Abstract
Rice (Oryza sativa) is an excellent model monocot with a known genome sequence for studying embryogenesis. Here we report the transcriptome profiling analysis of rice developing embryos using RNA-Seq as an attempt to gain insight into the molecular and cellular events associated with rice embryogenesis. RNA-Seq analysis generated 17,755,890 sequence reads aligned with 27,190 genes, which provided abundant data for the analysis of rice embryogenesis. A total of 23,971, 23,732, and 23,592 genes were identified from embryos at three developmental stages (3–5, 7, and 14 DAP), while an analysis between stages allowed the identification of a subset of stage-specific genes. The number of genes expressed stage-specifically was 1,131, 1,443, and 1,223, respectively. In addition, we investigated transcriptomic changes during rice embryogenesis based on our RNA-Seq data. A total of 1,011 differentially expressed genes (DEGs) (log2Ratio ≥1, FDR ≤0.001) were identified; thus, the transcriptome of the developing rice embryos changed considerably. A total of 672 genes with significant changes in expression were detected between 3–5 and 7 DAP; 504 DEGs were identified between 7 and 14 DAP. A large number of genes related to metabolism, transcriptional regulation, nucleic acid replication/processing, and signal transduction were expressed predominantly in the early and middle stages of embryogenesis. Protein biosynthesis-related genes accumulated predominantly in embryos at the middle stage. Genes for starch/sucrose metabolism and protein modification were highly expressed in the middle and late stages of embryogenesis. In addition, we found that many transcription factor families may play important roles at different developmental stages, not only in embryo initiation but also in other developmental processes. These results will expand our understanding of the complex molecular and cellular events in rice embryogenesis and provide a foundation for future studies on embryo development in rice and other cereal crops.
Highlights
Rice (Oryza sativa), which belongs to the grass family (Poaceae), together with barley, wheat, maize, and sorghum, are important cereal crops that support the global food supply
We report a comprehensive analysis of transcriptome dynamics that may serve as a gene expression profile blueprint for embryo development, which was used to investigate the regulation of gene expression during early embryo development events from 3 to 14 days after pollination (DAP)
RNA-Seq analysis created a comprehensive view of the participation of several multigene families in embryogenesis
Summary
Rice (Oryza sativa), which belongs to the grass family (Poaceae), together with barley, wheat, maize, and sorghum, are important cereal crops that support the global food supply. Rice offers various advantages as an experimental plant compared with other monocot species, including a small genome size and known genome sequence [1]. Patterning during embryogenesis begins with asymmetric zygote cell division that produces a small apical cell that becomes the embryo and a large basal cell that develops into the suspensor. The classification of gene expression patterns associated with specific stages of embryo development and a functional understanding of the encoded genes is critical for comprehending the molecular and biochemical events associated with embryogenesis. Embryo development is a major subject in plant growth and development research, there is still a long way to go in order to understand the mechanism of this developmental process. Given the availability of a genomic sequence database, rice is an excellent model monocot for studying embryogenesis
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