Integrating genome annotation and QTL position to identify candidate genes for productivity, architecture and water-use efficiency in Populus spp

Hybrid poplars species are candidates for biomass production but breeding efforts are needed to combine productivity and water use efficiency in improved cultivars. The understanding of the genetic architecture of growth in poplar by a Quantitative Trait Loci (QTL) approach can help us to elucidate...

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Published inBMC plant biology Vol. 12; no. 1; p. 173
Main Authors Monclus, Romain, Leplé, Jean-Charles, Bastien, Catherine, Bert, Pierre-François, Villar, Marc, Marron, Nicolas, Brignolas, Franck, Jorge, Véronique
Format Journal Article
LanguageEnglish
Published England BioMed Central Ltd 26.09.2012
BioMed Central
BMC
Subjects
Analysis
Arabidopsis
Arabidopsis thaliana
Architecture
Chromosome Mapping
Cloning
Confidence Intervals
Crosses, Genetic
Cultivars
Efficiency
France
Gene loci
Gene mapping
Genes
Genes, Plant - genetics
Genetic aspects
Genetic Association Studies
Genetic Linkage
Genetic Markers
Genetics
Genome, Plant - genetics
Genomes
Genomics
Genotype & phenotype
Leaves
Life Sciences
Molecular Sequence Annotation
Ontology
Physiological aspects
Plant genetics
Plant Leaves - genetics
Plant physiology
Poplar
Populus
Populus - anatomy & histology
Populus - genetics
Populus - growth & development
Populus trichocarpa
Productivity
Quantitative genetics
Quantitative trait loci
Quantitative Trait Loci - genetics
Quantitative Trait, Heritable
Vegetal Biology
Water
Water - metabolism
Water use
Water use efficiency
France
leaf trait
hybrid poplar
gene ontology
candidate gene
productivity
water-use efficiency
QTL
architecture
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Abstract Hybrid poplars species are candidates for biomass production but breeding efforts are needed to combine productivity and water use efficiency in improved cultivars. The understanding of the genetic architecture of growth in poplar by a Quantitative Trait Loci (QTL) approach can help us to elucidate the molecular basis of such integrative traits but identifying candidate genes underlying these QTLs remains difficult. Nevertheless, the increase of genomic information together with the accessibility to a reference genome sequence (Populus trichocarpa Nisqually-1) allow to bridge QTL information on genetic maps and physical location of candidate genes on the genome. The objective of the study is to identify QTLs controlling productivity, architecture and leaf traits in a P. deltoides x P. trichocarpa F1 progeny and to identify candidate genes underlying QTLs based on the anchoring of genetic maps on the genome and the gene ontology information linked to genome annotation. The strategy to explore genome annotation was to use Gene Ontology enrichment tools to test if some functional categories are statistically over-represented in QTL regions. Four leaf traits and 7 growth traits were measured on 330 F1 P. deltoides x P. trichocarpa progeny. A total of 77 QTLs controlling 11 traits were identified explaining from 1.8 to 17.2% of the variation of traits. For 58 QTLs, confidence intervals could be projected on the genome. An extended functional annotation was built based on data retrieved from the plant genome database Phytozome and from an inference of function using homology between Populus and the model plant Arabidopsis. Genes located within QTL confidence intervals were retrieved and enrichments in gene ontology (GO) terms were determined using different methods. Significant enrichments were found for all traits. Particularly relevant biological processes GO terms were identified for QTLs controlling number of sylleptic branches: intervals were enriched in GO terms of biological process like 'ripening' and 'adventitious roots development'. Beyond the simple identification of QTLs, this study is the first to use a global approach of GO terms enrichment analysis to fully explore gene function under QTLs confidence intervals in plants. This global approach may lead to identification of new candidate genes for traits of interest.
AbstractList Doc number: 173 Abstract Background: Hybrid poplars species are candidates for biomass production but breeding efforts are needed to combine productivity and water use efficiency in improved cultivars. The understanding of the genetic architecture of growth in poplar by a Quantitative Trait Loci (QTL) approach can help us to elucidate the molecular basis of such integrative traits but identifying candidate genes underlying these QTLs remains difficult. Nevertheless, the increase of genomic information together with the accessibility to a reference genome sequence (Populus trichocarpa Nisqually-1) allow to bridge QTL information on genetic maps and physical location of candidate genes on the genome. The objective of the study is to identify QTLs controlling productivity, architecture and leaf traits in a P. deltoides x P. trichocarpa F1 progeny and to identify candidate genes underlying QTLs based on the anchoring of genetic maps on the genome and the gene ontology information linked to genome annotation. The strategy to explore genome annotation was to use Gene Ontology enrichment tools to test if some functional categories are statistically over-represented in QTL regions. Results: Four leaf traits and 7 growth traits were measured on 330 F1 P. deltoides x P. trichocarpa progeny. A total of 77 QTLs controlling 11 traits were identified explaining from 1.8 to 17.2% of the variation of traits. For 58 QTLs, confidence intervals could be projected on the genome. An extended functional annotation was built based on data retrieved from the plant genome database Phytozome and from an inference of function using homology between Populus and the model plant Arabidopsis . Genes located within QTL confidence intervals were retrieved and enrichments in gene ontology (GO) terms were determined using different methods. Significant enrichments were found for all traits. Particularly relevant biological processes GO terms were identified for QTLs controlling number of sylleptic branches: intervals were enriched in GO terms of biological process like 'ripening' and 'adventitious roots development'. Conclusion: Beyond the simple identification of QTLs, this study is the first to use a global approach of GO terms enrichment analysis to fully explore gene function under QTLs confidence intervals in plants. This global approach may lead to identification of new candidate genes for traits of interest.
Background: Hybrid poplars species are candidates for biomass production but breeding efforts are needed to combine productivity and water use efficiency in improved cultivars. The understanding of the genetic architecture of growth in poplar by a Quantitative Trait Loci (QTL) approach can help us to elucidate the molecular basis of such integrative traits but identifying candidate genes underlying these QTLs remains difficult. Nevertheless, the increase of genomic information together with the accessibility to a reference genome sequence (Populus trichocarpa Nisqually-1) allow to bridge QTL information on genetic maps and physical location of candidate genes on the genome. The objective of the study is to identify QTLs controlling productivity, architecture and leaf traits in a P. deltoides x P. trichocarpa F1 progeny and to identify candidate genes underlying QTLs based on the anchoring of genetic maps on the genome and the gene ontology information linked to genome annotation. The strategy to explore genome annotation was to use Gene Ontology enrichment tools to test if some functional categories are statistically over-represented in QTL regions. Results: Four leaf traits and 7 growth traits were measured on 330 F1 P. deltoides x P. trichocarpa progeny. A total of 77 QTLs controlling 11 traits were identified explaining from 1.8 to 17.2% of the variation of traits. For 58 QTLs, confidence intervals could be projected on the genome. An extended functional annotation was built based on data retrieved from the plant genome database Phytozome and from an inference of function using homology between Populus and the model plant Arabidopsis. Genes located within QTL confidence intervals were retrieved and enrichments in gene ontology (GO) terms were determined using different methods. Significant enrichments were found for all traits. Particularly relevant biological processes GO terms were identified for QTLs controlling number of sylleptic branches: intervals were enriched in GO terms of biological process like 'ripening' and 'adventitious roots development'. Conclusion: Beyond the simple identification of QTLs, this study is the first to use a global approach of GO terms enrichment analysis to fully explore gene function under QTLs confidence intervals in plants. This global approach may lead to identification of new candidate genes for traits of interest.
Hybrid poplars species are candidates for biomass production but breeding efforts are needed to combine productivity and water use efficiency in improved cultivars. The understanding of the genetic architecture of growth in poplar by a Quantitative Trait Loci (QTL) approach can help us to elucidate the molecular basis of such integrative traits but identifying candidate genes underlying these QTLs remains difficult. Nevertheless, the increase of genomic information together with the accessibility to a reference genome sequence (Populus trichocarpa Nisqually-1) allow to bridge QTL information on genetic maps and physical location of candidate genes on the genome. The objective of the study is to identify QTLs controlling productivity, architecture and leaf traits in a P. deltoides x P. trichocarpa F1 progeny and to identify candidate genes underlying QTLs based on the anchoring of genetic maps on the genome and the gene ontology information linked to genome annotation. The strategy to explore genome annotation was to use Gene Ontology enrichment tools to test if some functional categories are statistically over-represented in QTL regions. Four leaf traits and 7 growth traits were measured on 330 F1 P. deltoides x P. trichocarpa progeny. A total of 77 QTLs controlling 11 traits were identified explaining from 1.8 to 17.2% of the variation of traits. For 58 QTLs, confidence intervals could be projected on the genome. An extended functional annotation was built based on data retrieved from the plant genome database Phytozome and from an inference of function using homology between Populus and the model plant Arabidopsis. Genes located within QTL confidence intervals were retrieved and enrichments in gene ontology (GO) terms were determined using different methods. Significant enrichments were found for all traits. Particularly relevant biological processes GO terms were identified for QTLs controlling number of sylleptic branches: intervals were enriched in GO terms of biological process like 'ripening' and 'adventitious roots development'. Beyond the simple identification of QTLs, this study is the first to use a global approach of GO terms enrichment analysis to fully explore gene function under QTLs confidence intervals in plants. This global approach may lead to identification of new candidate genes for traits of interest.
Abstract Background Hybrid poplars species are candidates for biomass production but breeding efforts are needed to combine productivity and water use efficiency in improved cultivars. The understanding of the genetic architecture of growth in poplar by a Quantitative Trait Loci (QTL) approach can help us to elucidate the molecular basis of such integrative traits but identifying candidate genes underlying these QTLs remains difficult. Nevertheless, the increase of genomic information together with the accessibility to a reference genome sequence (Populus trichocarpa Nisqually-1) allow to bridge QTL information on genetic maps and physical location of candidate genes on the genome. The objective of the study is to identify QTLs controlling productivity, architecture and leaf traits in a P. deltoides x P. trichocarpa F1 progeny and to identify candidate genes underlying QTLs based on the anchoring of genetic maps on the genome and the gene ontology information linked to genome annotation. The strategy to explore genome annotation was to use Gene Ontology enrichment tools to test if some functional categories are statistically over-represented in QTL regions. Results Four leaf traits and 7 growth traits were measured on 330 F1 P. deltoides x P. trichocarpa progeny. A total of 77 QTLs controlling 11 traits were identified explaining from 1.8 to 17.2% of the variation of traits. For 58 QTLs, confidence intervals could be projected on the genome. An extended functional annotation was built based on data retrieved from the plant genome database Phytozome and from an inference of function using homology between Populus and the model plant Arabidopsis. Genes located within QTL confidence intervals were retrieved and enrichments in gene ontology (GO) terms were determined using different methods. Significant enrichments were found for all traits. Particularly relevant biological processes GO terms were identified for QTLs controlling number of sylleptic branches: intervals were enriched in GO terms of biological process like ‘ripening’ and ‘adventitious roots development’. Conclusion Beyond the simple identification of QTLs, this study is the first to use a global approach of GO terms enrichment analysis to fully explore gene function under QTLs confidence intervals in plants. This global approach may lead to identification of new candidate genes for traits of interest.
Hybrid poplars species are candidates for biomass production but breeding efforts are needed to combine productivity and water use efficiency in improved cultivars. The understanding of the genetic architecture of growth in poplar by a Quantitative Trait Loci (QTL) approach can help us to elucidate the molecular basis of such integrative traits but identifying candidate genes underlying these QTLs remains difficult. Nevertheless, the increase of genomic information together with the accessibility to a reference genome sequence (Populus trichocarpa Nisqually-1) allow to bridge QTL information on genetic maps and physical location of candidate genes on the genome. The objective of the study is to identify QTLs controlling productivity, architecture and leaf traits in a P. deltoides x P. trichocarpa F1 progeny and to identify candidate genes underlying QTLs based on the anchoring of genetic maps on the genome and the gene ontology information linked to genome annotation. The strategy to explore genome annotation was to use Gene Ontology enrichment tools to test if some functional categories are statistically over-represented in QTL regions. Four leaf traits and 7 growth traits were measured on 330 F1 P. deltoides x P. trichocarpa progeny. A total of 77 QTLs controlling 11 traits were identified explaining from 1.8 to 17.2% of the variation of traits. For 58 QTLs, confidence intervals could be projected on the genome. An extended functional annotation was built based on data retrieved from the plant genome database Phytozome and from an inference of function using homology between Populus and the model plant Arabidopsis. Genes located within QTL confidence intervals were retrieved and enrichments in gene ontology (GO) terms were determined using different methods. Significant enrichments were found for all traits. Particularly relevant biological processes GO terms were identified for QTLs controlling number of sylleptic branches: intervals were enriched in GO terms of biological process like 'ripening' and 'adventitious roots development'. Beyond the simple identification of QTLs, this study is the first to use a global approach of GO terms enrichment analysis to fully explore gene function under QTLs confidence intervals in plants. This global approach may lead to identification of new candidate genes for traits of interest.
Hybrid poplars species are candidates for biomass production but breeding efforts are needed to combine productivity and water use efficiency in improved cultivars. The understanding of the genetic architecture of growth in poplar by a Quantitative Trait Loci (QTL) approach can help us to elucidate the molecular basis of such integrative traits but identifying candidate genes underlying these QTLs remains difficult. Nevertheless, the increase of genomic information together with the accessibility to a reference genome sequence (Populus trichocarpa Nisqually-1) allow to bridge QTL information on genetic maps and physical location of candidate genes on the genome. The objective of the study is to identify QTLs controlling productivity, architecture and leaf traits in a P. deltoides x P. trichocarpa F1 progeny and to identify candidate genes underlying QTLs based on the anchoring of genetic maps on the genome and the gene ontology information linked to genome annotation. The strategy to explore genome annotation was to use Gene Ontology enrichment tools to test if some functional categories are statistically over-represented in QTL regions.BACKGROUNDHybrid poplars species are candidates for biomass production but breeding efforts are needed to combine productivity and water use efficiency in improved cultivars. The understanding of the genetic architecture of growth in poplar by a Quantitative Trait Loci (QTL) approach can help us to elucidate the molecular basis of such integrative traits but identifying candidate genes underlying these QTLs remains difficult. Nevertheless, the increase of genomic information together with the accessibility to a reference genome sequence (Populus trichocarpa Nisqually-1) allow to bridge QTL information on genetic maps and physical location of candidate genes on the genome. The objective of the study is to identify QTLs controlling productivity, architecture and leaf traits in a P. deltoides x P. trichocarpa F1 progeny and to identify candidate genes underlying QTLs based on the anchoring of genetic maps on the genome and the gene ontology information linked to genome annotation. The strategy to explore genome annotation was to use Gene Ontology enrichment tools to test if some functional categories are statistically over-represented in QTL regions.Four leaf traits and 7 growth traits were measured on 330 F1 P. deltoides x P. trichocarpa progeny. A total of 77 QTLs controlling 11 traits were identified explaining from 1.8 to 17.2% of the variation of traits. For 58 QTLs, confidence intervals could be projected on the genome. An extended functional annotation was built based on data retrieved from the plant genome database Phytozome and from an inference of function using homology between Populus and the model plant Arabidopsis. Genes located within QTL confidence intervals were retrieved and enrichments in gene ontology (GO) terms were determined using different methods. Significant enrichments were found for all traits. Particularly relevant biological processes GO terms were identified for QTLs controlling number of sylleptic branches: intervals were enriched in GO terms of biological process like 'ripening' and 'adventitious roots development'.RESULTSFour leaf traits and 7 growth traits were measured on 330 F1 P. deltoides x P. trichocarpa progeny. A total of 77 QTLs controlling 11 traits were identified explaining from 1.8 to 17.2% of the variation of traits. For 58 QTLs, confidence intervals could be projected on the genome. An extended functional annotation was built based on data retrieved from the plant genome database Phytozome and from an inference of function using homology between Populus and the model plant Arabidopsis. Genes located within QTL confidence intervals were retrieved and enrichments in gene ontology (GO) terms were determined using different methods. Significant enrichments were found for all traits. Particularly relevant biological processes GO terms were identified for QTLs controlling number of sylleptic branches: intervals were enriched in GO terms of biological process like 'ripening' and 'adventitious roots development'.Beyond the simple identification of QTLs, this study is the first to use a global approach of GO terms enrichment analysis to fully explore gene function under QTLs confidence intervals in plants. This global approach may lead to identification of new candidate genes for traits of interest.CONCLUSIONBeyond the simple identification of QTLs, this study is the first to use a global approach of GO terms enrichment analysis to fully explore gene function under QTLs confidence intervals in plants. This global approach may lead to identification of new candidate genes for traits of interest.
ArticleNumber 173
Audience Academic
Author Bert, Pierre-François
Monclus, Romain
Villar, Marc
Marron, Nicolas
Bastien, Catherine
Brignolas, Franck
Leplé, Jean-Charles
Jorge, Véronique
AuthorAffiliation 2 UFR-Faculté des Sciences, UPRES EA 1207 Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans, F-45067, Orléans, France
3 INRA, USC1328 Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), F-45067, Orléans, France
6 Present address: INRA, UMR1287 Ecophysiologie et Génomique Fonctionnelle de la Vigne, F-33882, Villenave d'Ornon, France
4 INRA, UMR1137 Écologie et Écophysiologie Forestières (EEF), F-54280, Champenoux, France
5 Université de Lorraine, UMR 1137, Ecologie et Ecophysiologie Forestières (EEF), Faculté des Sciences, F-54500, Vandœuvre-lès-Nancy, France
1 INRA, UR0588 Amélioration Génétique et Physiologie Forestières (AGPF), F-45075, Orléans, France
AuthorAffiliation_xml – name: 5 Université de Lorraine, UMR 1137, Ecologie et Ecophysiologie Forestières (EEF), Faculté des Sciences, F-54500, Vandœuvre-lès-Nancy, France
– name: 1 INRA, UR0588 Amélioration Génétique et Physiologie Forestières (AGPF), F-45075, Orléans, France
– name: 2 UFR-Faculté des Sciences, UPRES EA 1207 Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans, F-45067, Orléans, France
– name: 4 INRA, UMR1137 Écologie et Écophysiologie Forestières (EEF), F-54280, Champenoux, France
– name: 6 Present address: INRA, UMR1287 Ecophysiologie et Génomique Fonctionnelle de la Vigne, F-33882, Villenave d'Ornon, France
– name: 3 INRA, USC1328 Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), F-45067, Orléans, France
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  surname: Monclus
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  givenname: Jean-Charles
  surname: Leplé
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/23013168$$D View this record in MEDLINE/PubMed
https://hal.inrae.fr/hal-02647348$$DView record in HAL
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2012 Monclus et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Copyright ©2012 Monclus et al.; licensee BioMed Central Ltd. 2012 Monclus et al.; licensee BioMed Central Ltd.
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– notice: 2012 Monclus et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
– notice: Distributed under a Creative Commons Attribution 4.0 International License
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Issue 1
Keywords leaf trait
hybrid poplar
gene ontology
candidate gene
productivity
water-use efficiency
QTL
architecture
Language English
License Distributed under a Creative Commons Attribution 4.0 International License: http://creativecommons.org/licenses/by/4.0
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Snippet Hybrid poplars species are candidates for biomass production but breeding efforts are needed to combine productivity and water use efficiency in improved...
Background Hybrid poplars species are candidates for biomass production but breeding efforts are needed to combine productivity and water use efficiency in...
Doc number: 173 Abstract Background: Hybrid poplars species are candidates for biomass production but breeding efforts are needed to combine productivity and...
Background: Hybrid poplars species are candidates for biomass production but breeding efforts are needed to combine productivity and water use efficiency in...
BACKGROUND: Hybrid poplars species are candidates for biomass production but breeding efforts are needed to combine productivity and water use efficiency in...
Abstract Background Hybrid poplars species are candidates for biomass production but breeding efforts are needed to combine productivity and water use...
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StartPage 173
SubjectTerms Analysis
Arabidopsis
Arabidopsis thaliana
Architecture
Chromosome Mapping
Cloning
Confidence Intervals
Crosses, Genetic
Cultivars
Efficiency
France
Gene loci
Gene mapping
Genes
Genes, Plant - genetics
Genetic aspects
Genetic Association Studies
Genetic Linkage
Genetic Markers
Genetics
Genome, Plant - genetics
Genomes
Genomics
Genotype & phenotype
Leaves
Life Sciences
Molecular Sequence Annotation
Ontology
Physiological aspects
Plant genetics
Plant Leaves - genetics
Plant physiology
Poplar
Populus
Populus - anatomy & histology
Populus - genetics
Populus - growth & development
Populus trichocarpa
Productivity
Quantitative genetics
Quantitative trait loci
Quantitative Trait Loci - genetics
Quantitative Trait, Heritable
Vegetal Biology
Water
Water - metabolism
Water use
Water use efficiency
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Title Integrating genome annotation and QTL position to identify candidate genes for productivity, architecture and water-use efficiency in Populus spp
URI https://www.ncbi.nlm.nih.gov/pubmed/23013168
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https://pubmed.ncbi.nlm.nih.gov/PMC3520807
https://doaj.org/article/61b6cdfccef64bc98fdf050b8e1113ba
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