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Eckert C, Wildhagen H, Paulo MJ, Scalabrin S, Ballauff J, Schnabel SK, Vendramin V, Keurentjes JJB, Bogeat-Triboulot MB, Taylor G, Polle A. Genotypic and tissue-specific variation of Populus nigra transcriptome profiles in response to drought. Sci Data 2022; 9:297. [PMID: 35701429 PMCID: PMC9197931 DOI: 10.1038/s41597-022-01417-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 05/23/2022] [Indexed: 11/14/2022] Open
Abstract
Climate change is one of the most important challenges for mankind in the far and near future. In this regard, sustainable production of woody crops on marginal land with low water availability is a major challenge to tackle. This dataset is part of an experiment, in which we exposed three genetically differentiated genotypes of Populus nigra originating from contrasting natural habitats to gradually increasing moderate drought. RNA sequencing was performed on fine roots, developing xylem and leaves of those three genotypes under control and moderate drought conditions in order to get a comprehensive dataset on the transcriptional changes at the whole plant level under water limiting conditions. This dataset has already provided insight in the transcriptional control of saccharification potential of the three Populus genotypes under drought conditions and we suggest that our data will be valuable for further in-depth analysis regarding candidate gene identification or, on a bigger scale, for meta-transcriptome analysis. Measurement(s) | transcriptome | Technology Type(s) | illumina sequencing | Factor Type(s) | treatment | Sample Characteristic - Organism | Populus nigra | Sample Characteristic - Environment | greenhouse experiment |
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Affiliation(s)
- Christian Eckert
- Forest Botany and Tree Physiology, University of Goettingen, Büsgenweg 2, Göttingen, Germany
| | - Henning Wildhagen
- HAWK University of Applied Sciences and Arts, Faculty of Resource Management, Büsgenweg 1a, 37077, Göttingen, Germany.
| | - Maria João Paulo
- Biometris, Wageningen UR Wageningen Plant Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | | | - Johannes Ballauff
- Forest Botany and Tree Physiology, University of Goettingen, Büsgenweg 2, Göttingen, Germany
| | - Sabine K Schnabel
- Biometris, Wageningen UR Wageningen Plant Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Vera Vendramin
- IGA Technology Services, via Jacopo Linussio 51, Udine, Italy
| | - Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | | | - Gail Taylor
- Department of Plant Sciences, University of California, One Shields Ave, Davis, CA, USA
| | - Andrea Polle
- Forest Botany and Tree Physiology, University of Goettingen, Büsgenweg 2, Göttingen, Germany
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2
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Quantitative genetic architecture of adaptive phenology traits in the deciduous tree, Populus trichocarpa (Torr. and Gray). Heredity (Edinb) 2020; 125:449-458. [PMID: 32901141 PMCID: PMC7784687 DOI: 10.1038/s41437-020-00363-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 12/02/2022] Open
Abstract
In a warming climate, the ability to accurately predict and track shifting environmental conditions will be fundamental for plant survival. Environmental cues define the transitions between growth and dormancy as plants synchronise development with favourable environmental conditions, however these cues are predicted to change under future climate projections which may have profound impacts on tree survival and growth. Here, we use a quantitative genetic approach to estimate the genetic basis of spring and autumn phenology in Populus trichocarpa to determine this species capacity for climate adaptation. We measured bud burst, leaf coloration, and leaf senescence traits across two years (2017–2018) and combine these observations with measures of lifetime growth to determine how genetic correlations between phenology and growth may facilitate or constrain adaptation. Timing of transitions differed between years, although we found strong cross year genetic correlations in all traits, suggesting that genotypes respond in consistent ways to seasonal cues. Spring and autumn phenology were correlated with lifetime growth, where genotypes that burst leaves early and shed them late had the highest lifetime growth. We also identified substantial heritable variation in the timing of all phenological transitions (h2 = 0.5–0.8) and in lifetime growth (h2 = 0.8). The combination of additive variation and favourable genetic correlations in phenology traits suggests that populations of cultivated varieties of P. Trichocarpa may have the capability to adapt their phenology to climatic changes without negative impacts on growth.
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Hallingbäck HR, Berlin S, Nordh NE, Weih M, Rönnberg-Wästljung AC. Genome Wide Associations of Growth, Phenology, and Plasticity Traits in Willow [ Salix viminalis (L.)]. FRONTIERS IN PLANT SCIENCE 2019; 10:753. [PMID: 31249579 PMCID: PMC6582754 DOI: 10.3389/fpls.2019.00753] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 05/23/2019] [Indexed: 05/10/2023]
Abstract
The short rotation biomass crop willow (Salix genera) has been of interest for bioenergy but recently also for biofuel production. For a faster development of new varieties molecular markers could be used as selection tool in an early stage of the breeding cycle. To identify markers associated with growth traits, genome-wide association mapping was conducted using a population of 291 Salix viminalis accessions collected across Europe and Russia and a large set of genotyping-by-sequencing markers. The accessions were vegetatively propagated and planted in replicated field experiments, one in Southern Sweden and one in Central Sweden. Phenology data, including bud burst and leaf senescence, as well as different growth traits were collected and measured repeatedly between 2010 and 2017 at both field environments. A value of the plasticity for each accession was calculated for all traits that were measured the same year in both environments as the normalized accession value in one environment subtracted by the corresponding value in the other environment. Broad-sense accession heritabilities and narrow-sense chip heritabilities ranged from 0.68 to 0.95 and 0.45 to 0.99, respectively for phenology traits and from 0.56 to 0.85 and 0.24 to 0.97 for growth traits indicating a considerable genetic component for most traits. Population structure and kinship between accessions were taken into account in the association analyses. In total, 39 marker-trait associations were found where four were specifically connected to plasticity and interestingly one particular marker was associated to several different plasticity growth traits. Otherwise association consistency was poor, possibly due to accession by environment interactions which were demonstrated by the low structure adjusted accession correlations across environments (ranging from 0.40 to 0.58). However, one marker association with biomass fresh weight was repeatedly observed in the same environment over two harvest years. For some traits where several associations were found, the markers jointly explained over 20% of the accession variation. The result from this study using a population of unrelated accessions has given useful information about marker-trait associations especially highlighting marker-plasticity associations and genotype-by-environment interactions as important factors to take account of in future strategies of Salix breeding.
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Affiliation(s)
- Henrik R. Hallingbäck
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sofia Berlin
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Nils-Erik Nordh
- Department of Crop Production Ecology, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Martin Weih
- Department of Crop Production Ecology, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ann-Christin Rönnberg-Wästljung
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Berlin S, Hallingbäck HR, Beyer F, Nordh NE, Weih M, Rönnberg-Wästljung AC. Genetics of phenotypic plasticity and biomass traits in hybrid willows across contrasting environments and years. ANNALS OF BOTANY 2017; 120:87-100. [PMID: 28449073 PMCID: PMC5737545 DOI: 10.1093/aob/mcx029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/22/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS Phenotypic plasticity can affect the geographical distribution of taxa and greatly impact the productivity of crops across contrasting and variable environments. The main objectives of this study were to identify genotype-phenotype associations in key biomass and phenology traits and the strength of phenotypic plasticity of these traits in a short-rotation coppice willow population across multiple years and contrasting environments to facilitate marker-assisted selection for these traits. METHODS A hybrid Salix viminalis × ( S. viminalis × Salix schwerinii ) population with 463 individuals was clonally propagated and planted in three common garden experiments comprising one climatic contrast between Sweden and Italy and one water availability contrast in Italy. Several key phenotypic traits were measured and phenotypic plasticity was estimated as the trait value difference between experiments. Quantitative trait locus (QTL) mapping analyses were conducted using a dense linkage map and phenotypic effects of S. schwerinii haplotypes derived from detected QTL were assessed. KEY RESULTS Across the climatic contrast, clone predictor correlations for biomass traits were low and few common biomass QTL were detected. This indicates that the genetic regulation of biomass traits was sensitive to environmental variation. Biomass QTL were, however, frequently shared across years and across the water availability contrast. Phenology QTL were generally shared between all experiments. Substantial phenotypic plasticity was found among the hybrid offspring, that to a large extent had a genetic origin. Individuals carrying influential S. schwerinii haplotypes generally performed well in Sweden but less well in Italy in terms of biomass production. CONCLUSIONS The results indicate that specific genetic elements of S. schwerinii are more suited to Swedish conditions than to those of Italy. Therefore, selection should preferably be conducted separately for such environments in order to maximize biomass production in admixed S. viminalis × S. schwerinii populations.
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Affiliation(s)
- Sofia Berlin
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, P.O. Box 7080, SE-750 07 Uppsala, Sweden
| | - Henrik R. Hallingbäck
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, P.O. Box 7080, SE-750 07 Uppsala, Sweden
| | - Friderike Beyer
- Swedish University of Agricultural Sciences, Department of Crop Production Ecology, Linnean Centre for Plant Biology, P.O. Box 7043, SE-750 07 Uppsala, Sweden
| | - Nils-Erik Nordh
- Swedish University of Agricultural Sciences, Department of Crop Production Ecology, Linnean Centre for Plant Biology, P.O. Box 7043, SE-750 07 Uppsala, Sweden
| | - Martin Weih
- Swedish University of Agricultural Sciences, Department of Crop Production Ecology, Linnean Centre for Plant Biology, P.O. Box 7043, SE-750 07 Uppsala, Sweden
| | - Ann-Christin Rönnberg-Wästljung
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, P.O. Box 7080, SE-750 07 Uppsala, Sweden
- For correspondence. E-mail
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Sun MY, Fu XL, Tan QP, Liu L, Chen M, Zhu CY, Li L, Chen XD, Gao DS. Analysis of basic leucine zipper genes and their expression during bud dormancy in peach (Prunus persica). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 104:54-70. [PMID: 27107182 DOI: 10.1016/j.plaphy.2016.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/01/2016] [Accepted: 03/03/2016] [Indexed: 06/05/2023]
Abstract
Dormancy is a biological characteristic developed to resist the cold conditions in winter. The bZIP transcription factors are present exclusively in eukaryotes and have been identified and classified in many species. bZIP proteins are known to regulate numerous biological processes, however, the role of bZIP in bud dodormancy has not been studied extensively. In total, 50 PpbZIP transcription factor-encoding genes were identified and categorized them into 10 groups (A-I and S). Similar intron/exon structures, additional conserved motifs, and DNA-binding site specificity supported our classification scheme. Additionally, chromosomal distribution and collinearity analyses suggested that expansion of the PpbZIP transcription factor family was due to segment/chromosomal duplications. We also predicted the dimerization properties based on characteristic features of the leucine zipper and classified PpbZIP proteins into 23 subfamilies. Furthermore, qRT-PCR results indicated that PpbZIPs genes may be involved in regulating dormancy. The same gene of different species might participate in different regulating networks through interactions with specific partners. Our expression profiling results complemented the microarray data, suggesting that co-expression patterns of bZIP transcription factors during dormancy differed among deciduous fruit trees. Our findings further clarify the molecular characteristics of the PpbZIP transcription factor family, including potential gene functions during dormancy. This information may facilitate further research on the evolutionary history and biological functions of bZIP proteins in peach and other rosaceae plants.
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Affiliation(s)
- Ming-Yue Sun
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, 61 Daizong Road, Taian 271018, China
| | - Xi-Ling Fu
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, 61 Daizong Road, Taian 271018, China
| | - Qiu-Ping Tan
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, 61 Daizong Road, Taian 271018, China
| | - Li Liu
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, 61 Daizong Road, Taian 271018, China
| | - Min Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, 61 Daizong Road, Taian 271018, China
| | - Cui-Ying Zhu
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, 61 Daizong Road, Taian 271018, China
| | - Ling Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, 61 Daizong Road, Taian 271018, China
| | - Xiu-De Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, 61 Daizong Road, Taian 271018, China
| | - Dong-Sheng Gao
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Taian 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, 61 Daizong Road, Taian 271018, China.
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Faivre-Rampant P, Zaina G, Jorge V, Giacomello S, Segura V, Scalabrin S, Guérin V, De Paoli E, Aluome C, Viger M, Cattonaro F, Payne A, PaulStephenRaj P, Le Paslier MC, Berard A, Allwright MR, Villar M, Taylor G, Bastien C, Morgante M. New resources for genetic studies in Populus nigra: genome-wide SNP discovery and development of a 12k Infinium array. Mol Ecol Resour 2016; 16:1023-36. [PMID: 26929265 DOI: 10.1111/1755-0998.12513] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 11/30/2022]
Abstract
Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed using Illumina platforms. A total number of 1 878 727 SNPs distributed along the P. nigra reference sequence were identified. The SNP calling accuracy was validated with Sanger sequencing. SNPs were selected within 14 previously identified QTL regions, 2916 expressional candidate genes related to rust resistance, wood properties, water-use efficiency and bud phenology and 1732 genes randomly spread across the genome. Over 10 000 SNPs were selected for the construction of a 12k Infinium Bead-Chip array dedicated to association mapping. The SNP genotyping assay was performed with 888 P. nigra individuals. The genotyping success rate was 91%. Our high success rate was due to the discovery panel design and the stringent parameters applied for SNP calling and selection. In the same set of P. nigra genotypes, linkage disequilibrium throughout the genome decayed on average within 5-7 kb to half of its maximum value. As an application test, ADMIXTURE analysis was performed with a selection of 600 SNPs spread throughout the genome and 706 individuals collected along 12 river basins. The admixture pattern was consistent with genetic diversity revealed by neutral markers and the geographical distribution of the populations. These newly developed SNP resources and genotyping array provide a valuable tool for population genetic studies and identification of QTLs through natural-population based genetic association studies in P. nigra.
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Affiliation(s)
| | - G Zaina
- DI4A, University of Udine, via delle Scienze 206, 33100, Udine, Italy
| | - V Jorge
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - S Giacomello
- IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
| | - V Segura
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - S Scalabrin
- IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
| | - V Guérin
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - E De Paoli
- IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
| | - C Aluome
- INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.,INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - M Viger
- Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK
| | - F Cattonaro
- IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
| | - A Payne
- Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK
| | | | | | - A Berard
- INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France
| | - M R Allwright
- Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK
| | - M Villar
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - G Taylor
- Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK
| | - C Bastien
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - M Morgante
- DI4A, University of Udine, via delle Scienze 206, 33100, Udine, Italy.,IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
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7
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Allwright MR, Payne A, Emiliani G, Milner S, Viger M, Rouse F, Keurentjes JJB, Bérard A, Wildhagen H, Faivre-Rampant P, Polle A, Morgante M, Taylor G. Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.). BIOTECHNOLOGY FOR BIOFUELS 2016; 9:195. [PMID: 27617034 PMCID: PMC5017058 DOI: 10.1186/s13068-016-0603-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/22/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Second generation (2G) bioenergy from lignocellulosic feedstocks has the potential to develop as a sustainable source of renewable energy; however, significant hurdles still remain for large-scale commercialisation. Populus is considered as a promising 2G feedstock and understanding the genetic basis of biomass yield and feedstock quality are a research priority in this model tree species. RESULTS We report the first coppiced biomass study for 714 members of a wide population of European black poplar (Populus nigra L.), a native European tree, selected from 20 river populations ranging in latitude and longitude between 40.5 and 52.1°N and 1.0 and 16.4°E, respectively. When grown at a single site in southern UK, significant Site of Origin (SO) effects were seen for 14 of the 15 directly measured or derived traits including biomass yield, leaf area and stomatal index. There was significant correlation (p < 0.001) between biomass yield traits over 3 years of harvest which identified leaf size and cell production as strong predictors of biomass yield. A 12 K Illumina genotyping array (constructed from 10,331 SNPs in 14 QTL regions and 4648 genes) highlighted significant population genetic structure with pairwise FST showing strong differentiation (p < 0.001) between the Spanish and Italian subpopulations. Robust associations reaching genome-wide significance are reported for main stem height and cell number per leaf; two traits tightly linked to biomass yield. These genotyping and phenotypic data were also used to show the presence of significant isolation by distance (IBD) and isolation by adaption (IBA) within this population. CONCLUSIONS The three associations identified reaching genome-wide significance at p < 0.05 include a transcription factor; a putative stress response gene and a gene of unknown function. None of them have been previously linked to bioenergy yield; were shown to be differentially expressed in a panel of three selected genotypes from the collection and represent exciting, novel candidates for further study in a bioenergy tree native to Europe and Euro-Asia. A further 26 markers (22 genes) were found to reach putative significance and are also of interest for biomass yield, leaf area, epidermal cell expansion and stomatal patterning. This research on European P. nigra provides an important foundation for the development of commercial native trees for bioenergy and for advanced, molecular breeding in these species.
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Affiliation(s)
- Mike Robert Allwright
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
| | - Adrienne Payne
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
| | - Giovanni Emiliani
- CNR-IVALSA, Sesto Fiorentino, via Madonna del Piano, 10, 50019 Sesto Fiorentino, FI Italy
| | - Suzanne Milner
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
| | - Maud Viger
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
| | - Franchesca Rouse
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
| | - Joost J. B. Keurentjes
- Laboratory of Genetics, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | | | | | | | - Andrea Polle
- Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Michele Morgante
- Dipartimento di Scienze agroalimentari, ambientali e animali, Università di Udine, Via delle Scienze 206, 33100 Udine, Italy
- Istituto di Genomica Applicata (IGA), via J. Linussio 51, 33100 Udine, Italy
| | - Gail Taylor
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton, SO17 1BJ UK
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Li F, Zhou C, Weng Q, Li M, Yu X, Guo Y, Wang Y, Zhang X, Gan S. Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus. PLoS One 2015; 10:e0145144. [PMID: 26695430 PMCID: PMC4687840 DOI: 10.1371/journal.pone.0145144] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 12/01/2015] [Indexed: 02/06/2023] Open
Abstract
Dense genetic maps, along with quantitative trait loci (QTLs) detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR), expressed sequence tag (EST) derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS), and diversity arrays technology (DArT) markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus) and with the E. grandis genome sequence. Fifty-three QTLs for growth (10-56 months of age) and wood density (56 months) were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa.
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Affiliation(s)
- Fagen Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Changpin Zhou
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Qijie Weng
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Mei Li
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Xiaoli Yu
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Yong Guo
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Yu Wang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Xiaohong Zhang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Siming Gan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
- * E-mail:
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Porth I, Klápště J, McKown AD, La Mantia J, Guy RD, Ingvarsson PK, Hamelin R, Mansfield SD, Ehlting J, Douglas CJ, El-Kassaby YA. Evolutionary Quantitative Genomics of Populus trichocarpa. PLoS One 2015; 10:e0142864. [PMID: 26599762 PMCID: PMC4658102 DOI: 10.1371/journal.pone.0142864] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 10/27/2015] [Indexed: 11/23/2022] Open
Abstract
Forest trees generally show high levels of local adaptation and efforts focusing on understanding adaptation to climate will be crucial for species survival and management. Here, we address fundamental questions regarding the molecular basis of adaptation in undomesticated forest tree populations to past climatic environments by employing an integrative quantitative genetics and landscape genomics approach. Using this comprehensive approach, we studied the molecular basis of climate adaptation in 433 Populus trichocarpa (black cottonwood) genotypes originating across western North America. Variation in 74 field-assessed traits (growth, ecophysiology, phenology, leaf stomata, wood, and disease resistance) was investigated for signatures of selection (comparing QST -FST) using clustering of individuals by climate of origin (temperature and precipitation). 29,354 SNPs were investigated employing three different outlier detection methods and marker-inferred relatedness was estimated to obtain the narrow-sense estimate of population differentiation in wild populations. In addition, we compared our results with previously assessed selection of candidate SNPs using the 25 topographical units (drainages) across the P. trichocarpa sampling range as population groupings. Narrow-sense QST for 53% of distinct field traits was significantly divergent from expectations of neutrality (indicating adaptive trait variation); 2,855 SNPs showed signals of diversifying selection and of these, 118 SNPs (within 81 genes) were associated with adaptive traits (based on significant QST). Many SNPs were putatively pleiotropic for functionally uncorrelated adaptive traits, such as autumn phenology, height, and disease resistance. Evolutionary quantitative genomics in P. trichocarpa provides an enhanced understanding regarding the molecular basis of climate-driven selection in forest trees and we highlight that important loci underlying adaptive trait variation also show relationship to climate of origin. We consider our approach the most comprehensive, as it uncovers the molecular mechanisms of adaptation using multiple methods and tests. We also provide a detailed outline of the required analyses for studying adaptation to the environment in a population genomics context to better understand the species’ potential adaptive capacity to future climatic scenarios.
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Affiliation(s)
- Ilga Porth
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Département des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et de Géomatique, Université Laval, Québec, QC, G1V 0A6 Canada
| | - Jaroslav Klápště
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Genetics and Physiology of Forest Trees, Czech University of Life Sciences, Prague, 165 21, Czech Republic
| | - Athena D. McKown
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jonathan La Mantia
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Corn, Soybean and Wheat Quality Research Unit, United States Department of Agriculture, Wooster, Ohio, 44691 United States of America
| | - Robert D. Guy
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Pär K. Ingvarsson
- Department of Ecology and Environmental Science, Umeå University, Umeå, SE-901 87, Sweden
| | - Richard Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Shawn D. Mansfield
- Department of Wood Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jürgen Ehlting
- Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC V8W 3N5, Canada
| | - Carl J. Douglas
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- * E-mail:
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10
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Guet J, Fichot R, Lédée C, Laurans F, Cochard H, Delzon S, Bastien C, Brignolas F. Stem xylem resistance to cavitation is related to xylem structure but not to growth and water-use efficiency at the within-population level in Populus nigra L. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:4643-52. [PMID: 25979998 DOI: 10.1093/jxb/erv232] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Xylem resistance to drought-induced cavitation is a key trait of plant water relations. This study assesses the genetic variation expressed for stem cavitation resistance within a population of a riparian species, the European black poplar (Populus nigra L.), and explores its relationships with xylem anatomy, water-use efficiency (WUE), and growth. Sixteen structural and physiological traits related to cavitation resistance, xylem anatomy, growth, bud phenology, and WUE were measured on 33 P. nigra genotypes grown under optimal irrigation in a 2-year-old clonal experiment in a nursery. Significant genetic variation was expressed for the xylem tension inducing 50% loss of hydraulic conductivity (Ψ50) within the studied population, as attested by the high value of broad-sense heritability estimated for this trait (H (2) ind = 0.72). Stem cavitation resistance was associated with xylem structure: the more cavitation-resistant genotypes exhibited lower hydraulic efficiency and higher mechanical reinforcement as assessed from stem xylem cross sections. By contrast, Ψ50 was not significantly related to shoot height increment, total above-ground dry mass, or bulk leaf carbon isotope discrimination, a proxy for intrinsic WUE. These findings indicate that the trade-offs between xylem resistance to cavitation, hydraulic efficiency, and mechanical reinforcement can occur at the within-population level. Given that the studied genotypes were exposed to the same environmental conditions and evolutionary drivers in situ, the trade-offs detected at this scale are expected to reflect true functional relationships.
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Affiliation(s)
- Justine Guet
- Université d'Orléans, INRA, EA 1207, Laboratoire de Biologie des Ligneux et des Grandes Cultures, F-45067 Orléans France INRA, UR 0588 'Amélioration, Génétique et Physiologie Forestières' (AGPF), Centre de Recherche Val de Loire, CS 40001 Ardon, F-45075 Orléans Cedex 2, France
| | - Régis Fichot
- Université d'Orléans, INRA, EA 1207, Laboratoire de Biologie des Ligneux et des Grandes Cultures, F-45067 Orléans France
| | - Camille Lédée
- Université d'Orléans, INRA, EA 1207, Laboratoire de Biologie des Ligneux et des Grandes Cultures, F-45067 Orléans France INRA, UR 0588 'Amélioration, Génétique et Physiologie Forestières' (AGPF), Centre de Recherche Val de Loire, CS 40001 Ardon, F-45075 Orléans Cedex 2, France
| | - Françoise Laurans
- INRA, UR 0588 'Amélioration, Génétique et Physiologie Forestières' (AGPF), Centre de Recherche Val de Loire, CS 40001 Ardon, F-45075 Orléans Cedex 2, France
| | - Hervé Cochard
- INRA, Université Blaise Pascal, UMR 547 PIAF, F-63100 Clermont-Ferrand, France
| | - Sylvain Delzon
- INRA, Université de Bordeaux, UMR 1202 BIOGECO, F-33405 Talence, France
| | - Catherine Bastien
- INRA, UR 0588 'Amélioration, Génétique et Physiologie Forestières' (AGPF), Centre de Recherche Val de Loire, CS 40001 Ardon, F-45075 Orléans Cedex 2, France
| | - Franck Brignolas
- Université d'Orléans, INRA, EA 1207, Laboratoire de Biologie des Ligneux et des Grandes Cultures, F-45067 Orléans France
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11
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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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12
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DeWoody J, Trewin H, Taylor G. Genetic and morphological differentiation in Populus nigra L.: isolation by colonization or isolation by adaptation? Mol Ecol 2015; 24:2641-55. [PMID: 25857321 PMCID: PMC4692097 DOI: 10.1111/mec.13192] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 03/26/2015] [Accepted: 04/02/2015] [Indexed: 01/19/2023]
Abstract
Identifying processes underlying the genetic and morphological differences among populations is a central question of evolutionary biology. Forest trees typically contain high levels of neutral genetic variation, and genetic differences are often correlated with geographic distance between populations [isolation by distance (IBD)] or are due to historic vicariance events [isolation by colonization (IBC)]. In contrast, morphological differences are largely due to local adaptation. Here, we examined genetic (microsatellite) and morphological (from a common garden experiment) variation in Populus nigra L., European black poplar, collected from 13 sites across western Europe and grown in a common garden in Belgium. Significant genetic differentiation was observed, with populations from France displaying greater admixture than the distinct Spanish and central European gene pools, consistent with previously described glacial refugia (IBC). Many quantitative traits displayed a bimodal distribution, approximately corresponding to small-leaf and large-leaf ecotypes. Examination of nine climatic variables revealed the sampling locations to have diverse climates, and although the correlation between morphological and climatic differences was significant, the pattern was not consistent with strict local adaptation. Partial Mantel tests based on multivariate summary statistics identified significant residual correlation in comparisons of small-leaf to large-leaf ecotypes, and within the small-leaf samples, but not within large-leaf ecotypes, indicating that variation within the small-leaf morphotype in particular may be adaptive. Some small-leaf populations experience climates very similar to those in large-leaf sites. We conclude that adaptive differentiation and persistent IBC acted in combination to produce the genetic and morphological patterns observed in P. nigra.
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Affiliation(s)
- Jennifer DeWoody
- Centre for Life Sciences, Unviersity of Southampton, Building 85, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Harriet Trewin
- Centre for Life Sciences, Unviersity of Southampton, Building 85, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Gail Taylor
- Centre for Life Sciences, Unviersity of Southampton, Building 85, Highfield Campus, Southampton, SO17 1BJ, UK
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13
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McKown AD, Klápště J, Guy RD, Geraldes A, Porth I, Hannemann J, Friedmann M, Muchero W, Tuskan GA, Ehlting J, Cronk QCB, El-Kassaby YA, Mansfield SD, Douglas CJ. Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa. THE NEW PHYTOLOGIST 2014; 203:535-553. [PMID: 24750093 DOI: 10.1111/nph.12815] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 03/14/2014] [Indexed: 05/02/2023]
Abstract
In order to uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa) from much of its range in western North America. Extensive data from large-scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34 K Populus single nucleotide polymorphism (SNP) array) of all accessions were used for gene discovery in a genome-wide association study (GWAS). We performed GWAS with 40 biomass, ecophysiology and phenology traits and 29,355 filtered SNPs representing 3518 genes. The association analyses were carried out using a Unified Mixed Model accounting for population structure effects among accessions. We uncovered 410 significant SNPs using a Bonferroni-corrected threshold (P<1.7×10(-6)). Markers were found across 19 chromosomes, explained 1-13% of trait variation, and implicated 275 unique genes in trait associations. Phenology had the largest number of associated genes (240 genes), followed by biomass (53 genes) and ecophysiology traits (25 genes). The GWAS results propose numerous loci for further investigation. Many traits had significant associations with multiple genes, underscoring their genetic complexity. Genes were also identified with multiple trait associations within and/or across trait categories. In some cases, traits were genetically correlated while in others they were not.
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Affiliation(s)
- Athena D McKown
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jaroslav Klápště
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Dendrology and Forest Tree Breeding, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, 165 21, Czech Republic
| | - Robert D Guy
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Armando Geraldes
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Ilga Porth
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jan Hannemann
- Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Michael Friedmann
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Wellington Muchero
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Gerald A Tuskan
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jürgen Ehlting
- Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Quentin C B Cronk
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Carl J Douglas
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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14
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Lind-Riehl JF, Sullivan AR, Gailing O. Evidence for selection on a CONSTANS-like gene between two red oak species. ANNALS OF BOTANY 2014; 113:967-75. [PMID: 24615344 PMCID: PMC3997637 DOI: 10.1093/aob/mcu019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 01/27/2014] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Hybridizing species such as oaks may provide a model to study the role of selection in speciation with gene flow. Discrete species' identities and different adaptations are maintained among closely related oak species despite recurrent gene flow. This is probably due to ecologically mediated selection at a few key genes or genomic regions. Neutrality tests can be applied to identify so-called outlier loci, which demonstrate locus-specific signatures of divergent selection and are candidate genes for further study. METHODS Thirty-six genic microsatellite markers, some with putative functions in flowering time and drought tolerance, and eight non-genic microsatellite markers were screened in two population pairs (n = 160) of the interfertile species Quercus rubra and Q. ellipsoidalis, which are characterized by contrasting adaptations to drought. Putative outliers were then tested in additional population pairs from two different geographic regions (n = 159) to support further their potential role in adaptive divergence. KEY RESULTS A marker located in the coding sequence of a putative CONSTANS-like (COL) gene was repeatedly identified as under strong divergent selection across all three geographically disjunct population pairs. COL genes are involved in the photoperiodic control of growth and development and are implicated in the regulation of flowering time. CONCLUSIONS The location of the polymorphism in the Quercus COL gene and given the potential role of COL genes in adaptive divergence and reproductive isolation makes this a promising candidate speciation gene. Further investigation of the phenological characteristics of both species and flowering time pathway genes is suggested in order to elucidate the importance of phenology genes for the maintenance of species integrity. Next-generation sequencing in multiple population pairs in combination with high-density genetic linkage maps could reveal the genome-wide distribution of outlier genes and their potential role in reproductive isolation between these species.
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Affiliation(s)
| | | | - Oliver Gailing
- Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
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15
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Alonso-Blanco C, Méndez-Vigo B. Genetic architecture of naturally occurring quantitative traits in plants: an updated synthesis. CURRENT OPINION IN PLANT BIOLOGY 2014; 18:37-43. [PMID: 24565952 DOI: 10.1016/j.pbi.2014.01.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 01/20/2014] [Accepted: 01/26/2014] [Indexed: 05/08/2023]
Abstract
Deciphering the genetic and molecular bases of quantitative variation is a long-standing challenge in plant biology because it is essential for understanding evolution and for accelerating plant breeding. Recent multi-trait analyses at different phenotypic levels are uncovering the pleiotropy and the genetic regulation underlying high-level complex traits. Thus, the number of known causal loci, genes and nucleotide polymorphisms is expanding. Current plant causal catalogs contain ∼400 genes and natural polymorphisms revealing several dysfunctional allelic series that involve multiple mutations. In addition, repeated evolution of quantitative traits mediated by large effect alleles is found across plant phylogeny. Finally, systematic analyses of genetic and environmental interactions are beginning to elucidate the molecular mechanisms of relevant interactions.
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Affiliation(s)
- Carlos Alonso-Blanco
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, Madrid 28049, Spain.
| | - Belén Méndez-Vigo
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, Madrid 28049, Spain
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16
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McKown AD, Guy RD, Klápště J, Geraldes A, Friedmann M, Cronk QCB, El-Kassaby YA, Mansfield SD, Douglas CJ. Geographical and environmental gradients shape phenotypic trait variation and genetic structure in Populus trichocarpa. THE NEW PHYTOLOGIST 2014; 201:1263-1276. [PMID: 24491114 DOI: 10.1111/nph.12601] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 10/09/2013] [Indexed: 05/18/2023]
Abstract
• Populus trichocarpa is widespread across western North America spanning extensive variation in photoperiod, growing season and climate. We investigated trait variation in P. trichocarpa using over 2000 trees from a common garden at Vancouver, Canada, representing replicate plantings of 461 genotypes originating from 136 provenance localities. • We measured 40 traits encompassing phenological events, biomass accumulation, growth rates, and leaf, isotope and gas exchange-based ecophysiology traits. With replicated plantings and 29,354 single nucleotide polymorphisms (SNPs) from 3518 genes, we estimated both broad-sense trait heritability (H(2)) and overall population genetic structure from principal component analysis. • Populus trichocarpa had high phenotypic variation and moderate/high H(2) for many traits. H(2) ranged from 0.3 to 0.9 in phenology, 0.3 to 0.8 in biomass and 0.1 to 0.8 in ecophysiology traits. Most traits correlated strongly with latitude, maximum daylength and temperature of tree origin, but not necessarily with elevation, precipitation or heat : moisture indices. Trait H(2) values reflected trait correlation strength with geoclimate variables. The population genetic structure had one significant principal component (PC1) which correlated with daylength and showed enrichment for genes relating to circadian rhythm and photoperiod. • Robust relationships between traits, population structure and geoclimate in P. trichocarpa reflect patterns which suggest that range-wide geographical and environment gradients have shaped its genotypic and phenotypic variability.
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Affiliation(s)
- Athena D McKown
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Robert D Guy
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jaroslav Klápště
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Dendrology and Forest Tree Breeding, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, 165 21, Czech Republic
| | - Armando Geraldes
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Michael Friedmann
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Quentin C B Cronk
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Carl J Douglas
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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17
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Romeu JF, Monforte AJ, Sánchez G, Granell A, García-Brunton J, Badenes ML, Ríos G. Quantitative trait loci affecting reproductive phenology in peach. BMC PLANT BIOLOGY 2014; 14:52. [PMID: 24559033 PMCID: PMC3941940 DOI: 10.1186/1471-2229-14-52] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 02/18/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND The reproductive phenology of perennial plants in temperate climates is largely conditioned by the duration of bud dormancy, and fruit developmental processes. Bud dormancy release and bud break depends on the perception of cumulative chilling and heat during the bud development. The objective of this work was to identify new quantitative trait loci (QTLs) associated to temperature requirements for bud dormancy release and flowering and to fruit harvest date, in a segregating population of peach. RESULTS We have identified QTLs for nine traits related to bud dormancy, flowering and fruit harvest in an intraspecific hybrid population of peach in two locations differing in chilling time accumulation. QTLs were located in a genetic linkage map of peach based on single nucleotide polymorphism (SNP) markers for eight linkage groups (LGs) of the peach genome sequence. QTLs for chilling requirements for dormancy release and blooming clustered in seven different genomic regions that partially coincided with loci identified in previous works. The most significant QTL for chilling requirements mapped to LG1, close to the evergrowing locus. QTLs for heat requirement related traits were distributed in nine genomic regions, four of them co-localizing with QTLs for chilling requirement trait. Two major loci in LG4 and LG6 determined fruit harvest time. CONCLUSIONS We identified QTLs associated to nine traits related to the reproductive phenology in peach. A search of candidate genes for these QTLs rendered different genes related to flowering regulation, chromatin modification and hormone signalling. A better understanding of the genetic factors affecting crop phenology might help scientists and breeders to predict changes in genotype performance in a context of global climate change.
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Affiliation(s)
- José F Romeu
- Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario (IMIDA), La Alberca, Murcia, Spain
| | - Antonio J Monforte
- Instituto de Biología Molecular y Celular de Plantas (IBMCP, CSIC-UPV), Valencia, Spain
| | - Gerardo Sánchez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP, CSIC-UPV), Valencia, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP, CSIC-UPV), Valencia, Spain
| | - Jesús García-Brunton
- Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario (IMIDA), La Alberca, Murcia, Spain
| | - María L Badenes
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Gabino Ríos
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
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Ghelardini L, Berlin S, Weih M, Lagercrantz U, Gyllenstrand N, Rönnberg-Wästljung AC. Genetic architecture of spring and autumn phenology in Salix. BMC PLANT BIOLOGY 2014; 14:31. [PMID: 24438179 PMCID: PMC3945485 DOI: 10.1186/1471-2229-14-31] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 01/03/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND In woody plants from temperate regions, adaptation to the local climate results in annual cycles of growth and dormancy, and optimal regulation of these cycles are critical for growth, long-term survival, and competitive success. In this study we have investigated the genetic background to growth phenology in a Salix pedigree by assessing genetic and phenotypic variation in growth cessation, leaf senescence and bud burst in different years and environments. A previously constructed linkage map using the same pedigree and anchored to the annotated genome of P. trichocarpa was improved in target regions and used for QTL analysis of the traits. The major aims in this study were to map QTLs for phenology traits in Salix, and to identify candidate genes in QTL hot spots through comparative mapping with the closely related Populus trichocarpa. RESULTS All traits varied significantly among genotypes and the broad-sense heritabilities ranged between 0.5 and 0.9, with the highest for leaf senescence. In total across experiment and years, 80 QTLs were detected. For individual traits, the QTLs explained together from 21.5 to 56.5% of the variation. Generally each individual QTL explained a low amount of the variation but three QTLs explained above 15% of the variation with one QTL for leaf senescence explaining 34% of the variation. The majority of the QTLs were recurrently identified across traits, years and environments. Two hotspots were identified on linkage group (LG) II and X where narrow QTLs for all traits co-localized. CONCLUSIONS This study provides the most detailed analysis of QTL detection for phenology in Salix conducted so far. Several hotspot regions were found where QTLs for different traits and QTLs for the same trait but identified during different years co-localised. Many QTLs co-localised with QTLs found in poplar for similar traits that could indicate common pathways for these traits in Salicaceae. This study is an important first step in identifying QTLs and candidate genes for phenology traits in Salix.
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Affiliation(s)
- Luisa Ghelardini
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden
- Present address: Institute for Plant Protection, Italian National Research Council CNR, 50019 Sesto fiorentino, Italy
| | - Sofia Berlin
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden
| | - Martin Weih
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden
| | - Ulf Lagercrantz
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Niclas Gyllenstrand
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden
| | - Ann Christin Rönnberg-Wästljung
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden
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Tognetti R, Cocozza C, Marchetti M. Shaping the multifunctional tree: the use of Salicaceae in environmental restoration. IFOREST - BIOGEOSCIENCES AND FORESTRY 2013. [PMID: 0 DOI: 10.3832/ifor0920-006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
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