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Genome Wide Association Study Identifies Candidate Genes Related to the Earlywood Tracheid Properties in Picea crassifolia Kom. FORESTS 2022. [DOI: 10.3390/f13020332] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Picea crassifolia Kom. is one of the timber and ecological conifers in China and its wood tracheid traits directly affect wood formation and adaptability under harsh environment. Molecular studies on P. crassifolia remain inadequate because relatively few genes have been associated with these traits. To identify markers and candidate genes that can potentially be used for genetic improvement of wood tracheid traits, we examined 106 clones of P. crassifolia, and investigated phenotypic data for 14 wood tracheid traits before specific-locus amplified fragment sequencing (SLAF-seq) was employed to perform a genome wide association study (GWAS). Subsequently, the results were used to screen single nucleotide polymorphism (SNP) loci and candidate genes that exhibited a significant correlation with the studied traits. We developed 4,058,883 SLAF-tags and 12,275,765 SNP loci, and our analyses identified a total of 96 SNP loci that showed significant correlations with three earlywood tracheid traits using a mixed linear model (MLM). Next, candidate genes were screened in the 100 kb zone (50 kb upstream, 50 kb downstream) of each of the SNP loci, whereby 67 candidate genes were obtained in earlywood tracheid traits, including 34 genes of known function and 33 genes of unknown function. We provide the most significant SNP for each trait-locus combination and candidate genes occurring within the GWAS hits. These resources provide a foundation for the development of markers that could be used in wood traits improvement and candidate genes for the development of earlywood tracheid in P. crassifolia.
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Klápště J, Kremer A, Burg K, Garnier-Géré P, El-Dien OG, Ratcliffe B, El-Kassaby YA, Porth I. Quercus species divergence is driven by natural selection on evolutionarily less integrated traits. Heredity (Edinb) 2021; 126:366-382. [PMID: 33110229 PMCID: PMC8027598 DOI: 10.1038/s41437-020-00378-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 10/07/2020] [Accepted: 10/07/2020] [Indexed: 11/09/2022] Open
Abstract
Functional traits are organismal attributes that can respond to environmental cues, thereby providing important ecological functions. In addition, an organism's potential for adaptation is defined by the patterns of covariation among groups of functionally related traits. Whether an organism is evolutionarily constrained or has the potential for adaptation is based on the phenotypic integration or modularity of these traits. Here, we revisited leaf morphology in two European sympatric white oaks (Quercus petraea (Matt.) Liebl. and Quercus robur L.), sampling 2098 individuals, across much of their geographical distribution ranges. At the phenotypic level, leaf morphology traditionally encompasses discriminant attributes among different oak species. Here, we estimated in situ heritability, genetic correlation, and integration across such attributes. Also, we performed Selection Response Decomposition to test these traits for potential differences in oak species' evolutionary responses. Based on the uncovered functional units of traits (modules) in our study, the morphological module "leaf size gradient" was highlighted among functionally integrated traits. Equally, this module was defined in both oaks as being under "global regulation" in vegetative bud establishment and development. Lamina basal shape and intercalary veins' number were not, or, less integrated within the initially defined leaf functional unit, suggesting more than one module within the leaf traits' ensemble. Since these traits generally show the greatest species discriminatory power, they potentially underwent effective differential response to selection among oaks. Indeed, the selection of these traits could have driven the ecological preferences between the two sympatric oaks growing under different microclimates.
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Affiliation(s)
- Jaroslav Klápště
- Department of Genetics and Physiology of Forest Trees, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences in Prague, Kamýcká 129, 165 21, Prague 6, Czechia.
- Scion (New Zealand Forest Research Institute Ltd.), 49 Sala Street, Whakarewarewa, Rotorua, 3010, New Zealand.
| | - Antoine Kremer
- INRA, UMR Biodiversité Gènes et Communautés, 69 route d'Arcachon, 33612, Cestas Cedex, France
- University of Bordeaux, UMR 1202, Biodiversité Gènes et Communautés, F-33400, Talence, France
| | - Kornel Burg
- Department of Health and Environment (Bioresources), AIT Austrian Institute of Technology, Konrad-Lorenz-Straβe 24, 3430, Tulln, Austria
| | - Pauline Garnier-Géré
- INRA, UMR Biodiversité Gènes et Communautés, 69 route d'Arcachon, 33612, Cestas Cedex, France
- University of Bordeaux, UMR 1202, Biodiversité Gènes et Communautés, F-33400, Talence, France
| | - Omnia Gamal El-Dien
- Pharmacognosy Department, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Blaise Ratcliffe
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Ilga Porth
- Département des sciences du bois et de la forêt, Université Laval, 1030, Avenue de la Médecine, Québec, QC, G1V 0A6, Canada
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Creyaufmüller FC, Chassignet I, Delb H, Dounavi A, Gailing O, Leinemann L, Kreuzwieser J, Teply-Szymanski J, Vornam B. Terpene Synthase Genes in Quercus robur - Gene Characterization, Expression and Resulting Terpenes Due to Cockchafer Feeding. FRONTIERS IN PLANT SCIENCE 2018; 9:1753. [PMID: 30559755 PMCID: PMC6287202 DOI: 10.3389/fpls.2018.01753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 11/12/2018] [Indexed: 06/09/2023]
Abstract
Root herbivory caused by larvae of the forest cockchafer (Melolontha hippocastani) enhances the impact of drought on trees, particularly in oak forest rejuvenations. In Germany, geographically distant oak stands show differences in infestation strength by the forest cockchafer. While in Southwestern Germany this insect causes severe damage, oak forests in northern Germany are rarely infested. It is known that root-released volatile organic compounds (VOCs) are perceived by soil herbivores, thus guiding the larvae toward the host roots. In this work, we exposed seedlings of two distant oak provenances to forest cockchafer larvae and studied their population genetic properties, their root-based VOC chemotypes, their attraction for larvae and terpene synthase gene expression. Based on nuclear and chloroplast marker analysis, we found both oak populations to be genetically highly variable while showing typical patterns of migration from different refugial regions. However, no clear association between genetic constitution of the different provenances and the abundance of cockchafer populations on site was observed. In contrast to observations in the field, bioassays revealed a preference of the larvae for the northeastern oak provenance. The behavior of larvae was most likely related to root-released volatile terpenes and benzenoids since their composition and quantity differed between oak populations. We assume repellent effects of these compounds because the populations attractive to insects showed low abundance of these compounds. Five different oak terpene synthase (TPS) genes were identified at the genomic level which can be responsible for biosynthesis of the released terpenes. TPS gene expression patterns in response to larval feeding revealed geographic variation rather than genotypic variation. Our results support the assumption that root-released VOC are influencing the perception of roots by herbivores.
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Affiliation(s)
| | - Isabelle Chassignet
- Department of Forest Protection, Forest Research Institute Baden-Württemberg, Freiburg, Germany
| | - Horst Delb
- Department of Forest Protection, Forest Research Institute Baden-Württemberg, Freiburg, Germany
| | - Aikaterini Dounavi
- Department of Forest Protection, Forest Research Institute Baden-Württemberg, Freiburg, Germany
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Germany
| | - Ludger Leinemann
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Germany
| | - Jürgen Kreuzwieser
- Chair of Tree Physiology, Institute of Forest Science, University of Freiburg, Freiburg, Germany
| | - Julia Teply-Szymanski
- Department of Forest Protection, Forest Research Institute Baden-Württemberg, Freiburg, Germany
| | - Barbara Vornam
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Germany
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Plomion C, Aury JM, Amselem J, Leroy T, Murat F, Duplessis S, Faye S, Francillonne N, Labadie K, Le Provost G, Lesur I, Bartholomé J, Faivre-Rampant P, Kohler A, Leplé JC, Chantret N, Chen J, Diévart A, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Bogeat-Triboulot MB, Bouffaud ML, Brachi B, Chancerel E, Cohen D, Couloux A, Da Silva C, Dossat C, Ehrenmann F, Gaspin C, Grima-Pettenati J, Guichoux E, Hecker A, Herrmann S, Hugueney P, Hummel I, Klopp C, Lalanne C, Lascoux M, Lasserre E, Lemainque A, Desprez-Loustau ML, Luyten I, Madoui MA, Mangenot S, Marchal C, Maumus F, Mercier J, Michotey C, Panaud O, Picault N, Rouhier N, Rué O, Rustenholz C, Salin F, Soler M, Tarkka M, Velt A, Zanne AE, Martin F, Wincker P, Quesneville H, Kremer A, Salse J. Oak genome reveals facets of long lifespan. NATURE PLANTS 2018; 4:440-452. [PMID: 29915331 PMCID: PMC6086335 DOI: 10.1038/s41477-018-0172-3] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 05/08/2018] [Indexed: 05/18/2023]
Abstract
Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times2. With 450 species spread throughout Asia, Europe and America3, oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical4 and modelling5 approaches have shown that intra-organismal genetic heterogeneity can be selected for6 and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes7. However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.
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Affiliation(s)
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | | | | | - Sébastien Faye
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | - Isabelle Lesur
- BIOGECO, INRA, Université de Bordeaux, Cestas, France
- HelixVenture, Mérignac, France
| | | | | | | | | | - Nathalie Chantret
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Jun Chen
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anne Diévart
- CIRAD, UMR AGAP, Montpellier, France
- Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Valérie Barbe
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Caroline Belser
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | | | - Marie-Lara Bouffaud
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle/Saale, Germany
| | | | | | - David Cohen
- UMR Silva, INRA, Université de Lorraine, AgroPariTech, Nancy, France
| | - Arnaud Couloux
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Carole Dossat
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | - Christine Gaspin
- Plateforme bioinformatique Toulouse Midi-Pyrénées, INRA, Auzeville Castanet-Tolosan, France
| | | | | | - Arnaud Hecker
- IAM, INRA, Université de Lorraine, Champenoux, France
| | - Sylvie Herrmann
- German Centre for Integrative Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | | | - Irène Hummel
- UMR Silva, INRA, Université de Lorraine, AgroPariTech, Nancy, France
| | - Christophe Klopp
- Plateforme bioinformatique Toulouse Midi-Pyrénées, INRA, Auzeville Castanet-Tolosan, France
| | | | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Eric Lasserre
- Université de Perpignan, UMR 5096, Perpignan, France
| | - Arnaud Lemainque
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | - Mohammed-Amin Madoui
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Sophie Mangenot
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | - Jonathan Mercier
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | | | | | - Olivier Rué
- Plateforme bioinformatique Toulouse Midi-Pyrénées, INRA, Auzeville Castanet-Tolosan, France
| | | | - Franck Salin
- BIOGECO, INRA, Université de Bordeaux, Cestas, France
| | - Marçal Soler
- Université de Toulouse, CNRS, UMR 5546, LRSV, Castanet-Tolosan, France
- Laboratori del Suro, University of Girona, Girona, Spain
| | - Mika Tarkka
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle/Saale, Germany
| | - Amandine Velt
- SVQV, Université de Strasbourg, INRA, Colmar, France
| | - Amy E Zanne
- Department of Biological Sciences, George Washington University, Washington, DC, USA
| | | | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université d'Evry, Université Paris-Saclay, Evry, France
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Apostol EN, Curtu AL, Daia LM, Apostol B, Dinu CG, Şofletea N. Leaf morphological variability and intraspecific taxonomic units for pedunculate oak and grayish oak (genus Quercus L., series Pedunculatae Schwz.) in Southern Carpathian Region (Romania). THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 609:497-505. [PMID: 28755599 DOI: 10.1016/j.scitotenv.2017.05.274] [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: 02/24/2017] [Revised: 05/30/2017] [Accepted: 05/30/2017] [Indexed: 06/07/2023]
Abstract
Even though pedunculate oak (Quercus robur L.) and grayish oak (Quercus pedunculiflora K. Koch) have different ecological requirements, they have been considered as having low differentiation at the level of morphological traits and genetic variation. The leaf morphology for 862 trees has been assessed in 16 natural populations, seven of Q. robur, eight of Q. pedunculiflora and a mixed forest were both taxa coexist. In total, fifteen descriptors have been analysed by using discriminant analysis, while it was found that with only four out of the fifteen leaf traits (abaxial pubescence, abaxial colour of the leaf, petiole length and basal shape of lamina) the two taxa could be clearly differentiated. A dendrogram has been constructed on the basis of these traits, where the populations of each taxon have been clustered together. PU and CL traits of Q. pedunculiflora were discussed for their adaptive value for drought resistance in the steppe habitats occupied by this taxon. Using the leaves' morphological descriptors and data from the literature, intra-taxonomic units (varieties, forms and sub-forms) have been identified in all analysed populations. Eight intraspecific units for Q. robur and six for Q. pedunculiflora have been identified in the investigated area. An analysis of spatial distribution of the two taxa and of their intraspecific units has been performed using maps of ecoregions for the study area.
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Affiliation(s)
- Ecaterina Nicoleta Apostol
- National Institute for Research and Development in Forestry (INCDS) "Marin Drăcea", Eroilor No. 128, Voluntari, Ilfov, Romania; "Transilvania" University of Braşov, Brașov, Romania.
| | | | - Liviu Mihai Daia
- National Forest Administration - ROMSILVA, Petricani Street, 9A, Bucharest, Romania
| | - Bogdan Apostol
- National Institute for Research and Development in Forestry (INCDS) "Marin Drăcea", Eroilor No. 128, Voluntari, Ilfov, Romania
| | - Cristiana Georgeta Dinu
- National Institute for Research and Development in Forestry (INCDS) "Marin Drăcea", Eroilor No. 128, Voluntari, Ilfov, Romania
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Jian H, Yang B, Zhang A, Zhang L, Xu X, Li J, Liu L. Screening of Candidate Leaf Morphology Genes by Integration of QTL Mapping and RNA Sequencing Technologies in Oilseed Rape (Brassica napus L.). PLoS One 2017; 12:e0169641. [PMID: 28068426 PMCID: PMC5222374 DOI: 10.1371/journal.pone.0169641] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 12/20/2016] [Indexed: 11/30/2022] Open
Abstract
Leaf size and shape play important roles in agronomic traits, such as yield, quality and stress responses. Wide variations in leaf morphological traits exist in cultivated varieties of many plant species. By now, the genetics of leaf shape and size have not been characterized in Brassica napus. In this study, a population of 172 recombinant inbred lines (RILs) was used for quantitative trait locus (QTL) analysis of leaf morphology traits. Furthermore, fresh young leaves of extreme lines with more leaf lobes (referred to as ‘A’) and extreme lines with fewer lobes (referred to as ‘B’) selected from the RIL population and leaves of dissected lines (referred to as ‘P’) were used for transcriptional analysis. A total of 31 QTLs for the leaf morphological traits tested in this study were identified on 12 chromosomes, explaining 5.32–39.34% of the phenotypic variation. There were 8, 6, 2, 5, 8, and 2 QTLs for PL (petiole length), PN (lobe number), LW (lamina width), LL (Lamina length), LL/LTL (the lamina size ratio) and LTL (leaf total length), respectively. In addition, 74, 1,166 and 1,272 differentially expressed genes (DEGs) were identified in ‘A vs B’, ‘A vs P’ and ‘B vs P’ comparisons, respectively. The Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used to predict the functions of these DEGs. Gene regulators of leaf shape and size, such as ASYMMETRIC LEAVES 2, gibberellin 20-oxidase 3, genes encoding gibberellin-regulated family protein, genes encoding growth-regulating factor and KNOTTED1-like homeobox were also detected in DEGs. After integrating the QTL mapping and RNA sequencing data, 33 genes, including a gene encoding auxin-responsive GH3 family protein and a gene encoding sphere organelles protein-related gene, were selected as candidates that may control leaf shape. Our findings should be valuable for studies of the genetic control of leaf morphological trait regulation in B. napus.
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Affiliation(s)
- Hongju Jian
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P. R. China
| | - Bo Yang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P. R. China
| | - Aoxiang Zhang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P. R. China
| | - Li Zhang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P. R. China
| | - Xinfu Xu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P. R. China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P. R. China
| | - Liezhao Liu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P. R. China
- * E-mail:
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Deacon NJ, Cavender-Bares J. Limited Pollen Dispersal Contributes to Population Genetic Structure but Not Local Adaptation in Quercus oleoides Forests of Costa Rica. PLoS One 2015; 10:e0138783. [PMID: 26407244 PMCID: PMC4583504 DOI: 10.1371/journal.pone.0138783] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/03/2015] [Indexed: 11/25/2022] Open
Abstract
Background Quercus oleoides Cham. and Schlect., tropical live oak, is a species of conservation importance in its southern range limit of northwestern Costa Rica. It occurs in high-density stands across a fragmented landscape spanning a contrasting elevation and precipitation gradient. We examined genetic diversity and spatial genetic structure in this geographically isolated and genetically distinct population. We characterized population genetic diversity at 11 nuclear microsatellite loci in 260 individuals from 13 sites. We monitored flowering time at 10 sites, and characterized the local environment in order to compare observed spatial genetic structure to hypotheses of isolation-by-distance and isolation-by-environment. Finally, we quantified pollen dispersal distances and tested for local adaptation through a reciprocal transplant experiment in order to experimentally address these hypotheses. Results High genetic diversity is maintained in the population and the genetic variation is significantly structured among sampled sites. We identified 5 distinct genetic clusters and average pollen dispersal predominately occurred over short distances. Differences among sites in flowering phenology and environmental factors, however, were not strictly associated with genetic differentiation. Growth and survival of upland and lowland progeny in their native and foreign environments was expected to exhibit evidence of local adaptation due to the more extreme dry season in the lowlands. Seedlings planted in the lowland garden experienced much higher mortality than seedlings in the upland garden, but we did not identify evidence for local adaptation. Conclusion Overall, this study indicates that the Costa Rican Q. oleoides population has a rich population genetic history. Despite environmental heterogeneity and habitat fragmentation, isolation-by-distance and isolation-by-environment alone do not explain spatial genetic structure. These results add to studies of genetic structure by examining a common, tropical tree over multiple habitats and provide information for managers of a successional forest in a protected area.
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Affiliation(s)
- Nicholas John Deacon
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
- Plant Biological Sciences Graduate Program, University of Minnesota, St. Paul, Minnesota, United States of America
- * E-mail:
| | - Jeannine Cavender-Bares
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
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8
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Drost DR, Puranik S, Novaes E, Novaes CRDB, Dervinis C, Gailing O, Kirst M. Genetical genomics of Populus leaf shape variation. BMC PLANT BIOLOGY 2015; 15:166. [PMID: 26122556 PMCID: PMC4486686 DOI: 10.1186/s12870-015-0557-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/16/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND Leaf morphology varies extensively among plant species and is under strong genetic control. Mutagenic screens in model systems have identified genes and established molecular mechanisms regulating leaf initiation, development, and shape. However, it is not known whether this diversity across plant species is related to naturally occurring variation at these genes. Quantitative trait locus (QTL) analysis has revealed a polygenic control for leaf shape variation in different species suggesting that loci discovered by mutagenesis may only explain part of the naturally occurring variation in leaf shape. Here we undertook a genetical genomics study in a poplar intersectional pseudo-backcross pedigree to identify genetic factors controlling leaf shape. The approach combined QTL discovery in a genetic linkage map anchored to the Populus trichocarpa reference genome sequence and transcriptome analysis. RESULTS A major QTL for leaf lamina width and length:width ratio was identified in multiple experiments that confirmed its stability. A transcriptome analysis of expanding leaf tissue contrasted gene expression between individuals with alternative QTL alleles, and identified an ADP-ribosylation factor (ARF) GTPase (PtARF1) as a candidate gene for regulating leaf morphology in this pedigree. ARF GTPases are critical elements in the vesicular trafficking machinery. Disruption of the vesicular trafficking function of ARF by the pharmacological agent Brefeldin A (BFA) altered leaf lateral growth in the narrow-leaf P. trichocarpa suggesting a molecular mechanism of leaf shape determination. Inhibition of the vesicular trafficking processes by BFA interferes with cycling of PIN proteins and causes their accumulation in intercellular compartments abolishing polar localization and disrupting normal auxin flux with potential effects on leaf expansion. CONCLUSIONS In other model systems, ARF proteins have been shown to control the localization of auxin efflux carriers, which function to establish auxin gradients and apical-basal cell polarity in developing plant organs. Our results support a model where PtARF1 transcript abundance changes the dynamics of endocytosis-mediated PIN localization in leaf cells, thus affecting lateral auxin flux and subsequently lamina leaf expansion. This suggests that evolution of differential cellular polarity plays a significant role in leaf morphological variation observed in subgenera of genus Populus.
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Affiliation(s)
- Derek R Drost
- School of Forest Resources and Conservation, University of Florida, P.O. Box 110410, Gainesville, FL, 32611, USA.
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, P.O. Box 110690, Gainesville, FL, 32611, USA.
- Seminis, Inc., 37437 State Highway 16, Woodland, CA, 95695, USA.
| | - Swati Puranik
- School of Forest Resourse and Environmental Sciences, Michigan Technological University, Houghton, MI, 49931, USA.
| | - Evandro Novaes
- School of Forest Resources and Conservation, University of Florida, P.O. Box 110410, Gainesville, FL, 32611, USA.
- Escola de Agronomia, Universidade Federal de Goiás, Rodovia Goiânia/Nova Veneza, Km0 - Caixa Postal 131, Goiânia, GO, 74690-900, Brazil.
| | - Carolina R D B Novaes
- School of Forest Resources and Conservation, University of Florida, P.O. Box 110410, Gainesville, FL, 32611, USA.
- Escola de Agronomia, Universidade Federal de Goiás, Rodovia Goiânia/Nova Veneza, Km0 - Caixa Postal 131, Goiânia, GO, 74690-900, Brazil.
| | - Christopher Dervinis
- School of Forest Resources and Conservation, University of Florida, P.O. Box 110410, Gainesville, FL, 32611, USA.
| | - Oliver Gailing
- School of Forest Resourse and Environmental Sciences, Michigan Technological University, Houghton, MI, 49931, USA.
| | - Matias Kirst
- School of Forest Resources and Conservation, University of Florida, P.O. Box 110410, Gainesville, FL, 32611, USA.
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, P.O. Box 110690, Gainesville, FL, 32611, USA.
- University of Florida Genetics Institute, University of Florida, P.O. Box 103610, Gainesville, FL, 32611, USA.
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9
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Kremer A, Potts BM, Delzon S. Genetic divergence in forest trees: understanding the consequences of climate change. Funct Ecol 2013. [DOI: 10.1111/1365-2435.12169] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Antoine Kremer
- INRA; UMR1202 Biodiversité Gènes et Communautés; Cestas F-33610, France
- Université de Bordeaux, UMR1202 Biodiversité Gènes et Communautés; Talence F-33410 France
| | - Brad M. Potts
- School of Plant Science and National Centre for Future Forest Industries; University of Tasmania; Private Bag 55 Hobart TAS 7001, Australia
| | - Sylvain Delzon
- INRA; UMR1202 Biodiversité Gènes et Communautés; Cestas F-33610, France
- Université de Bordeaux, UMR1202 Biodiversité Gènes et Communautés; Talence F-33410 France
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10
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Gailing O, Vornam B, Leinemann L, Finkeldey R. Genetic and genomic approaches to assess adaptive genetic variation in plants: forest trees as a model. PHYSIOLOGIA PLANTARUM 2009; 137:509-19. [PMID: 19627554 DOI: 10.1111/j.1399-3054.2009.01263.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
With the increasing availability of sequence information at putatively important genes or regulatory regions, the characterization of adaptive genetic diversity and their association with phenotypic trait variation becomes feasible for many non-model organisms such as forest trees. Especially in predominantly outcrossing forest tree populations with large effective size, a high genetic variation in relevant genes is maintained, that is the raw material for the adaptation to changing and variable environments, and likewise for plant breeding. Oaks (Quercus spp.) are excellent model species to study the adaptation of forest trees to changing environments. They show a wide geographic distribution in Europe as dominant tree species in many forests and grow under a wide range of climatic and edaphic conditions. With the availability of a growing amount of functional and expressional candidate genes, we are now able to test the functional importance of single nucleotide polymorphisms (SNPs) by associating nucleotide variation in these genes with phenotypic variation in adaptive traits in segregating or natural populations. Here, we report on quantitative trait locus (QTL), candidate gene and association mapping approaches that are applicable to characterize gene markers and SNPs associated with variation in adaptive traits, such as bud burst, drought resistance and other traits showing selective responses to environmental change and stress. Because genome-wide association mapping studies are not feasible because of the enormous amount of SNP markers required in outcrossing trees with high recombination rates, the success of such an approach depends largely on the reasonable selection of candidate genes.
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Affiliation(s)
- Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Germany.
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