Genome-Wide Analysis of Spatial Gene Expression in Arabidopsis Flowers[W]

Abstract

We have compared the gene expression profiles of inflorescences of the floral homeotic mutants apetala1, apetala2, apetala3, pistillata, and agamous with that of wild-type plants using a flower-specific cDNA microarray and a whole genome oligonucleotide array. By combining the data sets from the individual mutant/wild type comparisons, we were able to identify a large number of genes that are, within flowers, predicted to be specifically or at least predominantly expressed in one type of floral organ. We have analyzed the expression patterns of several of these genes by in situ hybridization and found that they match the predictions that were made based on the microarray experiments. Moreover, genes with known floral organ-specific expression patterns were correctly assigned by our analysis. The vast majority of the identified transcripts are found in stamens or carpels, whereas few genes are predicted to be expressed specifically or predominantly in sepals or petals. These findings indicate that spatially limited expression of a large number of genes is part of flower development and that its extent differs significantly between the reproductive organs and the organs of the perianth.

Global analysis of gene expression in flower buds of Ms-cd1 Brassica oleracea conferring male sterility by using an Arabidopsis microarray

“…To determine pollen stage specificity and co-expression information, present data were compared to array data from three other studies to which we will refer in the following ways: pollen transcriptome (''pollen transcriptome'' in this study refers to the dataset from Honys and Twell 2004), stamen transcriptome (''stamen transcriptome'' in this study refers to the dataset from Wellmer et al 2004) and mia mutant down regulated transcriptome (''mia transcriptome'' in this study refers to the mia mutant down regulated gene transcriptome from Jakobsen et al 2005). Microsoft Excel was used to manage and filter the microarray data.…”

“…For determining expression patterns of the downregulated genes, we compared differentially expressed genes identified in Ms-cd1 with published stamen, pollen and mia transcriptomes (Honys and Twell 2004;Wellmer et al 2004;Jakobsen et al 2005) (Table 2). In the rest of the paper, we will discuss expression specificity in relation to gene function; all expression specificities are from papers of stamen, pollen and mia transcriptome as described in the materials and methods section.…”

“…Out of the 277 suppressed genes, 189 (68%) were also listed in the stamen transcriptome dataset and 251 (90.6%) were also listed in the pollen transcriptome dataset. Furthermore, based on stamen and pollen transcriptomic data, we assigned genes as pollen specific (PS) if they were only expressed in pollen; pollen preferential (PP) if genes showed at least 4-fold higher expression in any of the four pollen stages relative to the highest level in any sporophytic tissue (MaxP/MaxS); pollen expressed (PE) if genes showed MaxP/MaxS less then 4 and stamen preferential (SP) if genes showed expression in stamen transcriptomic dataset (Honys and Twell 2004) and stamen transcriptome (Wellmer et al 2004). PS, pollen specific; SP, stamen preferential; PP, pollen preferential; PE, pollen expressed; NDP, not detected in pollen previously with no expression or not detected in pollen transcriptomic dataset.…”

“…Besides suppressed genes, we identified 14 up regulated genes in Ms-cd1 flower buds compared to wild type. None of these genes were described as pollen specific or pollen preferential genes based on the pollen transcriptome from Honys and Twell studys (2004), while only AT2G38940 is described as a stamen preferentially expressed gene (Wellmer et al 2004). Since there is no information on the function of these genes during anther development, we infer that some of these genes are not functionally involved in anther development.…”

“…Using mutants, which lack stamens due to the destruction of stamen identity genes, a large number of stamen specific genes were identified by microarrays (Zik and Irish 2003;Wellmer et al 2004). These genes provided a good basis for studying anther development.…”