Abstract
Drought tolerance (DT) in rice is known to be controlled by many quantitative trait loci (QTLs) and involved differential expression of large numbers of genes, but linking QTLs with their underlying genes remains the most challenging issue in plant molecular biology. To shed some light on this issue, differential gene expression in response to PEG simulated drought in 3 unique genetic materials (a lowland rice, IR64 and its derived line, PD86 which has 11 introgressed DT QTLs, and a upland rice IRAT109) was investigated using a PCR-based subtractive hybridization strategy. More than 300 unique subtracted cDNA sequences, covering genes of diverse cellular activities and functions, were identified and confirmed by semi-quantitative and quantitative RT-PCR. Detailed bioinformatics analyses of the data revealed two interesting results. First, the levels and mechanisms of DT of the three rice lines were associated with the number and types of differentially expressed genes, suggesting different DT mechanisms in rice are controlled by different sets of genes and different metabolic pathways, and most differentially expressed genes under drought were able to contribute to DT. Second, there appeared a high correspondence in genomic location between DT QTLs and clusters of differentially expressed genes in rice, suggesting some DT QTLs may represent clusters of co-regulated and functionally related genes. Thus, differential gene expression analyses using genetically characterized materials can provide additional insights into the molecular basis of QTLs and convergent evidence to shortlist the candidate genes for target QTLs.
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References
Abebe T, Guenzi AC, Martin B, Cushman JC (2003) Tolerance of mannitol-accumulating transgenic wheat to water stress and salinity. Plant Physiol 131:1748–1755
Babu RC, Pathan MS, Blum A, Nguyen HT (1999) Comparison of measurement methods of osmotic adjustment in rice cultivars. Crop Sci 39:150–158
Babu RC, Shashidhar HE, Lilley JM, Thanh ND, Ray JD, Sadasivam S, Sarkarung S, O’Toole JC, Nguyen HT (2001) Variation in root penetration ability, osmotic adjustment and dehydration tolerance among accessions of rice adapted to rainfed lowland and upland ecosystems. Plant Breed 120:233–238
Capell T, Bassie L, Christou P (2004) Modulation of the polyamine biosynthetic pathway in transgenic rice confers tolerance to drought stress. Proc Natl Acad Sci USA 101:9909–9914
Cruz RT, O’Toole JC (1984) Dry land rice response to an irrigation gradient at flowering stage. Agron J 76:178–183
Diatchenko L, Lau YF, Campbell AP, Chenchik A, Moqadam F, Huang B, Lukyanov S, Lukyanov K, Gurskaya N, Sverdlov ED, Siebert PD (1996) Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci USA 93(12):6025–6030
Fujita Y, Fujita M, Satoh R, Maruyama K, Parvez MM, Seki M, Hiratsu K, Ohme-Takagi M, Shinozaki K, Yamaguchi-Shinozaki K (2005) AREB1 is a transcription activator of novel ABRE-dependent ABA signaling that enhances drought stress tolerance in Arabidopsis. Plant Cell 17:3470–3488
Gaber A, Yoshimura K, Yamamoto T, Yabuta Y, Takeda T, Miyasaka H, Nakano Y, Shigeoka S (2006) Glutathione peroxidase-like protein of Synechocystis PCC 6803 confers tolerance to oxidative and environmental stresses in transgenic Arabidopsis. Physiol Plant 128:251–262
Gorantla M, Babu P R, Lachagari VBR, Feltus FA, Paterson AH, Reddy AR (2005) Functional genomics of drought stress response in rice: transcript mapping of annotated unigenes of an indica rice (Oryza sativa L cv Nagina 22). Curr Sci 89(3):496–514
Jonaliza CL, Pantuwan G, Jongdee B, Toojinda T (2004) Quantitative trait loci associated with drought tolerance at reproductive stage in rice. Plant Physiol 135(1):384–399
Lafitte HR, Courtois B, Arraudeau M (2002) Genetic improvement of rice in aerobic systems: progress from yield to genes. Field Crops Res 75:171–190
Lafitte HR, Li ZK, Vijayakumar CHM, Gao YM, Shi Y, Xu JL, Fu BY, Yu SB, Ali AJ, Domingo J, Maghirang R, Torres R, Mackill D (2006) Improvement of rice drought tolerance through backcross breeding: evaluation of donors and selection in drought nurseries. Field Crops Res 97:77–86
Li ZK (2001) QTL mapping in rice: a few critical considerations. In: Rice genetics VI proceedings of the fourth international rice genetics symposium, 22–27 Oct, 2000 Los Banos, Philippines, New Delhi (India), International Rice Research Institute. Science Publishers, Inc and Los Banos, Philippines, pp 153–171
Li ZK, Xu JL (2007) Breeding for drought and salt tolerant rice (Oryza sativa L): progress and perspectives. In: Jenks MA, Hasegawa PM, Jain SM (eds) Advances in molecular-breeding toward drought and salt tolerant crops. Springer, Heidelberg
Li ZK, Fu BY, Gao YM, Xu JL, Ali J, Lafitte R, Jiang YZ, Domingo-Rey J, Vijayakumar CHM, Dwivedi D, Maghirang R, Zheng TQ, Zhu LH (2005) Genome-wide introgression lines and a forward genetics strategy for genetic and molecular dissection of complex phenotypes in rice (Oryza sativa L). Plant Mol Biol 59(1):33–52
Lilley JM, Ludlow MM, McCouch SR, O’Toole JC (1996) Locating QTL for osmotic adjustment and dehydration tolerance in rice. J Exp Bot 47(302):1427–1436
Nguyen TT, Klueva N, Chamareck V, Aarti A, Magpantay G, Millena AC, Pathan MS, Nguyen HT (2004) Saturation mapping of QTL regions and identification of putative candidate genes for drought tolerance in rice. Mol Genet Genom 272(1):35–46
Oh SJ, Song SI, Kim YS, Jang HJ, Kim SY, Kim MJ, Kim YK, Nahm BH, Kim JK (2005) Arabidopsis CBF3/DREB1A and ABF3 in transgenic rice increased tolerance to abiotic stress without stunting growth. Plant Physiol 138:341–351
Pandey S, Behura D, Villano R, D Naik (2000) Economic cost of drought and farmers’ coping mechanisms: a study of rainfed rice in eastern India. IRRI Discuss Paper Ser 39:1–35
Price AH, Tomos AD (1997) Genetics dissection of root growth in rice (Oryza sativa L) II: Mapping quantitative trait loci using molecular markers. Theor Appl Genet 95:143–152
International Rice Genome Sequencing Project (2003) The map-based sequence of the rice genome. Nature 436:793–800
Robin S, Pathan MS, Courtois B, Lafitte R, Carandang S, Lanceras S, Amante M, Nguyen HT, Li Z (2003) Mapping osmotic adjustment in an advanced back-cross inbred population of rice. Theor Appl Genet 107:1288–1296
Rockman MV, Kruglyak L (2006) Genetics of global gene expression. Nat Rev Genet 7:862–872
Rohila JS, Rajinder K, Wu JR (2002) Genetic improvement of Basmati rice for salt and drought tolerance by regulated expression of a barley Hva1 cDNA. Plant Sci 163:525–532
Teng S, Qian Q, Zeng DL, Kunihiro Y, Fujimoto K, Huang DN, Zhu LH (2002) Analysis of gene loci and epistasis for drought tolerance in seedling stage of rice (Oryza sativa L). Acta Genetica Sin 29:235–240
Tuong TP, Bouman BAM, Mortimer M (2005) More rice, less water—integrated approaches for increasing water productivity in irrigated rice-based systems in Asia. Plant Prod Sci 8:231–241
Valliyodan B, Nguyen HT (2006) Understanding regulatory networks and engineering for enhanced drought tolerance in plants. Curr Opin Plant Biol 9:1–7
Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93(1):77–78
Xiong L, Zhu JK (2002) Molecular and genetic aspects of plant responses to osmotic stress. Plant Cell Environ 25(2):131–139
Yoshida S, Forno DA, Cock JH, Gomez KA (1976) Laboratory manual for physiological studies of rice, 3rd edn. The International Rice Research Institute, Manila
Yue B, Xue W, Xong L, Yu X, Luo L, Cui K, Jin D, Xing Y, Zhang Q (2006) Genetic basis of drought resistance at reproductive stage in rice: separation of drought tolerance from drought avoidance. Genetics 172:1213–1228
Zhang J, Zheng HG, Aarti A, Pantuwan G, Nguyen TT, Tripathy JN, Sarial AK, Robin S, Babu RC, Nguyen BD, Sarkarung S, Blum A, Nguyen HT (2001) Locating genomic regions associated with components of drought resistance in rice: comparative mapping within and across species. Theor Appl Genet 103:19–29
Zhou SX, Tian F, Zhu ZF, Fu YC, Wang XK, Sun CQ (2006) Identification of quantitative trait loci controlling drought tolerance at seedling stage in Chinese Dongxiang common wild rice. Acta Genetica Sinica 33(6):551–558
Acknowledgments
This study was supported by the National 973 project of Chinese Ministry of Science and Technology (grant no. 2003CB114308) and by a grant (#2005 FS029) from the Rockefeller Foundation.
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Communicated by J.-K. Zhu.
Bin-Ying Fu and Jian-Hua Xiong are contributed to this work equally.
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Fu, BY., Xiong, JH., Zhu, LH. et al. Identification of functional candidate genes for drought tolerance in rice. Mol Genet Genomics 278, 599–609 (2007). https://doi.org/10.1007/s00438-007-0276-3
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DOI: https://doi.org/10.1007/s00438-007-0276-3