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Open Access Highly Accessed Research article

Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds

Peter C McKeown1, Sylvia Laouielle-Duprat1, Pjotr Prins2, Philip Wolff34, Marc W Schmid5, Mark TA Donoghue1, Antoine Fort1, Dorota Duszynska1, Aurélie Comte1, Nga Thi Lao1, Trevor J Wennblom6, Geert Smant2, Claudia Köhler34, Ueli Grossniklaus5 and Charles Spillane1*

Author Affiliations

1 Genetics and Biotechnology Lab, Botany and Plant Science, National University of Ireland Galway (NUIG), C306 Aras de Brun, University Road, Galway, Ireland

2 Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands

3 Department of Biology and Zürich-Basel Plant Science Center, Swiss Federal Institute of Technology, ETH Centre, CH-8092 Zürich, Switzerland

4 Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden

5 Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland

6 Silicon Life Sciences, Minneapolis, MN, USA

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BMC Plant Biology 2011, 11:113  doi:10.1186/1471-2229-11-113

Published: 12 August 2011

Abstract

Background

Epigenetic regulation of gene dosage by genomic imprinting of some autosomal genes facilitates normal reproductive development in both mammals and flowering plants. While many imprinted genes have been identified and intensively studied in mammals, smaller numbers have been characterized in flowering plants, mostly in Arabidopsis thaliana. Identification of additional imprinted loci in flowering plants by genome-wide screening for parent-of-origin specific uniparental expression in seed tissues will facilitate our understanding of the origins and functions of imprinted genes in flowering plants.

Results

cDNA-AFLP can detect allele-specific expression that is parent-of-origin dependent for expressed genes in which restriction site polymorphisms exist in the transcripts derived from each allele. Using a genome-wide cDNA-AFLP screen surveying allele-specific expression of 4500 transcript-derived fragments, we report the identification of 52 maternally expressed genes (MEGs) displaying parent-of-origin dependent expression patterns in Arabidopsis siliques containing F1 hybrid seeds (3, 4 and 5 days after pollination). We identified these MEGs by developing a bioinformatics tool (GenFrag) which can directly determine the identities of transcript-derived fragments from (i) their size and (ii) which selective nucleotides were added to the primers used to generate them. Hence, GenFrag facilitates increased throughput for genome-wide cDNA-AFLP fragment analyses. The 52 MEGs we identified were further filtered for high expression levels in the endosperm relative to the seed coat to identify the candidate genes most likely representing novel imprinted genes expressed in the endosperm of Arabidopsis thaliana. Expression in seed tissues of the three top-ranked candidate genes, ATCDC48, PDE120 and MS5-like, was confirmed by Laser-Capture Microdissection and qRT-PCR analysis. Maternal-specific expression of these genes in Arabidopsis thaliana F1 seeds was confirmed via allele-specific transcript analysis across a range of different accessions. Differentially methylated regions were identified adjacent to ATCDC48 and PDE120, which may represent candidate imprinting control regions. Finally, we demonstrate that expression levels of these three genes in vegetative tissues are MET1-dependent, while their uniparental maternal expression in the seed is not dependent on MET1.

Conclusions

Using a cDNA-AFLP transcriptome profiling approach, we have identified three genes, ATCDC48, PDE120 and MS5-like which represent novel maternally expressed imprinted genes in the Arabidopsis thaliana seed. The extent of overlap between our cDNA-AFLP screen for maternally expressed imprinted genes, and other screens for imprinted and endosperm-expressed genes is discussed.