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

參考文獻

1. Bray, E.A., Plant responses to water deficit. Trends in Plant Science, 1997. 2(2): p. 48-54.
2. Barros, J., et al., The cell biology of lignification in higher plants. Annals of Botany, 2015. 115(7): p. 1053-1074.
3. Food and Agriculture Organization of the United Nations, The impact of disasters and crises on agriculture and food security. 2021.
4. Lin, O. and E. Syngle, Taiwan Drought Results in Rice Area Reduction and Crop Loss. 2021.
5. Basu, S., et al., Plant adaptation to drought stress. F1000Res, 2016. 5.
6. Shavrukov, Y., et al., Early Flowering as a Drought Escape Mechanism in Plants: How Can It Aid Wheat Production? Front Plant Sci, 2017. 8: p. 1950.
7. Fang, Y. and L. Xiong, General mechanisms of drought response and their application in drought resistance improvement in plants. Cell Mol Life Sci, 2015. 72(4): p. 673-89.
8. Izanloo, A., et al., Different mechanisms of adaptation to cyclic water stress in two South Australian bread wheat cultivars. J Exp Bot, 2008. 59(12): p. 3327-46.
9. Hasanuzzaman, M. and M. Fujita, Selenium pretreatment upregulates the antioxidant defense and methylglyoxal detoxification system and confers enhanced tolerance to drought stress in rapeseed seedlings. Biol Trace Elem Res, 2011. 143(3): p. 1758-76.
10. Guan, Y.S., et al., Simultaneously improving yield under drought stress and non-stress conditions: a case study of rice (Oryza sativa L.). J Exp Bot, 2010. 61(15): p. 4145-56.
11. Kaur, G. and B. Asthir, Molecular responses to drought stress in plants. Biologia Plantarum, 2017. 61(2): p. 201-209.
12. Shekoofa, A. and T.R. Sinclair Aquaporin Activity to Improve Crop Drought Tolerance. Cells, 2018. 7, DOI: 10.3390/cells7090123.
13. Jarzyniak, K.M. and M. Jasiński, Membrane transporters and drought resistance – a complex issue. Frontiers in Plant Science, 2014. 5.
14. Hong-Bo, S., L. Zong-Suo, and S. Ming-An, LEA proteins in higher plants: structure, function, gene expression and regulation. Colloids Surf B Biointerfaces, 2005. 45(3-4): p. 131-5.
15. Miller, G., et al., Reactive oxygen species homeostasis and signalling during drought and salinity stresses. Plant Cell Environ, 2010. 33(4): p. 453-67.
16. Laxa, M., et al., The Role of the Plant Antioxidant System in Drought Tolerance. Antioxidants (Basel), 2019. 8(4).
17. Ahmad, P., et al., Generation of ROS and non-enzymatic antioxidants during abiotic stress in plants. Botany Research International, 2009. 2(1): p. 11-20.
18. Ullah, A., et al., Phytohormones enhanced drought tolerance in plants: a coping strategy. Environmental Science and Pollution Research, 2018. 25(33): p. 33103-33118.
19. Singh, P.K., et al., Genomic and proteomic responses to drought stress and biotechnological interventions for enhanced drought tolerance in plants. Current Plant Biology, 2022. 29.
20. Shinozaki, K. and K. Yamaguchi-Shinozaki, Gene networks involved in drought stress response and tolerance. J Exp Bot, 2007. 58(2): p. 221-7.
21. Shailani, A., et al., Stacking for future: Pyramiding genes to improve drought and salinity tolerance in rice. Physiol Plant, 2021. 172(2): p. 1352-1362.
22. Sah, S.K., K.R. Reddy, and J. Li, Abscisic Acid and Abiotic Stress Tolerance in Crop Plants. Frontiers in Plant Science, 2016. 7.
23. Cutler, S.R., et al., Abscisic acid: emergence of a core signaling network. Annual review of plant biology, 2010. 61: p. 651-679.
24. Choi, H.-i., et al., ABFs, a family of ABA-responsive element binding factors. Journal of Biological Chemistry, 2000. 275(3): p. 1723-1730.
25. Agarwal, P.K., et al., Role of DREB transcription factors in abiotic and biotic stress tolerance in plants. Plant cell reports, 2006. 25: p. 1263-1274.
26. Yoshida, T., J. Mogami, and K. Yamaguchi-Shinozaki, ABA-dependent and ABA-independent signaling in response to osmotic stress in plants. Current Opinion in Plant Biology, 2014. 21: p. 133-139.
27. Joshi, R., et al., Transcription Factors and Plants Response to Drought Stress: Current Understanding and Future Directions. Front Plant Sci, 2016. 7: p. 1029.
28. Mukhopadhyay, M., T.K. Mondal, and P.K. Chand, Biotechnological advances in tea (Camellia sinensis [L.] O. Kuntze): a review. Plant Cell Reports, 2016. 35(2): p. 255-287.
29. Drew, L., The growth of tea. Nature, 2019. 566(7742): p. S2-s4.
30. Wei, C., et al., Draft genome sequence of <i>Camellia sinensis</i> var. <i>sinensis</i> provides insights into the evolution of the tea genome and tea quality. Proceedings of the National Academy of Sciences, 2018. 115(18): p. E4151-E4158.
31. Food and Agriculture Organization of the United Nations, International tea market: market situation, prospects and emerging issues. 2022.
32. Sun, Y., J. Zhou, and J. Guo, Advances in the knowledge of adaptive mechanisms mediating abiotic stress responses in Camellia sinensis. Front Biosci (Landmark Ed), 2021. 26(12): p. 1714-1722.
33. Cheruiyot, E.K., et al., High Fertilizer Rates Increase Susceptibility of Tea to Water Stress. Journal of Plant Nutrition, 2009. 33(1): p. 115-129.
34. Yang, H., et al., Genetic Divergence between Camellia sinensis and Its Wild Relatives Revealed via Genome-Wide SNPs from RAD Sequencing. PLoS One, 2016. 11(3): p. e0151424.
35. Koech, R.K., et al., Identification of novel QTL for black tea quality traits and drought tolerance in tea plants (Camellia sinensis). Tree Genetics & Genomes, 2018. 14(1).
36. Zhang, Z.B., et al., Understanding the Origin and Evolution of Tea (Camellia sinensis [L.]): Genomic Advances in Tea. J Mol Evol, 2023. 91(2): p. 156-168.
37. Wang, X., et al., Population sequencing enhances understanding of tea plant evolution. Nat Commun, 2020. 11(1): p. 4447.
38. Collard, B.C. and D.J. Mackill, Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philosophical Transactions of the Royal Society B: Biological Sciences, 2008. 363(1491): p. 557-572.
39. Hasan, N., et al., Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes. Journal of Genetic Engineering and Biotechnology, 2021. 19(1): p. 128.
40. Bali, S., et al., Construction of a genetic linkage map and mapping of drought tolerance trait in Indian beveragial tea. Molecular Breeding, 2015. 35(5).
41. Parmar, R., et al., Transcriptional profiling of contrasting genotypes revealed key candidates and nucleotide variations for drought dissection in Camellia sinensis (L.) O. Kuntze. Sci Rep, 2019. 9(1): p. 7487.
42. Gupta, S., et al., Identification of drought tolerant progenies in tea by gene expression analysis. Funct Integr Genomics, 2012. 12(3): p. 543-63.
43. Maritim, T.K., et al., Physiological and biochemical response of tea [Camellia sinensis(L.) O. Kuntze] to water-deficit stress. The Journal of Horticultural Science and Biotechnology, 2015. 90(4): p. 395-400.
44. Liu, S.-C., et al., Physiological changes and differential gene expression of tea plant under dehydration and rehydration conditions. Scientia Horticulturae, 2015. 184: p. 129-141.
45. Cheruiyot, E.K., et al., Polyphenols as potential indicators for drought tolerance in tea (Camellia sinensis L.). Biosci Biotechnol Biochem, 2007. 71(9): p. 2190-7.
46. Wang, W., et al., Overexpression of Camellia sinensis H1 histone gene confers abiotic stress tolerance in transgenic tobacco. Plant Cell Rep, 2014. 33(11): p. 1829-41.
47. Wang, M., et al., Overexpression of a Camellia sinensis DREB transcription factor gene (CsDREB) increases salt and drought tolerance in transgenic Arabidopsis thaliana. Journal of Plant Biology, 2017. 60(5): p. 452-461.
48. Lo, Y.H., et al., Teaghrelins, unique acylated flavonoid tetraglycosides in Chin-shin oolong tea, are putative oral agonists of the ghrelin receptor. J Agric Food Chem, 2014. 62(22): p. 5085-91.
49. Liu, S.C., et al., Transcriptomic Analysis of Tea Plant Responding to Drought Stress and Recovery. PLoS One, 2016. 11(1): p. e0147306.
50. Zhang, Q., et al., Transcriptome dynamics of Camellia sinensis in response to continuous salinity and drought stress. Tree Genetics & Genomes, 2017. 13(4).
51. Zhang, X., et al., Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis. Nature Genetics, 2021. 53(8): p. 1250-1259.
52. Kanehisa, M., Y. Sato, and K. Morishima, BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences. Journal of Molecular Biology, 2016. 428(4): p. 726-731.
53. Lu, D., et al., Transcriptional control of ROS homeostasis by KUODA1 regulates cell expansion during leaf development. Nat Commun, 2014. 5: p. 3767.
54. Jogawat, A., et al., Crosstalk between phytohormones and secondary metabolites in the drought stress tolerance of crop plants: A review. Physiol Plant, 2021. 172(2): p. 1106-1132.
55. Miura, K. and Y. Tada, Regulation of water, salinity, and cold stress responses by salicylic acid. Front Plant Sci, 2014. 5: p. 4.
56. Lefevere, H., L. Bauters, and G. Gheysen, Salicylic Acid Biosynthesis in Plants. Front Plant Sci, 2020. 11: p. 338.
57. Thomazella, D.P.T., et al., Loss of function of a DMR6 ortholog in tomato confers broad-spectrum disease resistance. Proc Natl Acad Sci U S A, 2021. 118(27).
58. Liu, N., et al., Transcriptional Analysis of Tea Plants (Camellia sinensis) in Response to Salicylic Acid Treatment. J Agric Food Chem, 2023. 71(5): p. 2377-2389.
59. Seyfferth, C. and K. Tsuda, Salicylic acid signal transduction: the initiation of biosynthesis, perception and transcriptional reprogramming. Front Plant Sci, 2014. 5: p. 697.
60. Zhang, S., et al., Cooperative Regulation of Flavonoid and Lignin Biosynthesis in Plants. Critical Reviews in Plant Sciences, 2021. 40(2): p. 109-126.
61. Wang, Y., et al., Proteomic analysis of Camellia sinensis (L.) reveals a synergistic network in the response to drought stress and recovery. J Plant Physiol, 2017. 219: p. 91-99.
62. Barragán, V., et al., Ion Exchangers NHX1 and NHX2 Mediate Active Potassium Uptake into Vacuoles to Regulate Cell Turgor and Stomatal Function in Arabidopsis The Plant Cell, 2012. 24(3): p. 1127-1142.
63. Klein, M., et al., Disruption of AtMRP4, a guard cell plasma membrane ABCC-type ABC transporter, leads to deregulation of stomatal opening and increased drought susceptibility. Plant J, 2004. 39(2): p. 219-36.
64. Remy, E., et al., A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis. Plant Cell, 2013. 25(3): p. 901-26.
65. Kuromori, T., et al., Functional relationship of AtABCG21 and AtABCG22 in stomatal regulation. Sci Rep, 2017. 7(1): p. 12501.
66. Nour-Eldin, H.H., et al., NRT/PTR transporters are essential for translocation of glucosinolate defence compounds to seeds. Nature, 2012. 488(7412): p. 531-4.
67. Chiba, Y., et al., Identification of Arabidopsis thaliana NRT1/PTR FAMILY (NPF) proteins capable of transporting plant hormones. J Plant Res, 2015. 128(4): p. 679-86.
68. Upadhyay, N., et al., The multitasking abilities of MATE transporters in plants. J Exp Bot, 2019. 70(18): p. 4643-4656.
69. Jiang, L., et al., SWEET Transporters and the Potential Functions of These Sequences in Tea (Camellia sinensis). Front Genet, 2021. 12: p. 655843.
70. Wang, P., et al., Exploration of the Effects of Different Blue LED Light Intensities on Flavonoid and Lipid Metabolism in Tea Plants via Transcriptomics and Metabolomics. International Journal of Molecular Sciences, 2020. 21(13).
71. Van Houtte, H., et al., Overexpression of the trehalase gene AtTRE1 leads to increased drought stress tolerance in Arabidopsis and is involved in abscisic acid-induced stomatal closure. Plant Physiol, 2013. 161(3): p. 1158-71.
72. Bird, D., et al., Characterization of Arabidopsis ABCG11/WBC11, an ATP binding cassette (ABC) transporter that is required for cuticular lipid secretion. Plant J, 2007. 52(3): p. 485-98.

指導教授

葉淑丹(Shu-Dan Yeh)

審核日期

2023-7-6

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