Research

Genetic subtraction profiling identifies genes essential for Arabidopsis reproduction and reveals interaction between the female gametophyte and the maternal sporophyte

Amal J Johnston^1,3* , Patrick Meier^1* , Jacqueline Gheyselinck¹ , Samuel EJ Wuest¹ , Michael Federer¹ , Edith Schlagenhauf¹ , Jörg D Becker² and Ueli Grossniklaus¹

¹  Institute of Plant Biology and Zürich-Basel Plant Science Center, Zollikerstrasse, University of Zürich, CH-8008 Zürich, Switzerland

²  Centro de Biologia do Desenvolvimento, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, PT-2780-156 Oeiras, Portugal

³  Current address: Institute of Plant Sciences and Zürich-Basel Plant Science Center, ETH Zürich, Universitätstrasse, CH-8092 Zürich, Switzerland

author email corresponding author email* Contributed equally

Genome Biology 2007, 8:R204doi:10.1186/gb-2007-8-10-r204

Published:	3 October 2007

Subject areas: Plant biology, Development, Genome studies

Abstract

Background

The embryo sac contains the haploid maternal cell types necessary for double fertilization and subsequent seed development in plants. Large-scale identification of genes expressed in the embryo sac remains cumbersome because of its inherent microscopic and inaccessible nature. We used genetic subtraction and comparative profiling by microarray between the Arabidopsis thaliana wild-type and a sporophytic mutant lacking an embryo sac in order to identify embryo sac expressed genes in this model organism. The influences of the embryo sac on the surrounding sporophytic tissues were previously thought to be negligible or nonexistent; we investigated the extent of these interactions by transcriptome analysis.

Results

We identified 1,260 genes as embryo sac expressed by analyzing both our dataset and a recently reported dataset, obtained by a similar approach, using three statistical procedures. Spatial expression of nine genes (for instance a central cell expressed trithorax-like gene, an egg cell expressed gene encoding a kinase, and a synergid expressed gene encoding a permease) validated our approach. We analyzed mutants in five of the newly identified genes that exhibited developmental anomalies during reproductive development. A total of 527 genes were identified for their expression in ovules of mutants lacking an embryo sac, at levels that were twofold higher than in the wild type.

Conclusion

Identification of embryo sac expressed genes establishes a basis for the functional dissection of embryo sac development and function. Sporophytic gain of expression in mutants lacking an embryo sac suggests that a substantial portion of the sporophytic transcriptome involved in carpel and ovule development is, unexpectedly, under the indirect influence of the embryo sac.