Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance
Abstract In Arabidopsis thaliana, gene expression level polymorphisms (ELPs) between natural accessions that exhibit simple, single locus inheritance are promising quantitative trait locus (QTL) candidates to explain phenotypic variability. It is assumed that such ELPs overwhelmingly represent regul...
Saved in:
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Springer Nature
2009-02-01
|
| Series: | Molecular Systems Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1038/msb.2008.79 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849225765518835712 |
|---|---|
| author | Stephanie Plantegenet Johann Weber Darlene R Goldstein Georg Zeller Cindy Nussbaumer Jérôme Thomas Detlef Weigel Keith Harshman Christian S Hardtke |
| author_facet | Stephanie Plantegenet Johann Weber Darlene R Goldstein Georg Zeller Cindy Nussbaumer Jérôme Thomas Detlef Weigel Keith Harshman Christian S Hardtke |
| author_sort | Stephanie Plantegenet |
| collection | DOAJ |
| description | Abstract In Arabidopsis thaliana, gene expression level polymorphisms (ELPs) between natural accessions that exhibit simple, single locus inheritance are promising quantitative trait locus (QTL) candidates to explain phenotypic variability. It is assumed that such ELPs overwhelmingly represent regulatory element polymorphisms. However, comprehensive genome‐wide analyses linking expression level, regulatory sequence and gene structure variation are missing, preventing definite verification of this assumption. Here, we analyzed ELPs observed between the Eil‐0 and Lc‐0 accessions. Compared with non‐variable controls, 5′ regulatory sequence variation in the corresponding genes is indeed increased. However, ∼42% of all the ELP genes also carry major transcription unit deletions in one parent as revealed by genome tiling arrays, representing a >4‐fold enrichment over controls. Within the subset of ELPs with simple inheritance, this proportion is even higher and deletions are generally more severe. Similar results were obtained from analyses of the Bay‐0 and Sha accessions, using alternative technical approaches. Collectively, our results suggest that drastic structural changes are a major cause for ELPs with simple inheritance, corroborating experimentally observed indel preponderance in cloned Arabidopsis QTL. |
| format | Article |
| id | doaj-art-5eedb722272f4eecb801337b17db36f1 |
| institution | Kabale University |
| issn | 1744-4292 |
| language | English |
| publishDate | 2009-02-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-5eedb722272f4eecb801337b17db36f12025-08-24T11:59:30ZengSpringer NatureMolecular Systems Biology1744-42922009-02-015111010.1038/msb.2008.79Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritanceStephanie Plantegenet0Johann Weber1Darlene R Goldstein2Georg Zeller3Cindy Nussbaumer4Jérôme Thomas5Detlef Weigel6Keith Harshman7Christian S Hardtke8Department of Plant Molecular Biology, University of Lausanne, Biophore BuildingLausanne DNA Array Facility, Center for Integrative Genomics, University of Lausanne, Genopode BuildingÉcole Polytechnique Fédérale de Lausanne (EPFL), Institut de mathématiques (IMA), Bâtiment MAFriedrich Miescher Laboratory of the Max Planck SocietyDepartment of Plant Molecular Biology, University of Lausanne, Biophore BuildingLausanne DNA Array Facility, Center for Integrative Genomics, University of Lausanne, Genopode BuildingMax Planck Institute for Developmental Biology, Department of Molecular BiologyLausanne DNA Array Facility, Center for Integrative Genomics, University of Lausanne, Genopode BuildingDepartment of Plant Molecular Biology, University of Lausanne, Biophore BuildingAbstract In Arabidopsis thaliana, gene expression level polymorphisms (ELPs) between natural accessions that exhibit simple, single locus inheritance are promising quantitative trait locus (QTL) candidates to explain phenotypic variability. It is assumed that such ELPs overwhelmingly represent regulatory element polymorphisms. However, comprehensive genome‐wide analyses linking expression level, regulatory sequence and gene structure variation are missing, preventing definite verification of this assumption. Here, we analyzed ELPs observed between the Eil‐0 and Lc‐0 accessions. Compared with non‐variable controls, 5′ regulatory sequence variation in the corresponding genes is indeed increased. However, ∼42% of all the ELP genes also carry major transcription unit deletions in one parent as revealed by genome tiling arrays, representing a >4‐fold enrichment over controls. Within the subset of ELPs with simple inheritance, this proportion is even higher and deletions are generally more severe. Similar results were obtained from analyses of the Bay‐0 and Sha accessions, using alternative technical approaches. Collectively, our results suggest that drastic structural changes are a major cause for ELPs with simple inheritance, corroborating experimentally observed indel preponderance in cloned Arabidopsis QTL.https://doi.org/10.1038/msb.2008.79ArabidopsiseQTLexpression level polymorphismheritability of expressionQTLstructural gene variation |
| spellingShingle | Stephanie Plantegenet Johann Weber Darlene R Goldstein Georg Zeller Cindy Nussbaumer Jérôme Thomas Detlef Weigel Keith Harshman Christian S Hardtke Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance Molecular Systems Biology Arabidopsis eQTL expression level polymorphism heritability of expression QTL structural gene variation |
| title | Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance |
| title_full | Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance |
| title_fullStr | Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance |
| title_full_unstemmed | Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance |
| title_short | Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance |
| title_sort | comprehensive analysis of arabidopsis expression level polymorphisms with simple inheritance |
| topic | Arabidopsis eQTL expression level polymorphism heritability of expression QTL structural gene variation |
| url | https://doi.org/10.1038/msb.2008.79 |
| work_keys_str_mv | AT stephanieplantegenet comprehensiveanalysisofarabidopsisexpressionlevelpolymorphismswithsimpleinheritance AT johannweber comprehensiveanalysisofarabidopsisexpressionlevelpolymorphismswithsimpleinheritance AT darlenergoldstein comprehensiveanalysisofarabidopsisexpressionlevelpolymorphismswithsimpleinheritance AT georgzeller comprehensiveanalysisofarabidopsisexpressionlevelpolymorphismswithsimpleinheritance AT cindynussbaumer comprehensiveanalysisofarabidopsisexpressionlevelpolymorphismswithsimpleinheritance AT jeromethomas comprehensiveanalysisofarabidopsisexpressionlevelpolymorphismswithsimpleinheritance AT detlefweigel comprehensiveanalysisofarabidopsisexpressionlevelpolymorphismswithsimpleinheritance AT keithharshman comprehensiveanalysisofarabidopsisexpressionlevelpolymorphismswithsimpleinheritance AT christianshardtke comprehensiveanalysisofarabidopsisexpressionlevelpolymorphismswithsimpleinheritance |