臺灣博碩士論文加值系統

摘要
近年來氣候變遷與環境變化所產生之逆境愈形劇烈，在各種非生物逆境下將導致作物品質與產量的水平下降，進而影響全球糧食的供給。隨著水稻基因組的解碼與功能性基因體技術的進步，專家學者們將能更進一步了解水稻抗逆境的機制並探索耐逆境相關的重要基因，以加速耐逆境水稻的育種過程。在此論文中，我們利用可耐低溫與鹽逆境之梗稻品種台農67號與對此兩種逆境敏感之秈稻品種台中在來1號為材料，並使用水稻表達譜晶片Rice OneArray® v1為轉錄分析平台進行研究。除了分析兩品種的莖部與根部於逆境下的基因表現，我們更進一步分析於逆境處理後之回復期的基因變化。結果顯示，台農67號於低溫下會促進檸檬酸循環(tricarboxylic acid)與程序性細胞凋亡 (programmed cell death)；於鹽逆境處理下會透過無氧呼吸(fermentation)產生能量並於鹽回復處理下提升卡爾文循環。此外，鹽逆境下Salt Overly Sensitive (SOS) 排鹽機制似乎對台農67號的耐鹽性有部分貢獻。根據與賀爾蒙相關之基因的表現趨勢進行推測，低溫下增強對離層酸(abscisic acid)、多元胺(polyamine)、茉莉花酸(jasmonic acid)與生長素(auxin)的反應會提升其低溫耐性。鹽逆境下，除了增加對離層酸、多元胺、茉莉花酸、生長素與乙烯(ethylene)的反應外，同時也需降低其對激勃素(gibberellin)及細胞分裂素(cytokinins)之反應，此結果顯示不同賀爾蒙之間的協同作用對耐鹽性之重要。而逆境消退後，乙烯與細胞分裂素的共同作用有利於水稻歷經低溫逆境後回復生長，而茉莉花酸則是參與在鹽逆境之回復期。在轉錄因子的調控方面，NAC與WRKY型之轉錄因子與低溫耐性具相關性，而MYB與AP2/ERF型之轉錄因子則可能參與耐鹽性機制。此外，兩品種於低溫與鹽逆境下所呈現出的“具差異性表現之基因”(differentially expressed genes)非常不同。雖然低溫與鹽逆境會導致類似的表徵性狀與生理損害，然而由其基因之表現可知，兩者於細胞層次上的分子調控機制存在很大的差異。若能愈清楚地了解水稻之低溫與鹽逆境耐性的機制，將有助於我們日後更精準的育成具不同非生物性逆境耐性的品種。

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.

Table of Contents
摘要 i
Abstract iii
Table of Contents 1
Tables 3
Figures 4
Abbreviations 6
Chapter 1 7
General introduction 7
Chapter 2 10
Comparative transcriptomics analysis of shoots and roots of TNG67 and TCN1 rice seedlings under cold stress and following subsequent recovery: insights into metabolic pathways, phytohormones, and transcription factors 10
Abstract 10
Introduction 11
Materials and Methods 16
Results 19
Discussion 34
Conclusions 47
Chapter 3 81
Transcriptomics analysis of shoots and roots in contrary salt-tolerance cultivars of TNG67 and TCN1 rice seedlings under salt stress and subsequent recovery 81
Abstract 81
Introduction 82
Materials and Methods 86
Results 87
Discussion 99
Conclusions 112
Chapter 4 136
Overall Conclusions and Future Perspectives 136
References 143

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