Genome-Wide Analysis of the Complex Transcriptional Networks of Rice Developing Seeds

Abstract

BackgroundThe development of rice (Oryza sativa) seed is closely associated with assimilates storage and plant yield, and is fine controlled by complex regulatory networks. Exhaustive transcriptome analysis of developing rice embryo and endosperm will help to characterize the genes possibly involved in the regulation of seed development and provide clues of yield and quality improvement.Principal FindingsOur analysis showed that genes involved in metabolism regulation, hormone response and cellular organization processes are predominantly expressed during rice development. Interestingly, 191 transcription factor (TF)-encoding genes are predominantly expressed in seed and 59 TFs are regulated during seed development, some of which are homologs of seed-specific TFs or regulators of Arabidopsis seed development. Gene co-expression network analysis showed these TFs associated with multiple cellular and metabolism pathways, indicating a complex regulation of rice seed development. Further, by employing a cold-resistant cultivar Hanfeng (HF), genome-wide analyses of seed transcriptome at normal and low temperature reveal that rice seed is sensitive to low temperature at early stage and many genes associated with seed development are down-regulated by low temperature, indicating that the delayed development of rice seed by low temperature is mainly caused by the inhibition of the development-related genes. The transcriptional response of seed and seedling to low temperature is different, and the differential expressions of genes in signaling and metabolism pathways may contribute to the chilling tolerance of HF during seed development.ConclusionsThese results provide informative clues and will significantly improve the understanding of rice seed development regulation and the mechanism of cold response in rice seed.

Global Analysis Reveals the Crucial Roles of DNA Methylation during Rice Seed Development

“…The central cell chromatin is less methylated than that of somatic cells (Jullien and Berger, 2010) and then reprogrammed in the offspring after double fertilization. The endosperm DNA of Arabidopsis and rice is globally hypomethylated (Gehring et al, 2009;Hsieh et al, 2009;Zemach et al, 2010). Analysis of the quantified methylation in rice embryo and endosperm at the milky stage by bisulfite sequencing indicated the globally reduced non-CG methylation and local CG hypomethylation in endosperm compared with that in embryo, resembling the phenomenon in Arabidopsis (Zemach et al, 2010).…”

“…In plants, DNA methylation occurs in the cytosine residue within three different sequence contexts (CG, CHG, and CHH;Cokus et al, 2008), of which methylation at CHG and CHH is predominantly found in TEs, while CG methylation occurs in TEs and genes (Feng et al, 2010;Zemach et al, 2010). Recent studies demonstrated the crucial roles of DNA methylation in plant development, including gametogenesis, seed development, and response to stresses (Boyko and Kovalchuk, 2008;Chen and Zhou, 2013).…”

“…Studies have shown that many factors are involved in the regulation of embryo and endosperm development, and genetics studies and functional genomics studies have identified some key regulators of seed development. Recent highthroughput transcriptome analysis using microarray and RNA sequencing provided detailed transcriptional profiles of genes at different developmental stages of developing seeds (Xu et al, 2012;Xue et al, 2012;Gao et al, 2013), which help to illustrate the regulatory networks of seed development.…”

“…The endosperm DNA of Arabidopsis and rice is globally hypomethylated (Gehring et al, 2009;Hsieh et al, 2009;Zemach et al, 2010). Analysis of the quantified methylation in rice embryo and endosperm at the milky stage by bisulfite sequencing indicated the globally reduced non-CG methylation and local CG hypomethylation in endosperm compared with that in embryo, resembling the phenomenon in Arabidopsis (Zemach et al, 2010). In addition, comparative analysis of transcriptome and methylome between two inbred parents, cv Nipponbare and indica varieties, and their hybrid offspring showed the variable epigenetic heritability and strong association between small interfering RNA differences and epimutation levels (Chodavarapu et al, 2012).…”

Genome-wide analysis of spatio-temporal gene expression patterns during early embryogenesis in rice

“…Although expression profiling of various embryonic tissues and stages has been reported in rice and maize (Jiao et al, 2009;Takacs et al, 2012;Xu et al, 2012;Xue et al, 2012;Lu et al, 2013;Chen et al, 2014), predicting the spatial expression pattern and dynamics of gene expression during early embryogenesis remains difficult.…”