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Silva PIT, Silva-Junior OB, Resende LV, Sousa VA, Aguiar AV, Grattapaglia D. A 3K Axiom SNP array from a transcriptome-wide SNP resource sheds new light on the genetic diversity and structure of the iconic subtropical conifer tree Araucaria angustifolia (Bert.) Kuntze. PLoS One 2020; 15:e0230404. [PMID: 32866150 PMCID: PMC7458329 DOI: 10.1371/journal.pone.0230404] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 08/05/2020] [Indexed: 12/30/2022] Open
Abstract
High-throughput SNP genotyping has become a precondition to move to higher precision and wider genome coverage genetic analysis of natural and breeding populations of non-model species. We developed a 44,318 annotated SNP catalog for Araucaria angustifolia, a grandiose subtropical conifer tree, one of the only two native Brazilian gymnosperms, critically endangered due to its valuable wood and seeds. Following transcriptome assembly and annotation, SNPs were discovered from RNA-seq and pooled RAD-seq data. From the SNP catalog, an Axiom® SNP array with 3,038 validated SNPs was developed and used to provide a comprehensive look at the genetic diversity and structure of 15 populations across the natural range of the species. RNA-seq was a far superior source of SNPs when compared to RAD-seq in terms of conversion rate to polymorphic markers on the array, likely due to the more efficient complexity reduction of the huge conifer genome. By matching microsatellite and SNP data on the same set of A. angustifolia individuals, we show that SNPs reflect more precisely the actual genome-wide patterns of genetic diversity and structure, challenging previous microsatellite-based assessments. Moreover, SNPs corroborated the known major north-south genetic cline, but allowed a more accurate attribution to regional versus among-population differentiation, indicating the potential to select ancestry-informative markers. The availability of a public, user-friendly 3K SNP array for A. angustifolia and a catalog of 44,318 SNPs predicted to provide ~29,000 informative SNPs across ~20,000 loci across the genome, will allow tackling still unsettled questions on its evolutionary history, toward a more comprehensive picture of the origin, past dynamics and future trend of the species' genetic resources. Additionally, but not less importantly, the SNP array described, unlocks the potential to adopt genomic prediction methods to accelerate the still very timid efforts of systematic tree breeding of A. angustifolia.
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Affiliation(s)
- Pedro Italo T. Silva
- Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology, DF, Brasilia, Brazil
- University of Brasília, Cell Biology Department, Campus Universitário, DF, Brasília, Brazil
| | - Orzenil B. Silva-Junior
- Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology, DF, Brasilia, Brazil
| | - Lucileide V. Resende
- Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology, DF, Brasilia, Brazil
| | - Valderes A. Sousa
- Empresa Brasileira de Pesquisa Agropecuária–EMBRAPA Florestas, PR, Colombo, Brazil
| | - Ananda V. Aguiar
- Empresa Brasileira de Pesquisa Agropecuária–EMBRAPA Florestas, PR, Colombo, Brazil
| | - Dario Grattapaglia
- Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology, DF, Brasilia, Brazil
- University of Brasília, Cell Biology Department, Campus Universitário, DF, Brasília, Brazil
- Graduate Program in Genomic Sciences, Universidade Católica de Brasília, Brasília, DF, Brazil
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Azaiez A, Pavy N, Gérardi S, Laroche J, Boyle B, Gagnon F, Mottet MJ, Beaulieu J, Bousquet J. A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies). BMC Genomics 2018; 19:942. [PMID: 30558528 PMCID: PMC6296092 DOI: 10.1186/s12864-018-5247-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Norway spruce [Picea abies (L.) Karst.] is ecologically and economically one of the most important conifer worldwide. Our main goal was to develop a large catalog of annotated high confidence gene SNPs that should sustain the development of genomic tools for the conservation of natural and domesticated genetic diversity resources, and hasten tree breeding efforts in this species. RESULTS Targeted sequencing was achieved by capturing P. abies exome with probes previously designed from the sequenced transcriptome of white spruce (Picea glauca (Moench) Voss). Capture efficiency was high (74.5%) given a high level of exome conservation between the two species. Using stringent criteria, we delimited a set of 61,771 high-confidence SNPs across 13,543 genes. To validate SNPs, a high-throughput genotyping array was developed for a subset of 5571 predicted SNPs representing as many different gene loci, and was used to genotype over 1000 trees. The estimated true positive rate of the resource was 84.2%, which was comparable with the genotyping success rate obtained for P. abies control SNPs recycled from previous genotyping efforts. We also analyzed SNP abundance across various gene functional categories. Several GO terms and gene families involved in stress response were found over-represented in highly polymorphic genes. CONCLUSION The annotated high-confidence SNP catalog developed herein represents a valuable genomic resource, being representative of over 13 K genes distributed across the P. abies genome. This resource should serve a variety of population genomics and breeding applications in Norway spruce.
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Affiliation(s)
- Aïda Azaiez
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Nathalie Pavy
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Jérôme Laroche
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Brian Boyle
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - France Gagnon
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Marie-Josée Mottet
- Direction de la recherche forestière, Ministère des Forêts, de la Faune et des Parcs du Québec, 2700 Einstein, Québec, Québec G1P 3W8 Canada
| | - Jean Beaulieu
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, Québec G1V 0A6 Canada
- Institute of Integrative Biology and Systems, Université Laval, Québec, Québec G1V 0A6 Canada
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Heer K, Ullrich KK, Hiss M, Liepelt S, Schulze Brüning R, Zhou J, Opgenoorth L, Rensing SA. Detection of somatic epigenetic variation in Norway spruce via targeted bisulfite sequencing. Ecol Evol 2018; 8:9672-9682. [PMID: 30386566 PMCID: PMC6202725 DOI: 10.1002/ece3.4374] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 06/18/2018] [Accepted: 06/22/2018] [Indexed: 12/24/2022] Open
Abstract
Epigenetic mechanisms represent a possible mechanism for achieving a rapid response of long-lived trees to changing environmental conditions. However, our knowledge on plant epigenetics is largely limited to a few model species. With increasing availability of genomic resources for many tree species, it is now possible to adopt approaches from model species that permit to obtain single-base pair resolution data on methylation at a reasonable cost. Here, we used targeted bisulfite sequencing (TBS) to study methylation patterns in the conifer species Norway spruce (Picea abies). To circumvent the challenge of disentangling epigenetic and genetic differences, we focused on four clone pairs, where clone members were growing in different climatic conditions for 24 years. We targeted >26.000 genes using TBS and determined the performance and reproducibility of this approach. We characterized gene body methylation and compared methylation patterns between environments. We found highly comparable capture efficiency and coverage across libraries. Methylation levels were relatively constant across gene bodies, with 21.3 ± 0.3%, 11.0 ± 0.4% and 1.3 ± 0.2% in the CG, CHG, and CHH context, respectively. The variance in methylation profiles did not reveal consistent changes between environments, yet we could identify 334 differentially methylated positions (DMPs) between environments. This supports that changes in methylation patterns are a possible pathway for a plant to respond to environmental change. After this successful application of TBS in Norway spruce, we are confident that this approach can contribute to broaden our knowledge of methylation patterns in natural tree populations.
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Affiliation(s)
- Katrin Heer
- Conservation BiologyFaculty of BiologyPhilipps University MarburgMarburgGermany
- Department of EcologyFaculty of BiologyPhilipps University MarburgMarburgGermany
| | - Kristian K. Ullrich
- Plant Cell BiologyFaculty of BiologyPhilipps University MarburgMarburgGermany
- Department of Evolutionary GeneticsMax Planck Institute for Evolutionary BiologyPloenGermany
| | - Manuel Hiss
- Plant Cell BiologyFaculty of BiologyPhilipps University MarburgMarburgGermany
| | - Sascha Liepelt
- Conservation BiologyFaculty of BiologyPhilipps University MarburgMarburgGermany
| | | | - Jiabin Zhou
- College of Life SciencesShaanxi Normal UniversityXi'anChina
- State Key Laboratory of Grassland Agro‐EcosystemsSchool of Life SciencesLanzhou UniversityLanzhouChina
| | - Lars Opgenoorth
- Department of EcologyFaculty of BiologyPhilipps University MarburgMarburgGermany
| | - Stefan A. Rensing
- Plant Cell BiologyFaculty of BiologyPhilipps University MarburgMarburgGermany
- BIOSS Biological Signaling StudiesUniversity of FreiburgFreiburgGermany
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Drought Sensitivity of Norway Spruce at the Species' Warmest Fringe: Quantitative and Molecular Analysis Reveals High Genetic Variation Among and Within Provenances. G3-GENES GENOMES GENETICS 2018; 8:1225-1245. [PMID: 29440346 PMCID: PMC5873913 DOI: 10.1534/g3.117.300524] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Norway spruce (Picea abies) is by far the most important timber species in Europe, but its outstanding role in future forests is jeopardized by its high sensitivity to drought. We analyzed drought response of Norway spruce at the warmest fringe of its natural range. Based on a 35-year old provenance experiment we tested for genetic variation among and within seed provenances across consecutively occurring strong drought events using dendroclimatic time series. Moreover, we tested for associations between ≈1,700 variable SNPs and traits related to drought response, wood characteristics and climate-growth relationships. We found significant adaptive genetic variation among provenances originating from the species’ Alpine, Central and Southeastern European range. Genetic variation between individuals varied significantly among provenances explaining up to 44% of the phenotypic variation in drought response. Varying phenotypic correlations between drought response and wood traits confirmed differences in selection intensity among seed provenances. Significant associations were found between 29 SNPs and traits related to drought, climate-growth relationships and wood properties which explained between 11 and 43% of trait variation, though 12 of them were due to single individuals having extreme phenotypes of the respective trait. The majority of these SNPs are located within exons of genes and the most important ones are preferentially expressed in cambium and xylem expansion layers. Phenotype-genotype associations were stronger if only provenances with significant quantitative genetic variation in drought response were considered. The present study confirms the high adaptive variation of Norway spruce in Central and Southeastern Europe and demonstrates how quantitative genetic, dendroclimatic and genomic data can be linked to understand the genetic basis of adaptation to climate extremes in trees.
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Ganthaler A, Stöggl W, Mayr S, Kranner I, Schüler S, Wischnitzki E, Sehr EM, Fluch S, Trujillo-Moya C. Association genetics of phenolic needle compounds in Norway spruce with variable susceptibility to needle bladder rust. PLANT MOLECULAR BIOLOGY 2017; 94:229-251. [PMID: 28190131 PMCID: PMC5443855 DOI: 10.1007/s11103-017-0589-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 01/24/2017] [Indexed: 05/15/2023]
Abstract
KEY MESSAGE Accumulation of phenolic needle metabolites in Norway spruce is regulated by many genes with small and additive effects and is correlated with the susceptibility against fungal attack. Norway spruce accumulates high foliar concentrations of secondary phenolic metabolites, with important functions for pathogen defence responses. However, the molecular genetic basis underlying the quantitative variation of phenolic compounds and their role in enhanced resistance of spruce to infection by needle bladder rust are unknown. To address these questions, a set of 1035 genome-wide single nucleotide polymorphisms (SNPs) was associated to the quantitative variation of four simple phenylpropanoids, eight stilbenes, nine flavonoids, six related arithmetic parameters and the susceptibility to infection by Chrysomyxa rhododendri in an unstructured natural population of Norway spruce. Thirty-one significant genetic associations for the flavonoids gallocatechin, kaempferol 3-glucoside and quercetin 3-glucoside and the stilbenes resveratrol, piceatannol, astringin and isorhapontin were discovered, explaining 22-59% of phenotypic variation, and indicating a regulation of phenolic accumulation by many genes with small and additive effects. The phenolics profile differed between trees with high and low susceptibility to the fungus, underlining the importance of phenolic compounds in the defence mechanisms of Norway spruce to C. rhododendri. Results highlight the utility of association studies in non-model tree species and may enable marker-assisted selection of Norway spruce adapted to severe pathogen attack.
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Affiliation(s)
- Andrea Ganthaler
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, 6020, Innsbruck, Austria.
- alpS - Centre for Climate Change Adaptation, Grabenweg 68, 6020, Innsbruck, Austria.
| | - Wolfgang Stöggl
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, 6020, Innsbruck, Austria
| | - Stefan Mayr
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, 6020, Innsbruck, Austria
| | - Ilse Kranner
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, 6020, Innsbruck, Austria
| | - Silvio Schüler
- Department of Forest Genetics, Federal Research and Training Centre for Forests, Natural Hazards and Landscapes (BFW), Seckendorff-Gudent-Weg 8, 1131, Vienna, Austria
| | - Elisabeth Wischnitzki
- Health and Environment Department, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430, Tulln, Austria
| | - Eva Maria Sehr
- Health and Environment Department, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430, Tulln, Austria
| | - Silvia Fluch
- Health and Environment Department, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430, Tulln, Austria
| | - Carlos Trujillo-Moya
- Department of Forest Genetics, Federal Research and Training Centre for Forests, Natural Hazards and Landscapes (BFW), Seckendorff-Gudent-Weg 8, 1131, Vienna, Austria
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