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Genome-Wide Analysis of Gene Expression during Early Arabidopsis Flower Development

Wellmer, Frank and Alves-Ferreira, Márcio and Dubois, Annick and Riechmann, José Luis and Meyerowitz, Elliot M. (2006) Genome-Wide Analysis of Gene Expression during Early Arabidopsis Flower Development. PLoS Genetics, 2 (7). pp. 1012-1024. ISSN 1553-7390. PMCID PMC1523247. http://resolver.caltech.edu/CaltechAUTHORS:WELplosgen06

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Abstract

Detailed information about stage-specific changes in gene expression is crucial for the understanding of the gene regulatory networks underlying development. Here, we describe the global gene expression dynamics during early flower development, a key process in the life cycle of a plant, during which floral patterning and the specification of floral organs is established. We used a novel floral induction system in Arabidopsis, which allows the isolation of a large number of synchronized floral buds, in conjunction with whole-genome microarray analysis to identify genes with differential expression at distinct stages of flower development. We found that the onset of flower formation is characterized by a massive downregulation of genes in incipient floral primordia, which is followed by a predominance of gene activation during the differentiation of floral organs. Among the genes we identified as differentially expressed in the experiment, we detected a significant enrichment of closely related members of gene families. The expression profiles of these related genes were often highly correlated, indicating similar temporal expression patterns. Moreover, we found that the majority of these genes is specifically up-regulated during certain developmental stages. Because co-expressed members of gene families in Arabidopsis frequently act in a redundant manner, these results suggest a high degree of functional redundancy during early flower development, but also that its extent may vary in a stage-specific manner.


Item Type:Article
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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1523247/PubMed CentralArticle
https://dx.doi.org/10.1371/journal.pgen.0020117.eorDOIArticle
ORCID:
AuthorORCID
Meyerowitz, Elliot M.0000-0003-4798-5153
Additional Information:© 2006 Wellmer et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Received: April 21, 2006; Accepted: June 12, 2006; Published: July 28, 2006. A previous version of this article appeared as an Early Online Release on June 12, 2006 (DOI:10.1371/journal.pgen.0020117.eor). We are indebted to Arnavaz Garda and David McKinney for technical assistance; to Dr. Igor Antoshechkin, Vijaya Rao, Kayla Smith, Brandon King, and Ali Mortazavi for help with data management and analysis; and to Drs. Adrienne Roeder, Carolyn Ohno, Emmanuelle Graciet, Patrick Sieber, and Zach Nimchuk for comments on the manuscript. Author contributions. FW, JLR, and EMM conceived and designed the experiments. FW, MAF, and AD performed the experiments. FW and JLR analyzed the data. FW, JLR, and EMM wrote the paper. Competing interests. The authors have declared that no competing interests exist. This work was supported by National Institutes of Health grant GM45697 to E.M.M. and by the Millard and Muriel Jacobs Genetics and Genomics Laboratory at the California Institute of Technology. M. A.-F. was supported by grants from CNPq (307219/2004–6, 400767/2004–0 and 475666/2004–6) and International Foundation for Science (C/3962–1), as well as by an IPBO fellowship sponsored by Aventis Crop Sciences. A.D. was supported by a Lavoisier fellowship. Microarray data have been deposited with the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo) under accession number GSE4594. Ratio and intensity data for all genes represented on the microarray used in this study are listed in Table S10. The Arabidopsis Genome Initiative (http://www.arabidopsis.org) identifiers for the genes and gene products discussed in this study are: AG (At4g18960), AGL24 (At4g24540), AGL42 (At5g62165), ANT (At4g37750), AP1 (At1g69120), AP2 (At4g36920), AP3 (At3g54340), ASK1 (At1g10940), BLR (At5g02030), CAL (At1g26310), CLF (At2g23380), CLV3 (At2g27250), CRC (At1g69180), FD (At4g35900), FDP (At2g17770), FIL (At2g45190), FT (At1g65480), FUL (At5g60910), GA2ox1 (At1g78440), GA4 (At1g15550), JAG (At1g68480), KNU (At5g14010), LEU (At4g32550), LFY (At5g61850), NAP (At1g69490), NUB (At1g13400), NZZ/SPL (At4g27330), PI (At5g20240), PIN2 (At5g57090), PIN3 (At1g70940), PIN4 (At2g01420), PIN6 (At1g77110), RBE (At5g06070), SAP (At5g35770), SEP1 (At5g15800), SEP2 (At3g02310), SEP3 (At1g24260), SEP4 (At2g03710), SEU (At1g43850), SHP1 (At3g58780), SHP2 (At2g42830), SOC1 (At2g45660), SUP (At3g23130), SVP (At2g22540), TCP2 (At4g18390), TCP3 (At1g53230), TCP4 (At3g15030), TCP5 (At5g60970), TCP10 (At2g31070), TCP13 (At3g02150), TCP17 (At5g08070), TFL1 (At5g03840), UFO (At1g30950), WUS (At2g17950), and YAB3 (At4g00180).
PubMed Central ID:PMC1523247
Record Number:CaltechAUTHORS:WELplosgen06
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:WELplosgen06
Alternative URL:http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pgen.0020117
Official Citation:Wellmer F, Alves-Ferreira M, Dubois A, Riechmann JL, Meyerowitz EM (2006) Genome-wide analysis of gene expression during early Arabidopsis flower development. PLoS Genet 2(7): e117. DOI: 10.1371/journal.pgen.0020117
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:4394
Collection:CaltechAUTHORS
Deposited By: Archive Administrator
Deposited On:21 Aug 2006
Last Modified:10 Dec 2016 20:06

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