IC4R020-RNA-Seq-2016-26752408

Project Title

• Transcriptome Analysis of Salt Stress Responsiveness in the Seedlings of Dongxiang Wild Rice (Oryza rufipogon Griff.)

The Background of This Project

• Rice (Oryza sativa L.) is one of the most important food crops in the world and also a model for genomic research in monocots. However, salinity is one of the most devastating abiotic stresses in rice, and the salt-affected soils currently account for about 20% of the total paddy rice planting area.More seriously, the area of salt-affected irrigated land is expanding and spreading in China.
• Dongxiang wild rice (Oryza rufipogon Griff., hereafter referred as DXWR) is the progenitor of cultivated rice (Oryza sativa L.). DXWR, a Chinese type of wild rice grown in Jiangxi Province (28°14’N latitude and 116°30’E longtitude), is considered to be the northernmost region in the world where O. rufipogon is found. DXWR grows in the natural habitats and possesses various characteristics resistant to biotic and abiotic stresses and abundant genetic diversity which have been lost in the cultivated rice. Thus, it is an extremely important resource for providing a valuable gene pool for rice genetic improvement.
• Recently, next-generation high-throughput RNA sequencing technology (RNA-Seq) could overcome the drawbacks of array-based technologies. With the high resolution and sensitivity, the RNA-Seq could be used for discovering novel splice junctions, novel transcripts, alternative transcription start sites and rare transcripts. Moreover, RNA-Seq data revealed a high level of reproducibility in both technical and biological replicates. So far, the global gene expression in various plants has been profiled by RNA-Seq.
• Core sets of transcription factor family genes are differentially expressed in response to elevated external salinity, including basic leucine zipper (bZIP), WRKY,APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF), MYB, basic helix-loophelix (bHLH) [38], and NAC [39] families. These transcription factors, in turn, regulate the expression levels of various genes that may ultimately influence the level of salt tolerance of plants. In rice, recent studies have indicated that a large number of transcription factors were involved in salt stress response, such as OsMYB91, OsbZIP71, OsWRKY42,SERF1, OsTZF1, and OsNAC5.

Plant Culture & Treatment

• Seeds of Dongxiang wild rice (Oryza rufipogon Griff.; Dongxiang County, Jiangxi Province) and rice Xieqingzao B (O. sativa L. ssp. indica) were immersed in distilled water in the dark,and the uniformly germinated seeds were sown in 96-well plates supported by a plastic container. Seeds were grown in a growth chamber, as previously described [12]. The growth culture solution was renewed every 3 days. After the seedlings had been grown for 14 days, they were transferred on their 96-well plates into containers filled with 200 mM NaCl solution, or with control solution for 12 days. The seedlings were then recovered under normal solution for 3 days, and survival rates were calculated. The experiment was a randomized complete block design with three replications. For RNA-Seq analysis, 14-day-old seedlings of Dongxiang wild rice were grown with or without 200 mM NaCl treatment for 3 days and then the leaves (penultimate leaves) and total roots (separated from the culture solution and washed carefully) of these seedlings were collected and immediately frozen in liquid nitrogen, respectively. For RNA extraction from each treatment group, 10 plants were collected and mixed, to minimize the effect of transcriptome unevenness among plants.

Labs working on this Project

• College of Life Sciences, Jiangxi Normal University, Nanchang, China
• Institute for Advanced Study,Jiangxi Normal University, Nanchang, China

Corresponding Author

• Yi Zhou:zhouyi25@mail2.sysu.edu.cn; & Jiankun Xie: xiejiankun@yahoo.com