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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT AND CHARACTERIZATION OF GENETIC RESOURCES FOR AGRONOMIC AND QUALITY TRAITS USING GENOMIC TOOLS Title: Deep transcriptome sequencing reveals the expression of key functional and regulatory genes involved in the abiotic stress signaling pathways in rice

Authors
item Venu, Reddyvaru-Chann -
item Sreerekha, M.V. -
item Nobuta, Kan -
item Madhav, Sheshu -
item Jia, Yulin
item Meyers, Blake -
item Wang, Guo-Liang -

Submitted to: Journal of Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 10, 2013
Publication Date: August 8, 2013
Repository URL: http://handle.nal.usda.gov/10113/57981
Citation: Venu, R.A., Sreerekha, M., Nobuta, K., Madhav, S.M., Jia, Y., Meyers, B.C., Wang, G. 2013. Deep transcriptome sequencing reveals the expression of key functional and regulatory genes involved in the abiotic stress signaling pathways in rice. Journal of Plant Biology. 56:216-231.

Interpretive Summary: Drought, cold and salt are the major abiotic stresses of rice that cause serious threat to secure stable rice production in the US and worldwide. In the present study, the transcription profiles of leaves and roots of the rice cultivar Nipponbare under cold, drought and salt stress conditions were investigated through deep transcriptome sequencing approaches using massively parallel signature sequencing (MPSS) and sequencing by synthesis (SBS). A total of 1.8 to 2.6 million transcript tags were sequenced from the 7 abiotic stressed and control libraries. Among them, a total of 102,630 and 1,414,788 distinct transcripts were obtained from MPSS and SBS technologies, respectively, and 80 to 85% of them matched the genome sequence. A clustering analysis was performed to identify up- and down-regulated genes specifically and commonly expressed in the cold, drought and salt treated plant leaves and roots. A total of 17 (up) and 131 (down) genes in leaves (cold, drought, salt) and 49 (up) and 35 (down) genes in roots (drought and salt) were identified by both MPSS and SBS methods. These differentially expressed genes encode MAPK, SnRK2s, transcription factors, ion transporters, detoxifying proteins, Late Embryogenesis Abundant (LEA) proteins, chaperons, heat shock proteins, and calmodulins. In addition, expressed genes involved in abscisic acid (ABA), ABA biosynthesis, and calcium dependent signaling pathway in the abiotic stress signaling pathways and 305 unique transcription factors (TFs) in the leaf, and 381 in root libraries were also identified. The conserved cis motifs in the promoter regions of up-regulated genes in the stressed libraries were identified. Furthermore, genes specifically induced in the cold, drought and salt stressed libraries were validated using a time course RT-PCR analysis. These validated expressed genes can be used as indicative expressed markers for these stresses. These results provide an unprecedented expression profile of rice genes that may be involved in the abiotic stress signaling pathways in rice.

Technical Abstract: Drought, salt and cold are the major abiotic stresses that limit the rice production and cause serious threat to food security. The identification of the key functional and regulatory genes in the abiotic stress signaling pathways is important for understanding the molecular basis of abiotic stress tolerance in plants. In this study, the transcriptomes of rice Nipponbare leaves and roots under cold, drought, and salt stresses were investigated using Illumina’s massively parallel signature sequencing (MPSS) and sequencing by synthesis (SBS) technologies. About 1.8 to 2.6 million individual signatures were obtained from the seven abiotic stressed and control libraries of the Japonica cultivar Nipponbare. A total of 102,630 and 1,414,788 distinct signatures were obtained from the libraries using MPSS and SBS technologies, respectively. Using the transcripts commonly identified by both MPSS and SBS technologies, we performed clustering analysis to identify up- and down-regulated genes specifically and commonly expressed in the cold, drought and salt-treated plant leaves and roots. Data mining revealed the expression of key functional and regulatory genes involved in the abiotic stress signaling pathways including those encoding mitogen-activated protein kinases (MAPKs), SNF1-related protein kinase 2 (SnRK2s), transcription factors, ion transporters, detoxifying proteins, late embryogenesis abundant (LEA) proteins, chaperons, heat shock proteins, and proteins in the calmodulin, abscisic acid (ABA) signaling, and ABA biosynthesis pathways. Furthermore, genes specifically induced in the cold-, drought-, and salt-stressed libraries were validated with a time-course RT-PCR method.

Last Modified: 10/21/2014