Comparative transcriptome analysis reveals key pathways underlying drought stress tolerance and characterizes genetic variations for selective breeding in tea plants, Camellia sinensis

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黎黃魁元(Le Hoang Khoi Nguyen) 查詢紙本館藏

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生命科學系

論文名稱

(Comparative transcriptome analysis reveals key pathways underlying drought stress tolerance and characterizes genetic variations for selective breeding in tea plants, Camellia sinensis)

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至系統瀏覽論文 (2029-7-31以後開放)

摘要(中)

栽培耐旱的茶樹（Camellia sinensis）可為解決日益頻繁且嚴重的乾旱問題提供一個永續性方法，然而，目前對茶樹耐旱分子遺傳機制的了解有限，致使此方法的執行仍然困難。本研究旨在比較具親緣關係但乾旱耐受性不同的四個茶樹品種，在缺水處理下彼此間的轉錄體調控差異，並且找出與耐旱相關的潛在分子標誌。分析結果顯示，參與苯丙素類生合成、抗氧化酶和主動穿膜運輸系統的基因表現量，在耐旱品種顯著升高，暗示著茶樹藉由累積二次代謝產物和抗氧化酶來防禦因缺水所導致的氧化壓力。此外，bZIP、bHLH、NAC、AP2/ERF、MYB、和WRKY等可能調控乾旱反應和抗氧化物生合成相關基因表現的轉錄因子，在耐旱茶樹品種缺水前後的表現量有顯著差異，在非耐旱品種則不然。從四個茶樹品種間的親緣關係可推導出位於蛋白質序列編碼區的34,426個非同義的單點核苷酸多型性位點（SNP）和1,184個插入/缺失，其中28個SNP座落於14個與耐旱性有關的關鍵轉錄因子基因上，更顯示這些遺傳變異作為遺傳標誌的潛能。本研究所得到的結果為茶樹耐旱性的分子機制提供新見解，並且在為了改良茶樹品種特性而進行遺傳操控和標記輔助篩選時，提供了重要基因體資訊。

摘要(英)

Breeding for drought adaptation in tea plants, Camellia sinensis, is a sustainable way to address the emerging issues of more frequent and severe droughts. However, this task remains difficult due to limited understanding of the genetic basis of drought tolerance in tea. This study aimed to investigate the transcriptomic profiles of four genetically-related tea cultivars differing in drought responses (tolerant and sensitive) under dehydration treatment and discover putative molecular markers associated with drought tolerance. Genes involved in salicylic biosynthesis and signal transduction, phenylpropanoid biosynthetic pathways, transmembrane transport systems were significantly up-regulated in tolerant cultivars, suggesting the accumulation of secondary metabolites induced by salicylic acid as an antioxidative defensive mechanism during water-deficit condition in tea. Additionally, several transcription factors (bZIP, bHLH, NAC, AP2/ERF, MYB, WRKY) probably engaging in the regulation of drought-responsive gene expression and biosynthetic pathways of antioxidants were differentially expressed in tolerant but not sensitive cultivars. A total of 34426 non-synonymous SNPs and 1184 InDels located on protein coding regions were inferred from the genetic inheritance of the four tea cultivars. Among these, 28 SNPs were characterized from 14 key transcription factors related to drought tolerance, highlighting their potential implications as genetic markers for genotyping in tea. These results provide novel insight of drought-defensive responses at molecular level and genomic resources for genetic manipulation and marker-assisted selection in tea crop improvement.

關鍵字(中)

★ Camellia sinensis
★ 耐旱
★ 轉錄
★ 遺傳變異

關鍵字(英)

★ Camellia sinensis
★ drought tolerance
★ transcriptome
★ genetic variation

論文目次

中文摘要 i
Abstract ii
Acknowledgements iii
Table of Contents iv
List of Figures vii
List of Tables viii
Abbreviations ix
Chapter I. Introduction 1
1.1 Plant adaptations to drought stress 1
1.2 Drought tolerance-related mechanisms in plants 2
1.2.1 Osmotic adjustments 2
1.2.2 Antioxidant defense systems 2
1.2.3 Phytohormonal activities 2
1.3 Molecular basis of drought tolerance in plants 3
1.4 Tea plant, Camellia sinensis 4
1.4.1 Tea plantation: importance and challenges due to drought 4
1.4.2 Breeding for drought tolerant tea cultivars 4
1.4.3 Molecular basis of drought tolerance in tea plants 5
1.4.4 Taiwanese tea cultivars 5
1.5 Specific aims of this study 7
Chapter II. Materials & Methods 8
2.1 Tea plant materials 8
2.2 Tea plant reference genome 8
2.3 Dehydration treatment 8
2.4 RNA isolation, cDNA library preparation and sequencing 8
2.5 Data analysis 9
2.5.1 Functional annotation for the reference genome 9
2.5.2 Quality control of RNA-seq data 10
2.5.3 Reference-based read mapping 10
2.5.4 Differential gene expression analysis 10
2.5.5 Functional enrichment analysis 10
2.5.6 Variant calling, filtering, and annotation 11
Chapter III. Results 12
3.1 Functional annotation of reference genome 12
3.2 Summary of RNA sequencing quality control 12
3.3 Differentially expressed genes in tea plants during dehydration treatment 12
3.3.1 Background genes and differentially expressed genes 12
3.3.2 Top significant drought-responsive DEGs 13
3.3.3 Common and unique drought-responsive DEGs among cultivars 13
3.4 Over-representation analysis of DEGs in response to dehydration treatment 14
3.4.1 GO enrichment analysis 14
3.4.2 KEGG enrichment analysis 16
3.5 Transcriptome dynamics of key genes related to drought tolerance 17
3.5.1 Plant hormone transduction 17
3.5.2 Phenylpropanoid biosynthetic pathways and antioxidant defenses 18
3.5.3 Transmembrane transporter and aquaporin activities 20
3.5.4 Differential expression of transcription factors 22
3.6 Identification of genetic variations related to drought tolerance 23
Chapter IV. Discussion 25
4.1 Quality of reference-base mapping and functional annotation of tea genome 25
4.2 Difference in the number of drought-responsive DEGs among tea cultivars 25
4.3 SA biosynthesis and signal transduction may induce drought tolerance 26
4.4 Phenylpropanoid biosynthetic pathways are involved in drought adaptation as an antioxidative defense 27
4.5 Diverse roles of transporters and aquaporins in drought tolerance-related processes 28
4.6 Key drought tolerance-related transcription factors 29
4.7 Molecular factors causing drought-sensitivity in Chin Shin Oolong 30
4.8 Effects of genetic variations and their implications in future tea breeding programs 30
Chapter V: Conclusion 31
References 32
Appendix A 36
Appendix B 37
Appendix C 38
Appendix D 40
Appendix E 41

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指導教授

葉淑丹(Shu-Dan Yeh)

審核日期

2023-7-6

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