IC4R012-RNA-Seq-2012-22347394

Project Title

• Transcriptomic Analysis of Rice (Oryza sativa) Developing Embryos Using the RNA-Seq Technique

The Background of This Project

• Although 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. 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. Rice (Oryza sativa) is an excellent model monocot with a known genome sequence for studying embryogenesis.
• RNA-Seq is suitable and affordable for comparative gene expression studies because it verifies direct transcript profiling without compromise and potential bias, thus allowing for more sensitive and accurate profiling of the transcriptome that more closely resembles the biology of the cell. This technology has been used in transcriptome profiling studies for various organisms, including maize, rice, and soybean. However, RNA-Seq technology has not been used to analyze embryogenesis in rice. In this research, the researchers reported 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.

Plant Culture & Treatment

• Rice (O. sativa L.ssp. indica cv.9311) plants were grown in a greenhouse at Wuhan University (30u330N, 114u190E), China. Some spikelets were tagged at the initiation of pollination, and harvested at 3–5, 7, and 14 DAP. Before 3 DAP, the zygote reiterates cell divisions to form a globular embryo with no apparent morphological differentiation. At 5 DAP, the first leaf primordium is visible on the opposite side of the coleoptile, and the shoot apical meristem becomes dome-shaped at 7 DAP [32]. Morphological maturity of the rice embryo was noted at approximately 14 DAP. Since the number of embryos at 3 DAP was extremely low, a mixture of embryos at 3–5 DAP was collected as one sample. The three-staged embryos were taken from spikelets with microdissection needles under a dissection microscope (Olympus, Tokyo, Japan) according to the manual microdissection method and frozen immediately in liquid nitrogen for total RNA extraction. Three embryo clusters were collected from 15 different plants at 3–5, 7, and 14 DAP during the growing season. The embryos were randomly selected from each cluster and pooled with embryos from other plants at the same greenhouse site, resulting in three independent pools for each developmental stage.

Labs working on this Project

• State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China

Corresponding Author

• jbwang@whu.edu.cn