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Niederhuth CE, Patharkar OR, Walker JC. Transcriptional profiling of the Arabidopsis abscission mutant hae hsl2 by RNA-Seq. BMC Genomics 2013; 14:37. [PMID: 23327667 PMCID: PMC3566969 DOI: 10.1186/1471-2164-14-37] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 01/14/2013] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Abscission is a mechanism by which plants shed entire organs in response to both developmental and environmental signals. Arabidopsis thaliana, in which only the floral organs abscise, has been used extensively to study the genetic, molecular and cellular processes controlling abscission. Abscission in Arabidopsis requires two genes that encode functionally redundant receptor-like protein kinases, HAESA (HAE) and HAESA-LIKE 2 (HSL2). Double hae hsl2 mutant plants fail to abscise their floral organs at any stage of floral development and maturation. RESULTS Using RNA-Seq, we compare the transcriptomes of wild-type and hae hsl2 stage 15 flowers, using the floral receptacle which is enriched for abscission zone cells. 2034 genes were differentially expressed with a False Discovery Rate adjusted p < 0.05, of which 349 had two fold or greater change in expression. Differentially expressed genes were enriched for hydrolytic, cell wall modifying, and defense related genes. Testing several of the differentially expressed genes in INFLORESCENCE DEFICIENT IN ABSCISSION (ida) mutants shows that many of the same genes are co-regulated by IDA and HAE HSL2 and support the role of IDA in the HAE and HSL2 signaling pathway. Comparison to microarray data from stamen abscission zones show distinct patterns of expression of genes that are dependent on HAE HSL2 and reveal HAE HSL2- independent pathways. CONCLUSION HAE HSL2-dependent and HAE HSL2-independent changes in genes expression are required for abscission. HAE and HSL2 affect the expression of cell wall modifying and defense related genes necessary for abscission. The HAE HSL2-independent genes also appear to have roles in abscission and additionally are involved in processes such as hormonal signaling, senescence and callose deposition.
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Affiliation(s)
- Chad E Niederhuth
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - O Rahul Patharkar
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - John C Walker
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
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Dubois A, Remay A, Raymond O, Balzergue S, Chauvet A, Maene M, Pécrix Y, Yang SH, Jeauffre J, Thouroude T, Boltz V, Martin-Magniette ML, Janczarski S, Legeai F, Renou JP, Vergne P, Le Bris M, Foucher F, Bendahmane M. Genomic approach to study floral development genes in Rosa sp. PLoS One 2011; 6:e28455. [PMID: 22194838 PMCID: PMC3237435 DOI: 10.1371/journal.pone.0028455] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 11/08/2011] [Indexed: 11/19/2022] Open
Abstract
Cultivated for centuries, the varieties of rose have been selected based on a number of flower traits. Understanding the genetic and molecular basis that contributes to these traits will impact on future improvements for this economically important ornamental plant. In this study, we used scanning electron microscopy and sections of meristems and flowers to establish a precise morphological calendar from early rose flower development stages to senescing flowers. Global gene expression was investigated from floral meristem initiation up to flower senescence in three rose genotypes exhibiting contrasted floral traits including continuous versus once flowering and simple versus double flower architecture, using a newly developed Affymetrix microarray (Rosa1_Affyarray) tool containing sequences representing 4765 unigenes expressed during flower development. Data analyses permitted the identification of genes associated with floral transition, floral organs initiation up to flower senescence. Quantitative real time PCR analyses validated the mRNA accumulation changes observed in microarray hybridizations for a selection of 24 genes expressed at either high or low levels. Our data describe the early flower development stages in Rosa sp, the production of a rose microarray and demonstrate its usefulness and reliability to study gene expression during extensive development phases, from the vegetative meristem to the senescent flower.
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Affiliation(s)
- Annick Dubois
- Laboratoire Reproduction et Développement des Plantes, Institut Nationale de la Recherche Agronomique, Centre National de la Recherche Scientifique, Ecole Normale Supérieure, Lyon, France
| | - Arnaud Remay
- UMR Génétique et Horticulture, Institut Nationale de la Recherche Agronomique, Agrocampus Ouest, Université d'Angers, Beaucouzé, France
| | - Olivier Raymond
- Laboratoire Reproduction et Développement des Plantes, Institut Nationale de la Recherche Agronomique, Centre National de la Recherche Scientifique, Ecole Normale Supérieure, Lyon, France
| | - Sandrine Balzergue
- Unité de Recherche en Génomique Végétale, Institut Nationale de la Recherche Agronomique, Centre National de la Recherche Scientifique, Evry, France
| | - Aurélie Chauvet
- Laboratoire Reproduction et Développement des Plantes, Institut Nationale de la Recherche Agronomique, Centre National de la Recherche Scientifique, Ecole Normale Supérieure, Lyon, France
| | - Marion Maene
- Laboratoire Reproduction et Développement des Plantes, Institut Nationale de la Recherche Agronomique, Centre National de la Recherche Scientifique, Ecole Normale Supérieure, Lyon, France
| | - Yann Pécrix
- Institut Méditerranéen d'Ecologie et de Paléoécologie, Centre National de la Recherche Scientifique, Université Paul Cézanne-Aix-Marseille III, Marseille, France
| | - Shu-Hua Yang
- Laboratoire Reproduction et Développement des Plantes, Institut Nationale de la Recherche Agronomique, Centre National de la Recherche Scientifique, Ecole Normale Supérieure, Lyon, France
| | - Julien Jeauffre
- UMR Génétique et Horticulture, Institut Nationale de la Recherche Agronomique, Agrocampus Ouest, Université d'Angers, Beaucouzé, France
| | - Tatiana Thouroude
- UMR Génétique et Horticulture, Institut Nationale de la Recherche Agronomique, Agrocampus Ouest, Université d'Angers, Beaucouzé, France
| | - Véronique Boltz
- Laboratoire Reproduction et Développement des Plantes, Institut Nationale de la Recherche Agronomique, Centre National de la Recherche Scientifique, Ecole Normale Supérieure, Lyon, France
| | - Marie-Laure Martin-Magniette
- Unité de Recherche en Génomique Végétale, Institut Nationale de la Recherche Agronomique, Centre National de la Recherche Scientifique, Evry, France
| | - Stéphane Janczarski
- Laboratoire Reproduction et Développement des Plantes, Institut Nationale de la Recherche Agronomique, Centre National de la Recherche Scientifique, Ecole Normale Supérieure, Lyon, France
| | - Fabrice Legeai
- UMR Bio3P IRISA Equipe Symbiose Campus de Beaulieu, Institut Nationale de la Recherche Agronomique, Rennes, France
| | - Jean-Pierre Renou
- Unité de Recherche en Génomique Végétale, Institut Nationale de la Recherche Agronomique, Centre National de la Recherche Scientifique, Evry, France
- UMR Génétique et Horticulture, Institut Nationale de la Recherche Agronomique, Agrocampus Ouest, Université d'Angers, Beaucouzé, France
| | - Philippe Vergne
- Laboratoire Reproduction et Développement des Plantes, Institut Nationale de la Recherche Agronomique, Centre National de la Recherche Scientifique, Ecole Normale Supérieure, Lyon, France
| | - Manuel Le Bris
- Institut Méditerranéen d'Ecologie et de Paléoécologie, Centre National de la Recherche Scientifique, Université Paul Cézanne-Aix-Marseille III, Marseille, France
| | - Fabrice Foucher
- UMR Génétique et Horticulture, Institut Nationale de la Recherche Agronomique, Agrocampus Ouest, Université d'Angers, Beaucouzé, France
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, Institut Nationale de la Recherche Agronomique, Centre National de la Recherche Scientifique, Ecole Normale Supérieure, Lyon, France
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