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Abiotic Stress Resistance

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Genetics and Genomics of Rice

Part of the book series: Plant Genetics and Genomics: Crops and Models ((PGG,volume 5))

Abstract

Abiotic stress resistance has complex genetic and molecular bases. Elucidation of the mechanisms underlying stress resistance of rice will accelerate the development of new varieties with enhanced tolerance. The progress in genetic, genomic, and molecular studies of stress resistance in rice is reviewed in this chapter. Drought resistance is regulated by a number of small-effect loci that are largely influenced by genetic background and environment. In contrast, submergence tolerance is controlled by a few master regulators that mediate various acclimation responses. Distinctive mechanisms are involved in the response of rice to other abiotic stresses. Recent functional studies uncovered hundreds of genes and signaling components that control various morphological and physiological responses to different stresses, providing new insight into understanding the complex mechanisms of stress resistance in rice.

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References

  1. Abbasi F, Onodera H, Toki S, Tanaka H, Komatsu S (2004) OsCDPK13, a calcium-dependent protein kinase gene from rice, is induced by cold and gibberellin in rice leaf sheath. Plant Mol Biol 55: 541–552

    Article  PubMed  CAS  Google Scholar 

  2. Agalou A, Purwantomo S, Overnas E, Johannesson H, Zhu X, Estiati A, de Kam RJ, Engstrom P, Slamet-Loedin IH, Zhu Z, Wang M, Xiong L, Meijer AH, Ouwerkerk PB (2008) A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members. Plant Mol Biol 66:87–103

    Article  PubMed  CAS  Google Scholar 

  3. Akimoto H (2003) Global air quality and pollution. Science 302:1716–1719

    Article  PubMed  CAS  Google Scholar 

  4. Ali ML, Pathan MS, Zhang J, Bai G, Sarkarung S, Nguyen HT (2000) Mapping QTLs for root traits in a recombinant inbred population from two indica ecotypes in rice. Theor Appl Genet 101:756–766

    Article  CAS  Google Scholar 

  5. Amir Hossain M, Lee Y, Cho JI, Ahn CH, Lee SK, Jeon JS, Kang H, Lee CH, An G, Park PB (2010) The bZIP transcription factor OsABF1 is an ABA responsive element binding factor that enhances abiotic stress signaling in rice. Plant Mol Biol 72:557–566

    Article  PubMed  CAS  Google Scholar 

  6. Andaya VC, Tai TH (2006) Fine mapping of the qCTS12 locus, a major QTL for seedling cold tolerance in rice. Theor Appl Genet 113:467–475

    Article  PubMed  CAS  Google Scholar 

  7. Arcade A, Labourdette A, Falque M, Mangin B, Chardon F, Charcosset A, Joets J (2004) BioMercator: integrating genetic maps and QTL towards discovery of candidate genes. Bioinformatics 20:2324–2326

    Article  PubMed  CAS  Google Scholar 

  8. Asano T, Hakata M, Nakamura H, Aoki N, Komatsu S, Ichikawa H, Hirochika H, Ohsugi R (2011) Functional characterisation of OsCPK21, a calcium-dependent protein kinase that confers salt tolerance in rice. Plant Mol Biol 75:179–191

    Article  PubMed  CAS  Google Scholar 

  9. Ashraf M (2010) Inducing drought tolerance in plants: recent advances. Biotechnol Adv 28:169–183

    Article  PubMed  CAS  Google Scholar 

  10. Babu R, Nguyen B, Chamarerk V, Shanmugasundaram P, Chezhian P, Jeyaprakash P, Ganesh S, Palchamy A, Sadasivam S, Sarkarung S, Wade L, Nguyen H (2003) Genetic analysis of drought resistance in rice by molecular markers: association between secondary traits and field performance. Crop Sci 43:1457–1469

    Article  CAS  Google Scholar 

  11. Bae H, Kim SK, Cho SK, Kang BG, Kim WT (2011) Overexpression of OsRDCP1, a rice RING domain-containing E3 ubiquitin ligase, increased tolerance to drought stress in rice (Oryza sativa L.). Plant Sci 180:775–782

    Article  PubMed  CAS  Google Scholar 

  12. Bailey-Serres J, Voesenek LA (2010) Life in the balance: a signaling network controlling survival of flooding. Curr Opin Plant Biol 13:489–494

    Article  PubMed  CAS  Google Scholar 

  13. Bernier J, Kumar A, Venuprasad R, Spaner D, Verulkar S, Mandal N, Sinha P, Peeraju P, Dongre P, Mahto R, Atlin G (2009) Characterization of the effect of a QTL for drought resistance in rice, qtl12.1, over a range of environments in the Philippines and eastern India. Euphytica 166:207–217

    Article  Google Scholar 

  14. Cao H, Guo S, Xu Y, Jiang K, Jones AM, Chong K (2011) Reduced expression of a gene encoding a Golgi localized monosaccharide transporter (OsGMST1) confers hypersensitivity to salt in rice (Oryza sativa). J Exp Bot 62:4595–4604

    Article  PubMed  CAS  Google Scholar 

  15. Chang CC, Huang PS, Lin HR, Lu CH (2007) Transactivation of protein expression by rice HSP101 in planta and using Hsp101 as a selection marker for transformation. Plant Cell Physiol 48:1098–1107

    Article  PubMed  CAS  Google Scholar 

  16. Chao DY, Luo YH, Shi M, Luo D, Lin HX (2005) Salt-responsive genes in rice revealed by cDNA microarray analysis. Cell Res 15:796–810

    Article  PubMed  CAS  Google Scholar 

  17. Chen CP, Frei M, Wissuwa M (2011) The OzT8 locus in rice protects leaf carbon assimilation rate and photosynthetic capacity under ozone stress. Plant Cell Environ 34:1141–1149

    Article  PubMed  CAS  Google Scholar 

  18. Chen G, Komatsuda T, Ma JF, Nawrath C, Pourkheirandish M, Tagiri A, Hu YG, Sameri M, Li X, Zhao X, Liu Y, Li C, Ma X, Wang A, Nair S, Wang N, Miyao A, Sakuma S, Yamaji N, Zheng X, Nevo E (2011) An ATP-binding cassette subfamily G full transporter is essential for the retention of leaf water in both wild barley and rice. Proc Natl Acad Sci U S A 108:12354–12359

    Article  PubMed  CAS  Google Scholar 

  19. Chen JQ, Meng XP, Zhang Y, Xia M, Wang XP (2008) Over-expression of OsDREB genes lead to enhanced drought tolerance in rice. Biotechnol Lett 30:2191–2198

    Article  PubMed  CAS  Google Scholar 

  20. Chen N, Xu Y, Wang X, Du C, Du J, Yuan M, Xu Z, Chong K (2011) OsRAN2, essential for mitosis, enhances cold tolerance in rice by promoting export of intranuclear tubulin and maintaining cell division under cold stress. Plant Cell Environ 34:52–64

    Article  PubMed  CAS  Google Scholar 

  21. Cheng C, Yun KY, Ressom HW, Mohanty B, Bajic VB, Jia Y, Yun SJ, de los Reyes BG (2007) An early response regulatory cluster induced by low temperature and hydrogen peroxide in seedlings of chilling-tolerant japonica rice. BMC Genomics 8:175

    Article  PubMed  CAS  Google Scholar 

  22. Chitteti BR, Peng Z (2007) Proteome and phosphoproteome differential expression under salinity stress in rice (Oryza sativa) roots. J Proteome Res 6:1718–1727

    Article  PubMed  CAS  Google Scholar 

  23. Coudert Y, Perin C, Courtois B, Khong NG, Gantet P (2010) Genetic control of root development in rice, the model cereal. Trends Plant Sci 15:219–226

    Article  PubMed  CAS  Google Scholar 

  24. Courtois B, Ahmadi N, Khowaja F, Price AH, Rami J-F, Frouin J, Hamelin C, Ruiz M (2009) Rice root genetic architecture: meta-analysis from a drought QTL database. Rice 2:115–128

    Article  Google Scholar 

  25. Courtois B, Shen L, Petalcorin W, Carandang S, Mauleon R, Li Z (2003) Locating QTLs controlling constitutive root traits in the rice population IAC165×Co39. Euphytica 134:335–345

    Article  CAS  Google Scholar 

  26. Cui M, Zhang W, Zhang Q, Xu Z, Zhu Z, Duan F, Wu R (2011) Induced over-expression of the transcription factor OsDREB2A improves drought tolerance in rice. Plant Physiol Biochem 49:1384–1391

    Article  PubMed  CAS  Google Scholar 

  27. Dai X, Xu Y, Ma Q, Xu W, Wang T, Xue Y, Chong K (2007) Overexpression of an R1R2R3 MYB gene, OsMYB3R-2, increases tolerance to freezing, drought, and salt stress in transgenic Arabidopsis. Plant Physiol 143:1739–1751

    Article  PubMed  CAS  Google Scholar 

  28. Degenkolbe T, Do PT, Zuther E, Repsilber D, Walther D, Hincha DK, Kohl KI (2009) Expression profiling of rice cultivars differing in their tolerance to long-term drought stress. Plant Mol Biol 69:133–153

    Article  PubMed  CAS  Google Scholar 

  29. Ding X, Hou X, Xie K, Xiong L (2009) Genome-wide identification of BURP domain-containing genes in rice reveals a gene family with diverse structures and responses to abiotic stresses. Planta 230:149–163

    Article  PubMed  CAS  Google Scholar 

  30. Ding X, Li X, Xiong L (2011) Evaluation of near-isogenic lines for drought resistance QTL and fine mapping of a locus affecting flag leaf width, spikelet number, and root volume in rice. Theor Appl Genet 123:815–826

    Article  PubMed  Google Scholar 

  31. Du H, Liu L, You L, Yang M, He Y, Li X, Xiong L (2011) Characterization of an inositol 1,3,4-trisphosphate 5/6-kinase gene that is essential for drought and salt stress responses in rice. Plant Mol Biol 77:547–563

    Article  PubMed  CAS  Google Scholar 

  32. Du H, Wang N, Cui F, Li X, Xiao J, Xiong L (2010) Characterization of the beta-carotene hydroxylase gene DSM2 conferring drought and oxidative stress resistance by increasing xanthophylls and abscisic acid synthesis in rice. Plant Physiol 154:1304–1318

    Article  PubMed  CAS  Google Scholar 

  33. Dubouzet JG, Sakuma Y, Ito Y, Kasuga M, Dubouzet EG, Miura S, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression. Plant J 33:751–763

    Article  PubMed  CAS  Google Scholar 

  34. Famoso AN, Zhao K, Clark RT, Tung CW, Wright MH, Bustamante C, Kochian LV, McCouch SR (2011) Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping. PLoS Genet 7:e1002221

    Article  PubMed  CAS  Google Scholar 

  35. Fang Y, You J, Xie K, Xie W, Xiong L (2008) Systematic sequence analysis and identification of tissue-specific or stress-responsive genes of NAC transcription factor family in rice. Mol Genet Genomics 280:547–563

    Article  PubMed  CAS  Google Scholar 

  36. Feng L, Wang K, Li Y, Tan Y, Kong J, Li H, Li Y, Zhu Y (2007) Overexpression of SBPase enhances photosynthesis against high temperature stress in transgenic rice plants. Plant Cell Rep 26:1635–1646

    Article  PubMed  CAS  Google Scholar 

  37. Frei M, Tanaka JP, Chen CP, Wissuwa M (2010) Mechanisms of ozone tolerance in rice: characterization of two QTLs affecting leaf bronzing by gene expression profiling and biochemical analyses. J Exp Bot 61:1405–1417

    Article  PubMed  CAS  Google Scholar 

  38. Frei M, Tanaka JP, Wissuwa M (2008) Genotypic variation in tolerance to elevated ozone in rice: dissection of distinct genetic factors linked to tolerance mechanisms. J Exp Bot 59:3741–3752

    Article  PubMed  CAS  Google Scholar 

  39. Fujino K, Sekiguchi H, Matsuda Y, Sugimoto K, Ono K, Yano M (2008) Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice. Proc Natl Acad Sci U S A 105:12623–12628

    Article  PubMed  CAS  Google Scholar 

  40. Fujino K, Sekiguchi H, Sato T, Kiuchi H, Nonoue Y, Takeuchi Y, Ando T, Lin SY, Yano M (2004) Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Theor Appl Genet 108:794–799

    Article  PubMed  CAS  Google Scholar 

  41. Fukao T, Bailey-Serres J (2008) Submergence tolerance conferred by Sub1A is mediated by SLR1 and SLRL1 restriction of gibberellin responses in rice. Proc Natl Acad Sci U S A 105:16814–16819

    Article  PubMed  CAS  Google Scholar 

  42. Fukao T, Xu K, Ronald PC, Bailey-Serres J (2006) A variable cluster of ethylene response factor-like genes regulates metabolic and developmental acclimation responses to submergence in rice. Plant Cell 18:2021–2034

    Article  PubMed  CAS  Google Scholar 

  43. Fukao T, Yeung E, Bailey-Serres J (2011) The submergence tolerance regulator SUB1A mediates crosstalk between submergence and drought tolerance in rice. Plant Cell 23:412–427

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  46. Fukuda A, Nakamura A, Tanaka Y (1999) Molecular cloning and expression of the Na+/H+ exchanger gene in Oryza sativa. Biochim Biophys Acta 1446:149–155

    Article  PubMed  CAS  Google Scholar 

  47. Gammulla CG, Pascovici D, Atwell BJ, Haynes PA (2010) Differential metabolic response of cultured rice (Oryza sativa) cells exposed to high- and low-temperature stress. Proteomics 10:3001–3019

    Article  PubMed  CAS  Google Scholar 

  48. Gao C, Han B (2009) Evolutionary and expression study of the aldehyde dehydrogenase (ALDH) gene superfamily in rice (Oryza sativa). Gene 431:86–94

    Article  PubMed  CAS  Google Scholar 

  49. Gao T, Wu Y, Zhang Y, Liu L, Ning Y, Wang D, Tong H, Chen S, Chu C, Xie Q (2011) OsSDIR1 overexpression greatly improves drought tolerance in transgenic rice. Plant Mol Biol 76:145–156

    Article  PubMed  CAS  Google Scholar 

  50. Gao LL, Xue HW (2011) Global analysis of expression profiles of rice receptor-like kinase genes. Mol Plant 5:143–153

    Article  PubMed  CAS  Google Scholar 

  51. Goffinet B, Gerber S (2000) Quantitative trait loci: a meta-analysis. Genetics 155:463–473

    PubMed  CAS  Google Scholar 

  52. Gothandam KM, Nalini E, Karthikeyan S, Shin JS (2010) OsPRP3, a flower specific proline-rich protein of rice, determines extracellular matrix structure of floral organs and its overexpression confers cold-tolerance. Plant Mol Biol 72:125–135

    Article  PubMed  CAS  Google Scholar 

  53. Han F, Chen H, Li XJ, Yang MF, Liu GS, Shen SH (2009) A comparative proteomic analysis of rice seedlings under various high-temperature stresses. Biochim Biophys Acta 1794:1625–1634

    Article  PubMed  CAS  Google Scholar 

  54. Hattori Y, Nagai K, Ashikari M (2010) Rice growth adapting to deepwater. Curr Opin Plant Biol 14:100–105

    Article  PubMed  Google Scholar 

  55. Hattori Y, Nagai K, Furukawa S, Song XJ, Kawano R, Sakakibara H, Wu J, Matsumoto T, Yoshimura A, Kitano H, Matsuoka M, Mori H, Ashikari M (2009) The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water. Nature 460:1026–1030

    Article  PubMed  CAS  Google Scholar 

  56. He X, Chen J, Zhang Z, Zhang J, Chen S (2002) Identification of salt-stress responsive genes in rice (Oryza sativa L.) by cDNA array. Sci China C Life Sci 45:477–484

    Article  PubMed  CAS  Google Scholar 

  57. Hemamalini G, Shashidhar H, Hittalmani S (2000) Molecular marker assisted tagging of morphological and physiological traits under two contrasting moisture regimes at peak vegetative stage in rice. Euphytica 1:69–78

    Article  Google Scholar 

  58. Hidema J, Teranishi M, Iwamatsu Y, Hirouchi T, Ueda T, Sato T, Burr B, Sutherland BM, Yamamoto K, Kumagai T (2005) Spontaneously occurring mutations in the cyclobutane pyrimidine dimer photolyase gene cause different sensitivities to ultraviolet-B in rice. Plant J 43:57–67

    Article  PubMed  CAS  Google Scholar 

  59. Horie T, Yoshida K, Nakayama H, Yamada K, Oiki S, Shinmyo A (2001) Two types of HKT transporters with different properties of Na+ and K+ transport in Oryza sativa. Plant J 27:129–138

    Article  PubMed  CAS  Google Scholar 

  60. Horii H, Nemoto K, Miyamoto N, Harada J (2006) Quantitative trait loci for adventitious and lateral roots in rice. Plant Breed 125:198–200

    Article  CAS  Google Scholar 

  61. Hou X, Xie K, Yao J, Qi Z, Xiong L (2009) A homolog of human ski-interacting protein in rice positively regulates cell viability and stress tolerance. Proc Natl Acad Sci U S A 106:6410–6415

    Article  PubMed  CAS  Google Scholar 

  62. Hu H, Dai M, Yao J, Xiao B, Li X, Zhang Q, Xiong L (2006) Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proc Natl Acad Sci U S A 103:12987–12992

    Article  PubMed  CAS  Google Scholar 

  63. Hu H, You J, Fang Y, Zhu X, Qi Z, Xiong L (2008) Characterization of transcription factor gene SNAC2 conferring cold and salt tolerance in rice. Plant Mol Biol 67:169–181

    Article  PubMed  CAS  Google Scholar 

  64. Huang XY, Chao DY, Gao JP, Zhu MZ, Shi M, Lin HX (2009) A previously unknown zinc finger protein, DST, regulates drought and salt tolerance in rice via stomatal aperture control. Genes Dev 23:1805–1817

    Article  PubMed  CAS  Google Scholar 

  65. Huang J, Wang MM, Jiang Y, Bao YM, Huang X, Sun H, Xu DQ, Lan HX, Zhang HS (2008) Expression analysis of rice A20/AN1-type zinc finger genes and characterization of ZFP177 that contributes to temperature stress tolerance. Gene 420:135–144

    Article  PubMed  CAS  Google Scholar 

  66. Huang Y, Xiao B, Xiong L (2007) Characterization of a stress responsive proteinase inhibitor gene with positive effect in improving drought resistance in rice. Planta 226:73–85

    Article  PubMed  CAS  Google Scholar 

  67. Huang CF, Yamaji N, Chen Z, Ma JF (2011) A tonoplast-localized half-size ABC transporter is required for internal detoxification of Al in rice. Plant J 69(5):857–867

    Article  PubMed  CAS  Google Scholar 

  68. Huang CF, Yamaji N, Mitani N, Yano M, Nagamura Y, Ma JF (2009) A bacterial-type ABC transporter is involved in aluminum tolerance in rice. Plant Cell 21:655–667

    Article  PubMed  CAS  Google Scholar 

  69. Igarashi Y, Yoshiba Y, Sanada Y, Yamaguchi-Shinozaki K, Wada K, Shinozaki K (1997) Characterization of the gene for delta1-pyrroline-5-carboxylate synthetase and correlation between the expression of the gene and salt tolerance in Oryza sativa L. Plant Mol Biol 33:857–865

    Article  PubMed  CAS  Google Scholar 

  70. Ishimaru K, Shirota K, Higa M, Kawamitsu Y (2001) Identification of quantitative trait loci for adaxial and abaxial stomatal frequencies in Oryza sativa. Plant Physiol Biochem 39:173–177

    Article  CAS  Google Scholar 

  71. Ishimaru K, Yano M, Aoki N, Ono K, Hirose T, Lin S, Monna L, Sasaki T, Ohsugi R (2001) Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and comparison between QTLs and expressed sequence tags. Theor Appl Genet 102:793–800

    Article  CAS  Google Scholar 

  72. Islam MA, Du H, Ning J, Ye H, Xiong L (2009) Characterization of Glossy1-homologous genes in rice involved in leaf wax accumulation and drought resistance. Plant Mol Biol 70:443–456

    Article  PubMed  CAS  Google Scholar 

  73. Ito Y, Katsura K, Maruyama K, Taji T, Kobayashi M, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2006) Functional analysis of rice DREB1/CBF-type transcription factors involved in cold-responsive gene expression in transgenic rice. Plant Cell Physiol 47:141–153

    Article  PubMed  CAS  Google Scholar 

  74. Jackson MB, Ram PC (2003) Physiological and molecular basis of susceptibility and tolerance of rice plants to complete submergence. Ann Bot 91:227–241

    Article  PubMed  CAS  Google Scholar 

  75. Jagadish SV, Muthurajan R, Oane R, Wheeler TR, Heuer S, Bennett J, Craufurd PQ (2010) Physiological and proteomic approaches to address heat tolerance during anthesis in rice (Oryza sativa L.). J Exp Bot 61:143–156

    Article  PubMed  CAS  Google Scholar 

  76. Jeong JS, Kim YS, Baek KH, Jung H, Ha SH, Do Choi Y, Kim M, Reuzeau C, Kim JK (2010) Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought conditions. Plant Physiol 153:185–197

    Article  PubMed  CAS  Google Scholar 

  77. Jeong D-H, Park S, Zhai J, Gurazada SGR, Paoli ED, Meyers BC, Green PJ (2011) Massive analysis of rice small RNAs: mechanistic implications of regulated microRNAs and variants for differential target RNA cleavage. Plant Cell 23:4185–4207

    Article  PubMed  CAS  Google Scholar 

  78. Jiang SY, Bhalla R, Ramamoorthy R, Luan HF, Venkatesh PN, Cai M, Ramachandran S (2011) Over-expression of OSRIP18 increases drought and salt tolerance in transgenic rice plants. Transgenic Res 21:785–795

    Article  PubMed  CAS  Google Scholar 

  79. Jiang SY, Ramamoorthy R, Bhalla R, Luan HF, Venkatesh PN, Cai M, Ramachandran S (2008) Genome-wide survey of the RIP domain family in Oryza sativa and their expression profiles under various abiotic and biotic stresses. Plant Mol Biol 67:603–614

    Article  PubMed  CAS  Google Scholar 

  80. Jung KH, Seo YS, Walia H, Cao P, Fukao T, Canlas PE, Amonpant F, Bailey-Serres J, Ronald PC (2010) The submergence tolerance regulator Sub1A mediates stress-responsive expression of AP2/ERF transcription factors. Plant Physiol 152:1674–1692

    Article  PubMed  CAS  Google Scholar 

  81. Kader MA, Seidel T, Golldack D, Lindberg S (2006) Expressions of OsHKT1, OsHKT2, and OsVHA are differentially regulated under NaCl stress in salt-sensitive and salt-tolerant rice (Oryza sativa L.) cultivars. J Exp Bot 57:4257–4268

    Article  PubMed  CAS  Google Scholar 

  82. Kamoshita A, Wade L, Ali M, Pathan M, Zhang J, Sarkarung S, Nguyen H (2002) Mapping QTL for root morphology of a rice population adapted to rainfed lowland conditions. Theor Appl Genet 104:880–893

    Article  PubMed  CAS  Google Scholar 

  83. Kamoshita A, Zhang J, Siopongco J, Sarkarung S, Nguyen H, Wade L (2002) Effects of phenotyping environment on identification of quantitative trait loci for rice root morphology under anaerobic conditions. Crop Sci 42:255–265

    Article  PubMed  CAS  Google Scholar 

  84. Kanneganti V, Gupta AK (2008) Overexpression of OsiSAP8, a member of stress associated protein (SAP) gene family of rice confers tolerance to salt, drought and cold stress in transgenic tobacco and rice. Plant Mol Biol 66:445–462

    Article  PubMed  CAS  Google Scholar 

  85. Kawakami A, Sato Y, Yoshida M (2008) Genetic engineering of rice capable of synthesizing fructans and enhancing chilling tolerance. J Exp Bot 59:793–802

    Article  PubMed  CAS  Google Scholar 

  86. Keith KA, Raskin I, Kende H (1986) A comparison of the submergence response of deepwater and non-deepwater rice. Plant Physiol 80:479–482

    Article  PubMed  CAS  Google Scholar 

  87. Khowaja FS, Norton GJ, Courtois B, Price AH (2009) Improved resolution in the position of drought-related QTLs in a single mapping population of rice by meta-analysis. BMC Genomics 10:276

    Article  PubMed  CAS  Google Scholar 

  88. Kim JY, Kim WY, Kwak KJ, Oh SH, Han YS, Kang H (2010) Glycine-rich RNA-binding proteins are functionally conserved in Arabidopsis thaliana and Oryza sativa during cold adaptation process. J Exp Bot 61:2317–2325

    Article  PubMed  CAS  Google Scholar 

  89. Kim JY, Kim WY, Kwak KJ, Oh SH, Han YS, Kang H (2010) Zinc finger-containing glycine-rich RNA-binding protein in Oryza sativa has an RNA chaperone activity under cold stress conditions. Plant Cell Environ 33:759–768

    Article  PubMed  CAS  Google Scholar 

  90. Kochian LV, Hoekenga OA, Pineros MA (2004) How do crop plants tolerate acid soils? Mechanisms of aluminum tolerance and phosphorous efficiency. Annu Rev Plant Biol 55:459–493

    Article  PubMed  CAS  Google Scholar 

  91. Koh S, Lee SC, Kim MK, Koh JH, Lee S, An G, Choe S, Kim SR (2007) T-DNA tagged knockout mutation of rice OsGSK1, an orthologue of Arabidopsis BIN2, with enhanced tolerance to various abiotic stresses. Plant Mol Biol 65:453–466

    Article  PubMed  CAS  Google Scholar 

  92. Komatsu S, Yang G, Khan M, Onodera H, Toki S, Yamaguchi M (2007) Over-expression of calcium-dependent protein kinase 13 and calreticulin interacting protein 1 confers cold tolerance on rice plants. Mol Genet Genomics 277:713–723

    Article  PubMed  CAS  Google Scholar 

  93. Koseki M, Kitazawa N, Yonebayashi S, Maehara Y, Wang ZX, Minobe Y (2010) Identification and fine mapping of a major quantitative trait locus originating from wild rice, controlling cold tolerance at the seedling stage. Mol Genet Genomics 284:45–54

    Article  PubMed  CAS  Google Scholar 

  94. Kumari S, Sabharwal VP, Kushwaha HR, Sopory SK, Singla-Pareek SL, Pareek A (2009) Transcriptome map for seedling stage specific salinity stress response indicates a specific set of genes as candidate for saline tolerance in Oryza sativa L. Funct Integr Genomics 9:109–123

    Article  PubMed  CAS  Google Scholar 

  95. Kuroki M, Saito K, Matsuba S, Yokogami N, Shimizu H, Ando I, Sato Y (2007) A quantitative trait locus for cold tolerance at the booting stage on rice chromosome 8. Theor Appl Genet 115:593–600

    Article  PubMed  Google Scholar 

  96. Laza M, Kondo M, Ideta O, Barlaan E, Imbe T (2010) Quantitative trait loci for stomatal density and size in lowland rice. Euphytica 172:149–158

    Article  Google Scholar 

  97. Lee SY, Ahn JH, Cha YS, Yun DW, Lee MC, Ko JC, Lee KS, Eun MY (2006) Mapping of quantitative trait loci for salt tolerance at the seedling stage in rice. Mol Cells 21:192–196

    PubMed  CAS  Google Scholar 

  98. Lee DG, Ahsan N, Lee SH, Kang KY, Bahk JD, Lee IJ, Lee BH (2007) A proteomic approach in analyzing heat-responsive proteins in rice leaves. Proteomics 7:3369–3383

    Article  PubMed  CAS  Google Scholar 

  99. Lenka SK, Katiyar A, Chinnusamy V, Bansal KC (2011) Comparative analysis of drought-responsive transcriptome in Indica rice genotypes with contrasting drought tolerance. Plant Biotechnol J 9:315–327

    Article  PubMed  CAS  Google Scholar 

  100. Li L, Li S, Tao Y, Kitagawa Y (2000) Molecular cloning of a novel water channel from rice: its products expression in Xenopus oocytes and involvement in chilling tolerance. Plant Sci 154:43–51

    Article  PubMed  CAS  Google Scholar 

  101. Li Z, Mu P, Li C, Zhang H, Gao Y, Wang X (2005) QTL mapping of root traits in a doubled haploid population from a cross between upland and lowland japonica rice in three environments. Theor Appl Genet 110:1244–1252

    Article  PubMed  CAS  Google Scholar 

  102. Li HW, Zang BS, Deng XW, Wang XP (2011) Overexpression of the trehalose-6-phosphate synthase gene OsTPS1 enhances abiotic stress tolerance in rice. Planta 234:1007–1018

    Article  PubMed  CAS  Google Scholar 

  103. Li GW, Zhang MH, Cai WM, Sun WN, Su WA (2008) Characterization of OsPIP2;7, a water channel protein in rice. Plant Cell Physiol 49:1851–1858

    Article  PubMed  CAS  Google Scholar 

  104. Lian HL, Yu X, Ye Q, Ding X, Kitagawa Y, Kwak SS, Su WA, Tang ZC (2004) The role of aquaporin RWC3 in drought avoidance in rice. Plant Cell Physiol 45:481–489

    Article  PubMed  CAS  Google Scholar 

  105. Lilley J, Ludlow M, McCouch S, O’Toole J (1996) Locating QTLs for osmotic adjustment and dehydration tolerance in rice. J Exp Bot 47:1427–1436

    Article  CAS  Google Scholar 

  106. Lin HX, Zhu MZ, Yano M, Gao JP, Liang ZW, Su WA, Hu XH, Ren ZH, Chao DY (2004) QTLs for Na+ and K+ uptake of the shoots and roots controlling rice salt tolerance. Theor Appl Genet 108:253–260

    Article  PubMed  CAS  Google Scholar 

  107. Liu JX, Bennett J (2011) Reversible and irreversible drought-induced changes in the anther proteome of rice (Oryza sativa L.) genotypes IR64 and Moroberekan. Mol Plant 4:59–69

    Article  PubMed  CAS  Google Scholar 

  108. Liu L, Mu P, Li X, Qu Y, Wang Y, Li Z (2008) Localization of QTL for basal root thickness in japonica rice and effect of marker-assisted selection for a major QTL. Euphytica 164:729–737

    Article  Google Scholar 

  109. Liu JG, Qin QL, Zhang Z, Peng RH, Xiong AS, Chen JM, Yao QH (2009) OsHSF7 gene in rice, Oryza sativa L., encodes a transcription factor that functions as a high temperature receptive and responsive factor. BMB Rep 42:16–21

    Article  PubMed  Google Scholar 

  110. Liu K, Wang L, Xu Y, Chen N, Ma Q, Li F, Chong K (2007) Overexpression of OsCOIN, a putative cold inducible zinc finger protein, increased tolerance to chilling, salt and drought, and enhanced proline level in rice. Planta 226:1007–1016

    Article  PubMed  CAS  Google Scholar 

  111. Liu H, Zou G, Liu G, Hu S, Li M, Yu X (2005) Correlation analysis and QTL identification for canopy temperature, leaf water potential and spikelet fertility in rice under contrasting moisture regimes. Chin Sci Bull 50:317–326

    CAS  Google Scholar 

  112. Lu G, Gao C, Zheng X, Han B (2009) Identification of OsbZIP72 as a positive regulator of ABA response and drought tolerance in rice. Planta 229:605–615

    Article  PubMed  CAS  Google Scholar 

  113. Ma Q, Dai X, Xu Y, Guo J, Liu Y, Chen N, Xiao J, Zhang D, Xu Z, Zhang X, Chong K (2009) Enhanced tolerance to chilling stress in OsMYB3R-2 transgenic rice is mediated by alteration in cell cycle and ectopic expression of stress genes. Plant Physiol 150:244–256

    Article  PubMed  CAS  Google Scholar 

  114. Ma X, Qian Q, Zhu D (2005) Expression of a calcineurin gene improves salt stress tolerance in transgenic rice. Plant Mol Biol 58:483–495

    Article  PubMed  CAS  Google Scholar 

  115. Ma JF, Shen R, Zhao Z, Wissuwa M, Takeuchi Y, Ebitani T, Yano M (2002) Response of rice to Al stress and identification of quantitative trait loci for Al tolerance. Plant Cell Physiol 43:652–659

    Article  PubMed  CAS  Google Scholar 

  116. MacMillan K, Emrich K, Piepho H, Mullins C, Price A (2006) Assessing the importance of genotype×environmental interaction for root traits in rice using a mapping population II: conventional QTL analysis. Theor Appl Genet 113:953–964

    Article  PubMed  CAS  Google Scholar 

  117. Mallikarjuna G, Mallikarjuna K, Reddy MK, Kaul T (2011) Expression of OsDREB2A transcription factor confers enhanced dehydration and salt stress tolerance in rice (Oryza sativa L.). Biotechnol Lett 33:1689–1697

    Article  PubMed  CAS  Google Scholar 

  118. Manavalan LP, Chen X, Clarke J, Salmeron J, Nguyen HT (2011) RNAi-mediated disruption of squalene synthase improves drought tolerance and yield in rice. J Exp Bot 63:163–175

    Article  PubMed  CAS  Google Scholar 

  119. Matsukura S, Mizoi J, Yoshida T, Todaka D, Ito Y, Maruyama K, Shinozaki K, Yamaguchi-Shinozaki K (2010) Comprehensive analysis of rice DREB2-type genes that encode transcription factors involved in the expression of abiotic stress-responsive genes. Mol Genet Genomics 283:185–196

    Article  PubMed  CAS  Google Scholar 

  120. Matsumoto T, Lian HL, Su WA, Tanaka D, Liu C, Iwasaki I, Kitagawa Y (2009) Role of the aquaporin PIP1 subfamily in the chilling tolerance of rice. Plant Cell Physiol 50:216–229

    Article  PubMed  CAS  Google Scholar 

  121. Mittal D, Chakrabarti S, Sarkar A, Singh A, Grover A (2009) Heat shock factor gene family in rice: genomic organization and transcript expression profiling in response to high temperature, low temperature and oxidative stresses. Plant Physiol Biochem 47:785–795

    Article  PubMed  CAS  Google Scholar 

  122. Morsy MR, Almutairi AM, Gibbons J, Yun SJ, de Los Reyes BG (2005) The OsLti6 genes encoding low-molecular-weight membrane proteins are differentially expressed in rice cultivars with contrasting sensitivity to low temperature. Gene 344:171–180

    Article  PubMed  CAS  Google Scholar 

  123. Mukhopadhyay A, Vij S, Tyagi AK (2004) Overexpression of a zinc-finger protein gene from rice confers tolerance to cold, dehydration, and salt stress in transgenic tobacco. Proc Natl Acad Sci U S A 101:6309–6314

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  125. Murakami T, Matsuba S, Funatsuki H, Kawaguchi K, Saruyama H, Tanida M, Sato Y (2004) Over-expression of a small heat shock protein, sHSP17. 7, confers both heat tolerance and UV-B resistance to rice plants. Plant Cell Rep 13:165–175

    CAS  Google Scholar 

  126. Nakashima K, Tran LS, Van Nguyen D, Fujita M, Maruyama K, Todaka D, Ito Y, Hayashi N, Shinozaki K, Yamaguchi-Shinozaki K (2007) Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice. Plant J 51:617–630

    Article  PubMed  CAS  Google Scholar 

  127. Neeraja CN, Maghirang-Rodriguez R, Pamplona A, Heuer S, Collard BC, Septiningsih EM, Vergara G, Sanchez D, Xu K, Ismail AM, Mackill DJ (2007) A marker-assisted backcross approach for developing submergence-tolerant rice cultivars. Theor Appl Genet 115:767–776

    Article  PubMed  CAS  Google Scholar 

  128. Nguyen BD, Brar DS, Bui BC, Nguyen TV, Pham LN, Nguyen HT (2003) Identification and mapping of the QTL for aluminum tolerance introgressed from the new source, Oryza Rufipogon Griff., into indica rice (Oryza sativa L.). Theor Appl Genet 106:583–593

    PubMed  CAS  Google Scholar 

  129. Nguyen VT, Burow MD, Nguyen HT, Le BT, Le TD, Paterson AH (2001) Molecular mapping of genes conferring aluminum tolerance in rice (Oryza sativa L.). Theor Appl Genet 102:1002–1010

    Article  CAS  Google Scholar 

  130. Nguyen VT, Nguyen BD, Sarkarung S, Martinez C, Paterson AH, Nguyen HT (2002) Mapping of genes controlling aluminum tolerance in rice: comparison of different genetic backgrounds. Mol Genet Genomics 267:772–780

    Article  PubMed  CAS  Google Scholar 

  131. Ning Y, Jantasuriyarat C, Zhao Q, Zhang H, Chen S, Liu J, Liu L, Tang S, Park CH, Wang X, Liu X, Dai L, Xie Q, Wang GL (2011) The SINA E3 ligase OsDIS1 negatively regulates drought response in rice. Plant Physiol 157:242–255

    Article  PubMed  CAS  Google Scholar 

  132. Ning J, Li X, Hicks LM, Xiong L (2010) A Raf-like MAPKKK gene DSM1 mediates drought resistance through reactive oxygen species scavenging in rice. Plant Physiol 152:876–890

    Article  PubMed  CAS  Google Scholar 

  133. Nohzadeh Malakshah S, Habibi Rezaei M, Heidari M, Salekdeh GH (2007) Proteomics reveals new salt responsive proteins associated with rice plasma membrane. Biosci Biotechnol Biochem 71:2144–2154

    Article  PubMed  CAS  Google Scholar 

  134. Obara M, Tamura W, Ebitani T, Yano M, Sato T, Yamaya T (2010) Fine-mapping of qRL6.1, a major QTL for root length of rice seedlings grown under a wide range of NH4+ concentrations in hydroponic conditions. Theor Appl Genet 121(3):535–547

    Article  PubMed  CAS  Google Scholar 

  135. Obata T, Kitamoto HK, Nakamura A, Fukuda A, Tanaka Y (2007) Rice shaker potassium channel OsKAT1 confers tolerance to salinity stress on yeast and rice cells. Plant Physiol 144:1978–1985

    Article  PubMed  CAS  Google Scholar 

  136. Oh SJ, Kim YS, Kwon CW, Park HK, Jeong JS, Kim JK (2009) Overexpression of the transcription factor AP37 in rice improves grain yield under drought conditions. Plant Physiol 150:1368–1379

    Article  PubMed  CAS  Google Scholar 

  137. Ohnishi T, Sugahara S, Yamada T, Kikuchi K, Yoshiba Y, Hirano HY, Tsutsumi N (2005) OsNAC6, a member of the NAC gene family, is induced by various stresses in rice. Genes Genet Syst 80:135–139

    Article  PubMed  CAS  Google Scholar 

  138. Ouyang SQ, Liu YF, Liu P, Lei G, He SJ, Ma B, Zhang WK, Zhang JS, Chen SY (2010) Receptor-like kinase OsSIK1 improves drought and salt stress tolerance in rice (Oryza sativa) plants. Plant J 62:316–329

    Article  PubMed  CAS  Google Scholar 

  139. Pandit A, Rai V, Bal S, Sinha S, Kumar V, Chauhan M, Gautam RK, Singh R, Sharma PC, Singh AK, Gaikwad K, Sharma TR, Mohapatra T, Singh NK (2010) Combining QTL mapping and transcriptome profiling of bulked RILs for identification of functional polymorphism for salt tolerance genes in rice (Oryza sativa L.). Mol Genet Genomics 284:121–136

    Article  PubMed  CAS  Google Scholar 

  140. Park GG, Park JJ, Yoon J, Yu SN, An G (2010) A RING finger E3 ligase gene, Oryza sativa Delayed Seed Germination 1 (OsDSG1), controls seed germination and stress responses in rice. Plant Mol Biol 74:467–478

    Article  PubMed  CAS  Google Scholar 

  141. Park MR, Yun KY, Mohanty B, Herath V, Xu F, Wijaya E, Bajic VB, Yun SJ, De Los Reyes BG (2010) Supra-optimal expression of the cold-regulated OsMyb4 transcription factor in transgenic rice changes the complexity of transcriptional network with major effects on stress tolerance and panicle development. Plant Cell Environ 33:2209–2230

    Article  PubMed  CAS  Google Scholar 

  142. Perata P, Voesenek LA (2007) Submergence tolerance in rice requires Sub1A, an ethylene-response-factor-like gene. Trends Plant Sci 12:43–46

    Article  PubMed  CAS  Google Scholar 

  143. Price AH, Cairns JE, Horton P, Jones HG, Griffiths H (2002) Linking drought-resistance mechanisms to drought avoidance in upland rice using a QTL approach: progress and new opportunities to integrate stomatal and mesophyll responses. J Exp Bot 53:989–1004

    Article  PubMed  CAS  Google Scholar 

  144. Price AH, Townend J, Jones MP, Audebert A, Courtois B (2002) Mapping QTLs associated with drought avoidance in upland rice grown in the Philippines and West Africa. Plant Mol Biol 48:683–695

    Article  PubMed  CAS  Google Scholar 

  145. Qin BX, Tang D, Huang J, Li M, Wu XR, Lu LL, Wang KJ, Yu HX, Chen JM, Gu MH, Cheng ZK (2011) Rice OsGL1-1 is involved in leaf cuticular wax and cuticle membrane. Mol Plant 4:985–995

    Article  PubMed  CAS  Google Scholar 

  146. Qin Y, Ye H, Tang N, Xiong L (2009) Systematic identification of X1-homologous genes reveals a family involved in stress responses in rice. Plant Mol Biol 71:483–496

    Article  PubMed  CAS  Google Scholar 

  147. Qu Y, Mu P, Li X, Tian Y, Wen F, Zhang H, Li Z (2008) QTL mapping and correlations between leaf water potential and drought resistance in rice under upland and lowland environments. Acta Agron Sin 34:198–206

    Article  CAS  Google Scholar 

  148. Qu Y, Mu P, Zhang H, Chen CY, Gao Y, Tian Y, Wen F, Li Z (2008) Mapping QTLs of root morphological traits at different growth stages in rice. Genetica 133:187–200

    Article  PubMed  Google Scholar 

  149. Quarrie SA, Laurie DA, Zhu J, Lebreton C, Semikhodskii A, Steed A, Witsenboer H, Calestani C (1997) QTL analysis to study the association between leaf size and abscisic acid accumulation in droughted rice leaves and comparisons across cereals. Plant Mol Biol 35:155–165

    Article  PubMed  CAS  Google Scholar 

  150. Ramamoorthy R, Jiang SY, Kumar N, Venkatesh PN, Ramachandran S (2008) A comprehensive transcriptional profiling of the WRKY gene family in rice under various abiotic and phytohormone treatments. Plant Cell Physiol 49:865–879

    Article  PubMed  CAS  Google Scholar 

  151. Ray S, Dansana PK, Giri J, Deveshwar P, Arora R, Agarwal P, Khurana JP, Kapoor S, Tyagi AK (2011) Modulation of transcription factor and metabolic pathway genes in response to water-deficit stress in rice. Funct Integr Genomics 11:157–178

    Article  PubMed  CAS  Google Scholar 

  152. Ren ZH, Gao JP, Li LG, Cai XL, Huang W, Chao DY, Zhu MZ, Wang ZY, Luan S, Lin HX (2005) A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat Genet 37:1141–1146

    Article  PubMed  CAS  Google Scholar 

  153. 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

    Article  PubMed  CAS  Google Scholar 

  154. Rose-John S, Kende H (1984) Effect of submergence on the cell wall composition of deep-water rice internodes. Plant Physiol 76:106–111

    Article  PubMed  CAS  Google Scholar 

  155. Saijo Y, Hata S, Kyozuka J, Shimamoto K, Izui K (2000) Over-expression of a single Ca2+-dependent protein kinase confers both cold and salt/drought tolerance on rice plants. Plant J 23:319–327

    Article  PubMed  CAS  Google Scholar 

  156. Sakamoto A, Alia, Murata N (1998) Metabolic engineering of rice leading to biosynthesis of glycinebetaine and tolerance to salt and cold. Plant Mol Biol 38:1011–1019

    Article  PubMed  CAS  Google Scholar 

  157. Sasaki T, Akutsu H, Shimada H, Miura S (2010) A rice cytochrome P450 OsCYP84A that may interact with the UV tolerance pathway. Biosci Biotechnol Biochem 74:1045–1049

    Article  PubMed  CAS  Google Scholar 

  158. Sato Y, Masuta Y, Saito K, Murayama S, Ozawa K (2011) Enhanced chilling tolerance at the booting stage in rice by transgenic overexpression of the ascorbate peroxidase gene, OsAPXa. Plant Cell Rep 30:399–406

    Article  PubMed  CAS  Google Scholar 

  159. Sato T, Ueda T, Fukuta Y, Kumagai T, Yano M (2003) Mapping of quantitative trait loci associated with ultraviolet-B resistance in rice (Oryza sativa L.). Theor Appl Genet 107:1003–1008

    Article  PubMed  CAS  Google Scholar 

  160. Sato Y, Yokoya S (2008) Enhanced tolerance to drought stress in transgenic rice plants overexpressing a small heat-shock protein, sHSP17.7. Plant Cell Rep 27:329–334

    Article  PubMed  CAS  Google Scholar 

  161. Scafaro AP, Haynes PA, Atwell BJ (2010) Physiological and molecular changes in Oryza meridionalis Ng, a heat-tolerant species of wild rice. J Exp Bot 61:191–202

    Article  PubMed  CAS  Google Scholar 

  162. Seo JS, Joo J, Kim MJ, Kim YK, Nahm BH, Song SI, Cheong JJ, Lee JS, Kim JK, Choi YD (2011) OsbHLH148, a basic helix-loop-helix protein, interacts with OsJAZ proteins in a jasmonate signaling pathway leading to drought tolerance in rice. Plant J 65:907–921

    Article  PubMed  CAS  Google Scholar 

  163. Septiningsih EM, Sanchez DL, Singh N, Sendon PM, Pamplona AM, Heuer S, Mackill DJ (2010) Identifying novel QTLs for submergence tolerance in rice cultivars IR72 and Madabaru. Theor Appl Genet 124:867–874

    Article  Google Scholar 

  164. Sharoni AM, Nuruzzaman M, Satoh K, Shimizu T, Kondoh H, Sasaya T, Choi IR, Omura T, Kikuchi S (2011) Gene structures, classification and expression models of the AP2/EREBP transcription factor family in rice. Plant Cell Physiol 52:344–360

    Article  PubMed  CAS  Google Scholar 

  165. Shen L, Courtois B, McNally KL, Robin S, Li Z (2001) Evaluation of near-isogenic lines of rice introgressed with QTLs for root depth through marker-aided selection. Theor Appl Genet 103:75–83

    Article  CAS  Google Scholar 

  166. Shen J, Xie K, Xiong L (2010) Global expression profiling of rice microRNAs by one-tube stem-loop reverse transcription quantitative PCR revealed important roles of microRNAs in abiotic stress responses. Mol Genet Genomics 284:477–488

    Article  PubMed  CAS  Google Scholar 

  167. Shimizu H, Sato K, Berberich T, Miyazaki A, Ozaki R, Imai R, Kusano T (2005) LIP19, a basic region leucine zipper protein, is a Fos-like molecular switch in the cold signaling of rice plants. Plant Cell Physiol 46:1623–1634

    Article  PubMed  CAS  Google Scholar 

  168. Shirasawa K, Takabe T, Takabe T, Kishitani S (2006) Accumulation of glycinebetaine in rice plants that overexpress choline monooxygenase from spinach and evaluation of their tolerance to abiotic stress. Ann Bot 98:565–571

    Article  PubMed  CAS  Google Scholar 

  169. Shu L, Lou Q, Ma C, Ding W, Zhou J, Wu J, Feng F, Lu X, Luo L, Xu G, Mei H (2011) Genetic, proteomic and metabolic analysis of the regulation of energy storage in rice seedlings in response to drought. Proteomics 11:4122–4138

    Article  PubMed  CAS  Google Scholar 

  170. Steele KA, Price AH, Shashidhar HE, Witcombe JR (2006) Marker-assisted selection to introgress rice QTLs controlling root traits into an Indian upland rice variety. Theor Appl Genet 112:208–221

    Article  PubMed  CAS  Google Scholar 

  171. Steele KA, Virk DS, Kumar R, Prasad SC, Witcombe JR (2007) Field evaluation of upland rice lines selected for QTLs controlling root traits. Field Crops Res 101:180–186

    Article  Google Scholar 

  172. Su CF, Wang YC, Hsieh TH, Lu CA, Tseng TH, Yu SM (2010) A novel MYBS3-dependent pathway confers cold tolerance in rice. Plant Physiol 153:145–158

    Article  PubMed  CAS  Google Scholar 

  173. Suh JP, Jeung JU, Lee JI, Choi YH, Yea JD, Virk PS, Mackill DJ, Jena KK (2010) Identification and analysis of QTLs controlling cold tolerance at the reproductive stage and validation of effective QTLs in cold-tolerant genotypes of rice (Oryza sativa L.). Theor Appl Genet 120:985–995

    Article  PubMed  CAS  Google Scholar 

  174. Sun SJ, Guo SQ, Yang X, Bao YM, Tang HJ, Sun H, Huang J, Zhang HS (2010) Functional analysis of a novel Cys2/His2-type zinc finger protein involved in salt tolerance in rice. J Exp Bot 61:2807–2818

    Article  PubMed  CAS  Google Scholar 

  175. Takai T, Fukuta Y, Sugimoto A, Shiraiwa T, Horie T (2006) Mapping of QTLs controlling carbon isotope discrimination in the photosynthetic system using recombinant inbred lines derived from a cross between two different rice (Oryza sativa L.) cultivars. Plant Prod Sci 9:271–280

    Article  CAS  Google Scholar 

  176. Tang N, Zhang H, Li X, Xiao J, Xiong L (2012) Constitutive activation of transcription factor OsbZIP46 improves drought tolerance in rice. Plant Physiol 158:1755–1768

    Article  PubMed  CAS  Google Scholar 

  177. Tao Z, Kou Y, Liu H, Li X, Xiao J, Wang S (2011) OsWRKY45 alleles play different roles in abscisic acid signalling and salt stress tolerance but similar roles in drought and cold tolerance in rice. J Exp Bot 62:4863–4874

    Article  PubMed  CAS  Google Scholar 

  178. Teulat B, This D, Khairallah M, Borries C, Ragot C, Sourdille P, Leroy P, Monneveux P, Charrier A (1998) Several QTLs involved in osmotic adjustment trait variation in barley. Theor Appl Genet 96:688–698

    Article  CAS  Google Scholar 

  179. Toojinda T, Siangliw M, Tragoonrung S, Vanavichit A (2003) Molecular genetics of submergence tolerance in rice: QTL analysis of key traits. Ann Bot 91(Spec No):243–253

    Article  PubMed  CAS  Google Scholar 

  180. Tripathy JN, Zhang J, Robin S, Nguyen TT, Nguyen HT (2000) QTLs for cell-membrane stability mapped in rice (Oryza sativa L.) under drought stress. Theor Appl Genet 118:1197–1202

    Article  Google Scholar 

  181. Turoczy Z, Kis P, Torok K, Cserhati M, Lendvai A, Dudits D, Horvath GV (2011) Overproduction of a rice aldo-keto reductase increases oxidative and heat stress tolerance by malondialdehyde and methylglyoxal detoxification. Plant Mol Biol 75:399–412

    Article  PubMed  CAS  Google Scholar 

  182. Ueda T, Sato T, Hidema J, Hirouchi T, Yamamoto K, Kumagai T, Yano M (2005) qUVR-10, a major quantitative trait locus for ultraviolet-B resistance in rice, encodes cyclobutane pyrimidine dimer photolyase. Genetics 171:1941–1950

    Article  PubMed  CAS  Google Scholar 

  183. Uga Y, Okuno K, Yano M (2010) Fine mapping of Sta1, a quantitative trait locus determining stele transversal area, on rice chromosome 9. Mol Breed 26:533–538

    Article  Google Scholar 

  184. Uga Y, Okuno K, Yano M (2011) Dro1, a major QTL involved in deep rooting of rice under upland field conditions. J Exp Bot 62:2485–2494

    Article  PubMed  CAS  Google Scholar 

  185. Vannini C, Locatelli F, Bracale M, Magnani E, Marsoni M, Osnato M, Mattana M, Baldoni E, Coraggio I (2004) Overexpression of the rice Osmyb4 gene increases chilling and freezing tolerance of Arabidopsis thaliana plants. Plant J 37:115–127

    Article  PubMed  CAS  Google Scholar 

  186. Veyrieras JB, Goffinet B, Charcosset A (2007) MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments. BMC Bioinformatics 8:49

    Article  PubMed  CAS  Google Scholar 

  187. Voesenek LA, Bailey-Serres J (2009) Plant biology: genetics of high-rise rice. Nature 460:959–960

    Article  PubMed  CAS  Google Scholar 

  188. Walia H, Wilson C, Condamine P, Liu X, Ismail AM, Zeng L, Wanamaker SI, Mandal J, Xu J, Cui X, Close TJ (2005) Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage. Plant Physiol 139:822–835

    Article  PubMed  CAS  Google Scholar 

  189. Wan B, Lin Y, Mou T (2007) Expression of rice Ca(2+)-dependent protein kinases (CDPKs) genes under different environmental stresses. FEBS Lett 581:1179–1189

    Article  PubMed  CAS  Google Scholar 

  190. Wang Q, Guan Y, Wu Y, Chen H, Chen F, Chu C (2008) Overexpression of a rice OsDREB1F gene increases salt, drought, and low temperature tolerance in both Arabidopsis and rice. Plant Mol Biol 67:589–602

    Article  PubMed  CAS  Google Scholar 

  191. Wang H, Hao J, Chen X, Hao Z, Wang X, Lou Y, Peng Y, Guo Z (2007) Overexpression of rice WRKY89 enhances ultraviolet B tolerance and disease resistance in rice plants. Plant Mol Biol 65:799–815

    Article  PubMed  CAS  Google Scholar 

  192. Wang D, Pan Y, Zhao X, Zhu L, Fu B, Li Z (2011) Genome-wide temporal-spatial gene expression profiling of drought responsiveness in rice. BMC Genomics 12:149

    Article  PubMed  CAS  Google Scholar 

  193. Wang N, Xiao B, Xiong L (2011) Identification of a cluster of PR4-like genes involved in stress responses in rice. J Plant Physiol 168:2212–2224

    Article  PubMed  CAS  Google Scholar 

  194. Wang YJ, Zhang ZG, He XJ, Zhou HL, Wen YX, Dai JX, Zhang JS, Chen SY (2003) A rice transcription factor OsbHLH1 is involved in cold stress response. Theor Appl Genet 107:1402–1409

    Article  PubMed  CAS  Google Scholar 

  195. Wathugala DL, Richards SA, Knight H, Knight MR (2011) OsSFR6 is a functional rice orthologue of SENSITIVE TO FREEZING-6 and can act as a regulator of COR gene expression, osmotic stress and freezing tolerance in Arabidopsis. New Phytol 191:984–995

    Article  PubMed  CAS  Google Scholar 

  196. Wen JQ, Oono K, Imai R (2002) Two novel mitogen-activated protein signaling components, OsMEK1 and OsMAP1, are involved in a moderate low-temperature signaling pathway in rice. Plant Physiol 129:1880–1891

    Article  PubMed  CAS  Google Scholar 

  197. Wu P, Liao CY, Hu B, Yi KK, Jin WZ, Ni JJ, He C (2000) QTLs and epistasis for aluminum tolerance in rice (Oryza sativa L.) at different seedling stages. Theor Appl Genet 100:1295–1303

    Article  CAS  Google Scholar 

  198. Wu X, Shiroto Y, Kishitani S, Ito Y, Toriyama K (2009) Enhanced heat and drought tolerance in transgenic rice seedlings overexpressing OsWRKY11 under the control of HSP101 promoter. Plant Cell Rep 28:21–30

    Article  PubMed  CAS  Google Scholar 

  199. Xia J, Yamaji N, Kasai T, Ma JF (2010) Plasma membrane-localized transporter for aluminum in rice. Proc Natl Acad Sci U S A 107:18381–18385

    Article  PubMed  CAS  Google Scholar 

  200. Xiang Y, Huang Y, Xiong L (2007) Characterization of stress-responsive CIPK genes in rice for stress tolerance improvement. Plant Physiol 144:1416–1428

    Article  PubMed  CAS  Google Scholar 

  201. Xiang Y, Tang N, Du H, Ye H, Xiong L (2008) Characterization of OsbZIP23 as a key player of the basic leucine zipper transcription factor family for conferring abscisic acid sensitivity and salinity and drought tolerance in rice. Plant Physiol 148:1938–1952

    Article  PubMed  CAS  Google Scholar 

  202. Xiao B, Huang Y, Tang N, Xiong L (2007) Over-expression of a LEA gene in rice improves drought resistance under the field conditions. Theor Appl Genet 115:35–46

    Article  PubMed  CAS  Google Scholar 

  203. Xing Y, Zhang Q (2010) Genetic and molecular bases of rice yield. Annu Rev Plant Biol 61:421–442

    Article  PubMed  CAS  Google Scholar 

  204. Xiong L, Yang Y (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

    Article  PubMed  CAS  Google Scholar 

  205. Xu DQ, Huang J, Guo SQ, Yang X, Bao YM, Tang HJ, Zhang HS (2008) Overexpression of a TFIIIA-type zinc finger protein gene ZFP252 enhances drought and salt tolerance in rice (Oryza sativa L.). FEBS Lett 582:1037–1043

    Article  PubMed  CAS  Google Scholar 

  206. Xu C, Li X, Xue Y, Huang Y, Gao J, Xing Y (2004) Comparison of quantitative trait loci controlling seedling characteristics at two seedling stages using rice recombinant inbred lines. Theor Appl Genet 109:640–647

    PubMed  CAS  Google Scholar 

  207. Xu GY, Rocha PS, Wang ML, Xu ML, Cui YC, Li LY, Zhu YX, Xia X (2011) A novel rice calmodulin-like gene, OsMSR2, enhances drought and salt tolerance and increases ABA sensitivity in Arabidopsis. Planta 234:47–59

    Article  PubMed  CAS  Google Scholar 

  208. Xu Y, This D, Pausch RC, Vonhof WM, Coburn JR, Comstock JP, McCouch SR (2009) Leaf-level water use efficiency determined by carbon isotope discrimination in rice seedlings: genetic variation associated with population structure and QTL mapping. Theor Appl Genet 118:1065–1081

    Article  PubMed  CAS  Google Scholar 

  209. Xu K, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail AM, Bailey-Serres J, Ronald PC, Mackill DJ (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442:705–708

    Article  PubMed  CAS  Google Scholar 

  210. Xu K, Xu X, Ronald PC, Mackill DJ (2000) A high-resolution linkage map of the vicinity of the rice submergence tolerance locus Sub1. Mol Gen Genet 263:681–689

    Article  PubMed  CAS  Google Scholar 

  211. Xue Y, Jiang L, Su N, Wang JK, Deng P, Ma JF, Zhai HQ, Wan JM (2007) The genetic basic and fine-mapping of a stable quantitative-trait loci for aluminium tolerance in rice. Planta 227:255–262

    Article  PubMed  CAS  Google Scholar 

  212. Xue Y, Wan JM, Jiang L, Wang CM, Liu LL, Zhang YM, Zhai HQ (2006) Identification of quantitative trait loci associated with aluminum tolerance in rice (Oryza Sativa L.). Euphytica 150:37–45

    Article  CAS  Google Scholar 

  213. Yamaji N, Huang CF, Nagao S, Yano M, Sato Y, Nagamura Y, Ma JF (2009) A zinc finger transcription factor ART1 regulates multiple genes implicated in aluminum tolerance in rice. Plant Cell 21:3339–3349

    Article  PubMed  CAS  Google Scholar 

  214. Yan YS, Chen XY, Yang K, Sun ZX, Fu YP, Zhang YM, Fang RX (2010) Overexpression of an F-box protein gene reduces abiotic stress tolerance and promotes root growth in rice. Mol Plant 4:190–197

    Article  PubMed  CAS  Google Scholar 

  215. Yang Z, Wu Y, Li Y, Ling HQ, Chu C (2009) OsMT1a, a type 1 metallothionein, plays the pivotal role in zinc homeostasis and drought tolerance in rice. Plant Mol Biol 70:219–229

    Article  PubMed  CAS  Google Scholar 

  216. Ye H, Du H, Tang N, Li X, Xiong L (2009) Identification and expression profiling analysis of TIFY family genes involved in stress and phytohormone responses in rice. Plant Mol Biol 71:291–305

    Article  PubMed  CAS  Google Scholar 

  217. Yokotani N, Ichikawa T, Kondou Y, Matsui M, Hirochika H, Iwabuchi M, Oda K (2008) Expression of rice heat stress transcription factor OsHsfA2e enhances tolerance to environmental stresses in transgenic Arabidopsis. Planta 227:957–967

    Article  PubMed  CAS  Google Scholar 

  218. Yu X, Peng YH, Zhang MH, Shao YJ, Su WA, Tang ZC (2006) Water relations and an expression analysis of plasma membrane intrinsic proteins in sensitive and tolerant rice during chilling and recovery. Cell Res 16:599–608

    Article  PubMed  CAS  Google Scholar 

  219. Yue B, Xiong L, Xue W, Xing Y, Luo L, Xu C (2005) Genetic analysis for drought resistance of rice at reproductive stage in field with different types of soil. Theor Appl Genet 111:1127–1136

    Article  PubMed  Google Scholar 

  220. Yue B, Xue W, Xiong 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

    Article  PubMed  Google Scholar 

  221. Zang J, Sun Y, Wang Y, Yang J, Li F, Zhou Y, Zhu L, Jessica R, Mohammadhosein F, Xu J, Li Z (2008) Dissection of genetic overlap of salt tolerance QTLs at the seedling and tillering stages using backcross introgression lines in rice. Sci China C Life Sci 51:583–591

    Article  PubMed  Google Scholar 

  222. Zhang Q (2007) Strategies for developing Green Super Rice. Proc Natl Acad Sci U S A 104:16402–16409

    Article  PubMed  CAS  Google Scholar 

  223. Zhang Y, Chen C, Jin XF, Xiong AS, Peng RH, Hong YH, Yao QH, Chen JM (2009) Expression of a rice DREB1 gene, OsDREB1D, enhances cold and high-salt tolerance in transgenic Arabidopsis. BMB Rep 42:486–492

    Article  PubMed  CAS  Google Scholar 

  224. Zhang SW, Li CH, Cao J, Zhang YC, Zhang SQ, Xia YF, Sun DY, Sun Y (2009) Altered architecture and enhanced drought tolerance in rice via the down-regulation of indole-3-acetic acid by TLD1/OsGH3.13 activation. Plant Physiol 151:1889–1901

    Article  PubMed  CAS  Google Scholar 

  225. Zhang W, Shen X, Wu P, Hu B, Liao C (2001) QTL and epistasis for seminal root length under a different water supply in rice. Theor Appl Genet 103:118–123

    Article  CAS  Google Scholar 

  226. 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

    Article  CAS  Google Scholar 

  227. Zhao L, Liu F, Xu W, Di C, Zhou S, Xue Y, Yu J, Su Z (2009) Increased expression of OsSPX1 enhances cold/subfreezing tolerance in tobacco and Arabidopsis thaliana. Plant Biotechnol J 7:550–561

    Article  PubMed  CAS  Google Scholar 

  228. Zheng X, Chen B, Lu G, Han B (2009) Overexpression of a NAC transcription factor enhances rice drought and salt tolerance. Biochem Biophys Res Commun 379:985–989

    Article  PubMed  CAS  Google Scholar 

  229. Zheng BS, Yang L, Mao CZ, Zhang WP, Wu P (2006) QTLs and candidate genes for rice root growth under flooding and upland conditions. Acta Genet Sin 33:141–151

    Article  PubMed  Google Scholar 

  230. Zheng BS, Yang L, Zhang WP, Mao CZ, Wu YR, Yi KK, Liu FY, Wu P (2003) Mapping QTLs and candidate genes for rice root traits under different water-supply conditions and comparative analysis across three populations. Theor Appl Genet 107:1505–1515

    Article  PubMed  CAS  Google Scholar 

  231. Zhou G, Liu F, Cao J, Yue B, Xiong L (2011) Detecting quantitative trait loci for water use efficiency in rice using a recombinant inbred line population. Chin Sci Bull 56:1481–1487

    Article  CAS  Google Scholar 

  232. Zhou L, Liu Y, Liu Z, Kong D, Duan M, Luo L (2010) Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa. J Exp Bot 61:4157–4168

    Article  PubMed  CAS  Google Scholar 

  233. Zhou J, Wang X, Jiao Y, Qin Y, Liu X, He K, Chen C, Ma L, Wang J, Xiong L, Zhang Q, Fan L, Deng XW (2007) Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle. Plant Mol Biol 63:591–608

    Article  PubMed  CAS  Google Scholar 

  234. Zhou L, Zeng Y, Zheng W, Tang B, Yang S, Zhang H, Li J, Li Z (2010) Fine mapping a QTL qCTB7 for cold tolerance at the booting stage on rice chromosome 7 using a near-isogenic line. Theor Appl Genet 121:895–905

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

The authors thank Xipeng Ding, Hao Du, Yujie Fang, Jun You, Ning Tang, and Jianping Huang, Huazhong Agricultural University, for collecting references and draft preparation. Due to limited space of the chapter, the authors apologize for any missing or incomplete citing of references related to the theme. For the same reason, nutrient deficit stresses are not included in this chapter. This work was supported by grants from the National Natural Science Foundation of China (30725021 and 30921091), the National Program on High Technology Development (2012AA10A303), and the Project from the Ministry of Agriculture of China for Transgenic Research.

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Correspondence to Lizhong Xiong Ph.D. .

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Xiong, L. (2013). Abiotic Stress Resistance. In: Zhang, Q., Wing, R. (eds) Genetics and Genomics of Rice. Plant Genetics and Genomics: Crops and Models, vol 5. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-7903-1_13

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