population history derived from reference SNPs. Genetic differentiation between these two species was higher at the candidate genes than at the reference loci. Moreover, analysis using the isolation-with-migration model indicated that gene flow between the species has been more restricted for climate-related candidate genes than the reference loci, in both directions. Taken together, our results suggest that species-specific and divergent climatic selection at the candidate genes might have counteracted interspecific gene flow and played a key role in the ecological divergence of these two closely related pine species.
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Affiliation(s)
- Yongfeng Zhou
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, China; Plant Genetics Group, Department of Biology, University of Oulu, 90014, Oulu, Finland
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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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