Genome-Wide Gene Expression Profiling Reveals Conserved and Novel Molecular Functions of the Stigma in Rice

Abstract

In angiosperms, the stigma provides initial nutrients and guidance cues for pollen grain germination and tube growth. However, little is known about the genes that regulate these processes in rice (Oryza sativa). Here, we generate rice stigmaspecific or -preferential gene expression profiles through comparing genome-wide expression patterns of hand-dissected, unpollinated stigma at anthesis with seven tissues, including seedling shoot, seedling root, mature anther, ovary at anthesis, seeds 5 d after pollination, 10-d-old embryo, 10-d-old endosperm, and suspension-cultured cells by using both 57 K Affymetrix rice whole-genome array and 10 K rice cDNA microarray. A high reproducibility of the microarray results was detected between the two different technology platforms. In total, we identified 548 genes to be expressed specifically or predominantly in the stigma papillar cells of rice. Real-time quantitative reverse transcription-polymerase chain reaction analysis of 34 selected genes all confirmed their stigma-specific expression. The expression of five selected genes was further validated by RNA in situ hybridization. Gene Ontology analysis shows that several auxin-signaling components, transcription, and stressrelated genes are significantly overrepresented in the rice stigma gene set. Interestingly, most of them also share several cisregulatory elements with known stress-responsive genes, supporting the notion of an overlap of genetic programs regulating pollination and stress/defense responses. We also found that genes involved in cell wall metabolism and cellular communication appear to be conserved in the stigma between rice and Arabidopsis (Arabidopsis thaliana). Our results indicate that the stigmas appear to have conserved and novel molecular functions between rice and Arabidopsis.

Analysis of theNicotiana tabacumStigma/Style Transcriptome Reveals Gene Expression Differences between Wet and Dry Stigma Species

“…The "Intracellular trafficking, secretion, and vesicular transport" (2.8%), "Carbohydrate transport and metabolism" (2.6%), and "Lipid transport and metabolism" (2.3%) categories contain the gene functions important for the roles exerted by the stigmatic secretory zone and the stylar transmitting tissue in secreting the exudate, which is rich in carbohydrates and lipids (Cresti et al, 1986). The "Defense mechanisms" (2.3%) category is also well represented, consistent with what was observed for the Arabidopsis stigma and transmitting tract gene sets (Tung et al, 2005) and for the rice stigma gene set (Li et al, 2007). Our data corroborate the notion of an overlap of genetic programs regulating reproduction processes and stress/defense responses, as proposed by Li et al (2007).…”

“…It is expected that many of these genes are stigma/style specific or preferential. Recent large-scale studies have identified stigma/style-specific genes in the dry stigma species Arabidopsis and rice (Swanson et al, 2005;Tung et al, 2005;Li et al, 2007). However, in wet stigma species, only a few individual genes have been characterized so far, and little is known about the stigma/style-specific genes important for successful pollination and reproduction.…”

Mapping Metabolic and Transcript Temporal Switches during Germination in Rice Highlights Specific Transcription Factors and the Role of RNA Instability in the Germination Process

“…This normalization allowed cross-comparison of arrays from all of the different studies at once. The arrays analyzed included all of the arrays from this study, together with publicly available rice genome arrays carried out from different tissues/ conditions, including 7-d-old seedlings that were untreated, drought stressed, salt stressed, or cold stressed (GSE6901; Jain et al, 2007); seeds collected at 5 d following pollination, 10-d-old embryos, 10-d-old endosperms, seedling roots, seedling shoots, unpollinated stigmas (at antithesis), ovaries (at antithesis), mature anthers, and suspension cells (GSE7951; Li et al, 2007); aerobically grown coleoptiles (4 d) and anoxically grown coleoptiles (4 d; GSE6908; Lasanthi- Kudahettige et al, 2007); crowns and growing points under salt stress and control conditions in sensitive and tolerant mutants in subspecies indica and japonica (GSE4438; Walia et al, 2007); crowns and growing points under control and salt stress conditions in subspecies indica and japonica (GDS1383; Walia et al, 2005); and leaves following biotic stress and control treatments (GSE7256; Ribot et al, 2008).…”

Comparative Network Analysis Reveals That Tissue Specificity and Gene Function Are Important Factors Influencing the Mode of Expression Evolution in Arabidopsis and Rice

“…We obtained 203 and 322 Affymetrix CEL files for rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana), respectively, from the National Center for Biotechnology Information Gene Expression Omnibus database monitoring the transcriptional activity in different tissues and developmental stages (Schmid et al, 2005;Jain et al, 2007;Li et al, 2007), root cell types (Birnbaum et al, 2003;Norton et al, 2008), and under different stress conditions (Walia et al, 2005;Kilian et al, 2007;Swarbrick et al, 2008). The ATH1 microarray slides were processed with a custom-made CDF measuring 19,937 genes as described before .…”