Comparative Analyses of Shoots and Roots Transcriptomics of Two Rice Seedlings (TNG67 vs. TCN1) under Cold or Salt Stress and Subsequent Recovery
Date Issued
2015
Date
2015
Author(s)
Yang, Yun-Wei
Abstract
Abstract Climate changes and environmental stresses become severe over the past few decades. In particular, different abiotic stresses reduce the yield and quality of crop, leading to the threaten of global food security. With the deciphering of rice genome and advancement of functional genomics technology, researchers were able to gradually reveal the mechanism of abiotic stress tolerance mechanisms in rice and to identify essential genes for breeding to improve stress tolerance. In this thesis, we used TNG67 (japonica) and TCN1 (indica) rice cultivars with contrastive tolerance to cold and salt stresses as studying materials. A custom designed oligonucleotide array, Rice OneArray® v1 microarray platform (Phalanx Biotech Group Inc.) was used for transcriptomic analysis of shoot and root tissues of these two cultivars under cold or salt treatment and subsequent recovery. The results showed that TNG67 which is tolerant to cold and salt stresses can enhance TCA (tricarboxylic acid) cycle and PCD (programmed cell death) pathways under cold stress while it shifts to fermentation pathway for energy production and enhances the efficiency of Calvin cycle under salt stress and recovery, respectively. In addition, activation of SOS pathway may partially contribute to salt tolerance of TNG67. Increase of genes expressions related to phytohormone biosynthesis and response of ABA, PA, JA, and auxin can help TNG67 in cold stress tolerance. Besides, maintaining the balance and crosstalk of different hormones through the induction of gene expressions related to ABA, ET, PA, auxin, JA and the decrease of gene expressions associated with GA and CK responses may also be quite important for salt tolerance of TNG67. The crosstalk of ET with CK and JA in rice may play a role in the restoration of cold and salt stress. Also, we investigated the possible transcription factors (TFs) which may be the candidate genes that control cold or salt stress tolerance in rice. The induction or repression of TFs under stresses includes NACs and WRKYs, and MYB and AP2/ERF. NACs and WRKYs were the major TFs that may participate in cold tolerance, and MYB and AP2/ERF may involve in salt stress tolerance. Taken together aforementioned results, the cold- and salt-tolerance exhibit distinct regulatory mechanisms in TNG67 vs. TCN1. Interestingly, comparing the DEGs in shoots or roots of both rice cultivars under stresses, the venn diagram analysis showed that TNG67 and TCN1 shared less differentially expressed genes (DEGs) between cold and salt treatment. Although cold and salt stress can cause similar phenotypes and physiological damages, the molecular basis of cellular regulation mechanism can be quite different. Understanding the difference of cold and salt tolerance mechanisms in details is important in the future for us to breed rice precisely to cope with various abiotic stresses.
Subjects
Rice (Oryza sativa L.)
cold tolerance
gene expression profiling
transcription factor
plant hormone
homeostasis
salt tolerance
ion transporter
Type
thesis
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