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研究生:陳冠全
研究生(外文):Kuan-Chuan Chen
論文名稱:水稻幼苗於鹽害下根部及地上部光合作用數量性狀之基因座定位與分析
論文名稱(外文):QTL mapping for root traits and shoot photosynthesis under salinity stress in rice seedling
指導教授:董致韡
口試委員:劉力瑜蔡育彰
口試日期:2016-05-11
學位類別:碩士
校院名稱:國立臺灣大學
系所名稱:農藝學研究所
學門:農業科學學門
學類:一般農業學類
論文種類:學術論文
論文出版年:2016
畢業學年度:104
語文別:英文
論文頁數:164
中文關鍵詞:水稻幼苗根部性狀葉綠素螢光關聯性定位鹽逆境
外文關鍵詞:association mappingchlorophyll fluorescencerice seedlingroot traitsalinity stress
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水稻為世界上重要的糧食作物,而隨著環境的變遷及人口的急遽飆升,大量增加水稻的產量為重要的課題,為了使得水稻能種植於更多的區域以增加產量,提升水稻抗逆境的能力是有效的方法之一,鹽害為主要的非生物性逆境之一,水稻又屬於極度不耐鹽的作物,因此增加水稻的耐鹽能力有助於提升整體的產量。本研究中,我們使用東南亞地區的種原,觀察三種不同型態的根的表現。在全基因體關聯性分析(genome-wide association mapping, GWAS)中,共偵測到16個顯著的基因座與根長變化相關。其中兩個基因座與前人使用不同族群進行關聯性分析的結果相當接近。此外,我們使用葉綠素螢光來測量鹽害下葉片的光合作用利用效率,而從預備試驗的結果可以發現,鹽害下,水稻幼苗於第九天的實際光合作用利用效率 (effective PSII quantum yield, ΦPSII) 與第十一天的鹽害指數 (Injury score) 呈現中度相關 (r = -0.588),推測葉片的光合作用利用效率以及其修復系統的受損程度對於水稻的耐鹽性是重要的。在全基因體關聯性分析中,共偵測到32個與葉綠素螢光性狀相關的基因座。有兩個與耐鹽機制相關的基因 - OsNHX3 與 OsCBL4則座落於我們所定義的候選區域。最後,我們利用全球水稻種,同時分析水稻根部與地上部的性狀,發現此兩種性狀的表現是互相獨立的。然而我們也觀察到在根部及地上部皆表現優良的品種。我們期望這些品種能用於未來水稻育種並提升水稻的耐鹽性。

To increase the yield production, the crops may have to grow in the harsh environment. Salinity is one of the major abiotic stresses, and rice is very sensitive to increasing salts. In this study, we evaluated three different root types performance in South East Asia rice varieties, total sixteen loci were detected using genome-wide association mapping (GWAS), and two were found in previous study. In addition, chlorophyll fluorescence was used to measure the leaf photosynthesis rate under salt stress. The pilot experiment showed the effective PSII quantum yield (ΦPSII) on day 9 and Injury score (IS) on day 11 was moderately correlated (r = -0.588), suggesting the damage level of leaf photosynthesis rate and its repairing mechanism may be crucial for salinity tolerance in rice. Total 32 significant loci were detected by GWAS in five chlorophyll fluorescence related traits. Among these loci, two genes OsNHX3 and OsCBL4 related to salinity tolerance mechanisms were detected in the candidate regions. Finally, we analyzed root and shoot traits in diverse accessions and found that performance of shoot and root is independent under salt stress We expect these varieties could be used to improve salt tolerance through QTLs pyramiding approach in rice breeding program.

口試委員會審定書 i
誌謝 ii
摘要 iii
Abstract iv
Table of contents v
Figure index vii
Table index xi
Abbreviation xiv
Chapter 1. Introduction 1
Background 1
Salinity tolerance mechanisms in rice 1
Salinity-related QTL mapping in rice 3
Root performance under salinity stress 5
Photosynthetic performance under salinity stress 7
Chlorophyll fluorescence 9
Chapter 2. Materials and Methods 14
Plant material and growth condition 14
Root length measurement 17
Chlorophyll fluorescence imaging for pilot 1 experiment 18
Chlorophyll fluorescence imaging for pilot 2 and GWAS experiment 20
Traits used for GWAS 21
Genome-wide Association Analysis 23
Statistical analysis 24
Chapter 3. QTL mapping of root trait in rice seedling stage under the salinity stress 25
Phenotypic variation of root length 25
GWAS result of root traits 26
Chapter 4. QTL mapping of shoot trait in rice seedling stage under the salinity stress 31
Pilot experiment 1 31
Pilot experiment 2 32
GWAS of fluorescence parameters on salt-treated second leaf 35
Chapter 5. Discussion 46
Root 46
Shoot 50
Salt tolerance: a complex trait 59
Conclusion 59
Reference 61
R scripts used in analysis 158


林士弘 (2014). 水稻幼苗在鹽逆境之根部數量性狀基因座定位分析, 國立臺灣大學.
Abdelkader, A. F., S. El-khawas, N. A. S. E.-D. El-Sherif, R. A. Hassanein, M. A. Emam and R. E.-S. Hassan (2012). Expression of aquaporin gene (OsPIP1-3) in salt-stressed rice (Oryza sativa L.) plants pre-treated with the neurotransmitter (dopamine). Plant Omics 5(6): 532-541.

Ahmadi, J. and M.-H. Fotokian (2011). Identification and mapping of quantitative trait loci associated with salinity tolerance in rice (Oryza sativa) using SSR markers. Iran. J. Biotechnol. 9(1): 21-30.

Allakhverdiev, S. I., D. A. Los, P. Mohanty, Y. Nishiyama and N. Murata (2007). Glycinebetaine alleviates the inhibitory effect of moderate heat stress on the repair of photosystem II during photoinhibition. Biochim Biophys Acta 1767(12): 1363-1371.

Allakhverdiev, S. I., Y. Nishiyama, S. Miyairi, H. Yamamoto, N. Inagaki, Y. Kanesaki and N. Murata (2002). Salt stress inhibits the repair of photodamaged photosystem II by suppressing the transcription and translation of psbA genes in Synechocystis. Plant Physiology 130(3): 1443-1453.

Ammar, M. H. M., R. K. Singh, A. K. Singh, T. Mohapatra, T. R. Sharma and N. K. Singh (2007). Mapping QTLs for salinity tolerance at seedling stage in rice (Oryza sativa L.). African Crop Sci. Conf. Proceed. 8: 617-620.

Ashraf, M. and P. J. C. Harris (2013). Photosynthesis under stressful environments: An overview. Photosynthetica 51(2): 163-190.

Baker, N. R. (2008). Chlorophyll fluorescence: a probe of photosynthesis in vivo. Annu Rev Plant Biol 59: 89-113.



Balkan, A., T. Genctan, O. Bilgin and H. Ulukan (2015). Response of rice (Oryza sativa L.) to salinity stress at germination and early seedling stages. Pakistan Journal of Agricultural Sciences 52(2): 455-461.

Barrett, J. C., B. Fry, J. Maller and M. J. Daly (2005). Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21(2): 263-265.

Björkman, O. and B. Demmig (1987). Photon tield of O2 evolution and chlorophyll flourescence characteristics at 77K among vascular plant of diverse origins. Planta 170: 489-504.

Bradbury, P. J., Z. Zhang, D. E. Kroon, T. M. Casstevens, Y. Ramdoss and E. S. Buckler (2007). TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23(19): 2633-2635.

Bulter, W. L. (1978). Energy distribution in the photochemical apparatus of photosynthesis. Ann. Rev. Plant Physiol 29: 345-378

Cheng, L., Y. Wang, L. Meng, X. Hu, Y. Cui, Y. Sun, L. Zhu, J. Ali, J. Xu and Z. Li (2012). Identification of salt-tolerant QTLs with strong genetic background effect using two sets of reciprocal introgression lines in rice. Genome 55(1): 45-55.

Clark, R. T., A. N. Famoso, K. Zhao, J. E. Shaff, E. J. Craft, C. D. Bustamante, S. R. McCouch, D. J. Aneshansley and L. V. Kochian (2013). High-throughput two-dimensional root system phenotyping platform facilitates genetic analysis of root growth and development. Plant Cell Environ 36(2): 454-466.

Costa, E. S., R. Bressan-Smith, J. Goncalves de Oliveira, E. Campostrini and C. Pimentel (2002). Photochemical efficiency in bean plants (Phaseolus vulgaris L. and Vigna unguiculata L. Walp) during recovery from high temperature stress. Brazilian Journal of Plant Physiology 14(2): 105-110.

Dionisio-Sese, M. L. and S. Tobita (2000). Effects of salinity on sodium content and photosynthetic responses of rice seedlings differing in salt tolerance. Journal of Plant Physiology 157(1): 54-58.

Fukuda, A., A. Nakamura, N. Hara, S. Toki and Y. Tanaka (2011). Molecular and functional analyses of rice NHX-type Na+/H+ antiporter genes. Planta 233(1): 175-188.

Fukuda, A., A. Nakamura, A. Tagiri, H. Tanaka, A. Miyao, H. Hirochika and Y. Tanaka (2004). Function, intracellular localization and the importance in salt tolerance of a vacuolar Na+/H+ antiporter from rice. Plant and Cell Physiology 45(2): 146-159.

Ghomi, K., B. Rabiei, H. Sabouri and A. Sabouri (2013). Mapping QTLs for traits related to salinity tolerance at seedling stage of rice (Oryza sativa L.): an agrigenomics study of an Iranian rice population. OMICS 17(5): 242-251.

Gu, Z., B. Ma, Y. Jiang, Z. Chen, X. Su and H. Zhang (2008). Expression analysis of the calcineurin B-like gene family in rice (Oryza sativa L.) under environmental stresses. Gene 415(1-2): 1-12.

Guo, L., Z. Y. Wang, H. Lin, W. E. Cui, J. Chen, M. Liu, Z. L. Chen, L. J. Qu and H. Gu (2006). Expression and functional analysis of the rice plasma-membrane intrinsic protein gene family. Cell Res 16(3): 277-286.

Gururani, M. A., J. Venkatesh and L. S. Tran (2015). Regulation of Photosynthesis during Abiotic Stress-Induced Photoinhibition. Mol Plant 8(9): 1304-1320.

Hairmansis, A., B. Berger, M. Tester and S. J. Roy (2014). Image-based phenotyping for non-destructive screening of different salinity tolerance traits in rice. Rice 7, 16.

Hakim, M. A., A. S. Juraimi, M. Begum, M. M. Hanafi, M. R. Ismail and A. Selamat (2010). Effect of salt stress on germination and early seedling growth of rice (Oryza sativa L.). African Journal of Biotechnology 9(13): 1911-1918.

Haq, T. U., J. Gorham, J. Akhtar, N. Akhtar and K. A. Steele (2010). Dynamic quantitative trait loci for salt stress components on chromosome 1 of rice. Functional Plant Biology 37(7): 634-645.

Hill, W. and A. Robertson (1968). Linkage disequilibrium in finite populations. Theoretical and Applied Genetics 38: 226-231.
IRRI (2002). Standard Evaluation System for rice, International Rice Research Institute. Philippine: 38.

Kawahara, Y., M. de la Bastide, J. P. Hamilton, H. Kanamori, W. R. McCombie, S. Ouyang, D. C. Schwartz, T. Tanaka, J. Wu, S. Zhou, K. L. Childs, R. M. Davidson, H. Lin, L. Quesada-Ocampo, B. Vaillancourt, H. Sakai, S. S. Lee, J. Kim, H. Numa, T. Itoh, C. R. Buell and T. Matsumoto (2013). Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice 6, 4.

Kim, S. G., S. Lee, P. J. Seo, S. K. Kim, J. K. Kim and C. M. Park (2010). Genome-scale screening and molecular characterization of membrane-bound transcription factors in Arabidopsis and rice. Genomics 95(1): 56-65.

Kornyeyev, D., B. A. Logan, P. Payton, R. D. Allen and A. S. Holaday (2001). Enhanced photochemical light utilization and decreased chilling-induced photoinhibition of photosystem II in cotton overexpressing genes encoding chloroplast-targeted antioxidant enzymes. Physiologia Plantarum 113(3): 323-331.

Kumar, V., A. Singh, S. V. Mithra, S. L. Krishnamurthy, S. K. Parida, S. Jain, K. K. Tiwari, P. Kumar, A. R. Rao, S. K. Sharma, J. P. Khurana, N. K. Singh and T. Mohapatra (2015). Genome-wide association mapping of salinity tolerance in rice (Oryza sativa). DNA Res 22(2): 133-145.

Kusumi, K., Y. Chono, H. Shimada, E. Gotoh, M. Tsuyama and K. Iba (2010). Chloroplast biogenesis during the early stage of leaf development in rice. Plant Biotechnology 27(1): 85-90.

Lee, M. H., E. J. Cho, S. G. Wi, H. Bae, J. E. Kim, J. Y. Cho, S. Lee, J. H. Kim and B. Y. Chung (2013). Divergences in morphological changes and antioxidant responses in salt-tolerant and salt-sensitive rice seedlings after salt stress. Plant Physiol Biochem 70: 325-335.

Lee, S. Y., J. H. Ahn, Y. S. Cha, D. W. Yun, M. C. Lee, J. C. Ko, K. S. Lee and M. Y. Eun (2007). Mapping QTLs related to salinity tolerance of rice at the young seedling stage. Plant Breeding 126(1): 43-46.
Lin, H. X., M. Z. Zhu, M. Yano, J. P. Gao, Z. W. Liang, W. A. Su, X. H. Hu, Z. H. Ren and D. Y. Chao (2004). QTLs for Na+ and K+ uptake of the shoots and roots controlling rice salt tolerance. Theor Appl Genet 108(2): 253-260.

Lipka, A. E., F. Tian, Q. Wang, J. Peiffer, M. Li, P. J. Bradbury, M. A. Gore, E. S. Buckler and Z. Zhang (2012). GAPIT: genome association and prediction integrated tool. Bioinformatics 28(18): 2397-2399.

Lutts, S., J. M. Kinet and J. Bouharmont (1996). NaCl-induced senescence in leaves of rice (Oryza sativa L) cultivars differing in salinity resistance. Annals of Botany 78(3): 389-398.

Martinez-Atienza, J., X. Jiang, B. Garciadeblas, I. Mendoza, J. K. Zhu, J. M. Pardo and F. J. Quintero (2007). Conservation of the salt overly sensitive pathway in rice. Plant Physiol 143(2): 1001-1012.

Misra, AN., M. Misra and R. Singh (2012). Chlorophyll Fluorescence in Plant Biology. In Misra AN (ed) Biophysics. InTech. DOI: 10.5772/35111.

Moradi, F. and A. M. Ismail (2007). Responses of Photosynthesis, Chlorophyll Fluorescence and ROS-Scavenging Systems to Salt Stress During Seedling and Reproductive Stages in Rice. Annals of Botany 99(6): 1161-1173.

Munns, R. and M. Tester (2008). Mechanisms of salinity tolerance. Annu Rev Plant Biol 59: 651-681.

Negrão, S., B. Courtois, N. Ahmadi, I. Abreu, N. Saibo and M. M. Oliveira (2011). Recent Updates on Salinity Stress in Rice: From Physiological to Molecular Responses. Critical Reviews in Plant Sciences 30(4): 329-377.

Nishiyama, Y. and N. Murata (2014). Revised scheme for the mechanism of photoinhibition and its application to enhance the abiotic stress tolerance of the photosynthetic machinery. Appl Microbiol Biotechnol 98(21): 8777-8796.



Prasad, S. R., P. G. Bagali, S. Hittalmani and H. E. Shashidhar (2000). Molecular mapping of quantitative trait loci associated with seedling tolerance to salt stress in rice (Oryza sativa L.). Current Science 78(2): 162-164.

Price, A. L., N. J. Patterson, R. M. Plenge, M. E. Weinblatt, N. A. Shadick and D. Reich (2006). Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38(8): 904-909.

Qiu, X., Z. Yuan, H. Liu, X. Xiang, L. Yang, W. He, B. Du, G. Ye, J. Xu, D. Xing and S. N. Ahn (2015). Identification of salt tolerance-improving quantitative trait loci alleles from a salt-susceptible rice breeding line by introgression breeding. Plant Breeding 134(6): 653-660.

Rajendran, K., M. Tester and S. J. Roy (2009). Quantifying the three main components of salinity tolerance in cereals. Plant Cell Environ 32(3): 237-249.

Ren, Z. H., J. P. Gao, L. G. Li, X. L. Cai, W. Huang, D. Y. Chao, M. Z. Zhu, Z. Y. Wang, S. Luan and H. X. Lin (2005). A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat Genet 37(10): 1141-1146.

Roy, S. J., S. Negrao and M. Tester (2014). Salt resistant crop plants. Curr Opin Biotechnol 26: 115-124.

Sabouri, H. and A. Sabouri (2008). New evidence of QTLs attributed to salinity tolerance in rice. African Journal of Biotechnology 7(24): 4376-4383.

Sanchez-Barrena, M. J., M. Martinez-Ripoll, J. K. Zhu and A. Albert (2005). The structure of the Arabidopsis thaliana SOS3: molecular mechanism of sensing calcium for salt stress response. J Mol Biol 345(5): 1253-1264.

Sarkar, R. K., K. R. Mahata and D. P. Singh (2013). Differential responses of antioxidant system and photosynthetic characteristics in four rice cultivars differing in sensitivity to sodium chloride stress. Acta Physiologiae Plantarum 35(10): 2915-2926.


Shabala, S., H. Wu and J. Bose (2015). Salt stress sensing and early signalling events in plant roots: Current knowledge and hypothesis. Plant Sci 241: 109-119.

Shobbar, M.-S., O. Azhari, Z.-S. Shobbar, V. Niknam, H. Askari, M. Pessarakli and H. Ebrahimzadeh (2012). Comparative Analysis of Some Physiological Responses of Rice Seedlings to Cold, Salt, and Drought Stresses. Journal of Plant Nutrition 35(7): 1037-1052.

Singh, D. P. and R. K. Sarkar (2014). Distinction and characterisation of salinity tolerant and sensitive rice cultivars as probed by the chlorophyll fluorescence characteristics and growth parameters. Functional Plant Biology 41(7): 727-736.

Singh, V. P., H. U. Neue and M. Akbar (1982). Costal saline soils for rice cultivation. Rice and problem soils in south and southeast asia. D. Senadhira, International Rice Research Institute: 20-35.

Sun, J., D. T. Zou, F. S. Luan, H. W. Zhao, J. G. Wang, H. L. Liu, D. W. Xie, D. Q. Su, J. Ma and Z. L. Liu (2014). Dynamic QTL analysis of the Na+ content, K+ content, and Na+/K+ ratio in rice roots during the field growth under salt stress. Biologia Plantarum 58(4): 689-696.

Takahashi, S. and N. Murata (2008). How do environmental stresses accelerate photoinhibition? Trends Plant Sci 13(4): 178-182.

Tester, M. and P. Langridge (2010). Breeding technologies to increase crop production in a changing world. Science 327(5967): 818-822.

Wang, Z., J. Cheng, Z. Chen, J. Huang, Y. Bao, J. Wang and H. Zhang (2012). Identification of QTLs with main, epistatic and QTL x environment interaction effects for salt tolerance in rice seedlings under different salinity conditions. Theor Appl Genet 125(4): 807-815.

Xiong, L. (2003). Disease Resistance and Abiotic Stress Tolerance in Rice Are Inversely Modulated by an Abscisic Acid-Inducible Mitogen-Activated Protein Kinase. Plant Cell 15: 745-759.

Yamane, K., M. Kawasaki, M. Taniguchi and H. Miyake (2008). Correlation between chloroplast ultrastructure and chlorophyll fluorescence characteristics in the leaves of rice (Oryza sativa L.) grown under salinity. Plant Production Science 11(1): 139-145.

Zhao, K., C. W. Tung, G. C. Eizenga, M. H. Wright, M. L. Ali, A. H. Price, G. J. Norton, M. R. Islam, A. Reynolds, J. Mezey, A. M. McClung, C. D. Bustamante and S. R. McCouch (2011). Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun 2: 467.

Zheng, H., H. Zhao, H. Liu, J. Wang and D. Zou (2014). QTL analysis of Na+ and K+ concentrations in shoots and roots under NaCl stress based on linkage and association analysis in japonica rice. Euphytica 201(1): 109-121.



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