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Genomic Approaches to Understand Varietal Differences in Rice Species and Genotypes with Respect to Stress Response and Quality Traits

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Rice Research for Quality Improvement: Genomics and Genetic Engineering

Abstract

Rice is one of the major food crops feeding more than 3.5 million people worldwide, especially in developing countries. The emerging population demands increased production of rice with improved quality and traits which is a challenge for sustainable rice cultivation. Although the rice production over the past decade is increasing annually, yet it is not sufficient to meet the need. Elevated demands for rice need increased production for which abundant arable land is unavailable, especially in Asian countries where more than 90% of rice is produced and consumed. Under a variable range of agroclimatic conditions, rice is produced across the world, so it is highly prone to a wide range of abiotic stress conditions including extreme temperature changes, heavy metal toxicity, salinity, and drought stress. Conjunction of various abiotic stresses is more common in field conditions, and abiotic stresses seldom occur singly. Different rice genotypes respond differentially to abiotic stress, and variance of intraspecific responses can be noted within indica and japonica varieties. Responses to abiotic stress tolerance is a complex trait, although many genes related to abiotic stress response have been identified, yet there remain gaps which are needed to be bridged for complete understanding of the differential varietal traits. Functional genomics has revealed more than 2000 genes which have been cloned and partially characterized; genome-wide expression profiling of rice varieties, mutants, and transgenics have also aided the development as well. Molecular regulatory networks involved in several agronomic traits have been investigated. Newer fields of proteomics, metabolomics, phenomics, and epigenomics have also aided the functional genomics research in the recent times. We briefly review here the recent developments in rice functional genomics research that are of paramount significance in understanding the responses and quality traits of rice varieties to abiotic stress.

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References

  • Abdullah T, Pawar DD, Kale KD (2015) Water and nutrient use efficiencies of wheat (Triticum aestivum L.) under drip fertigation. Agric Sustain Dev 3(1):52–56

    Google Scholar 

  • Abrol IP, Bhumbla DR (1978) Some comments on terminology relating to salt-affected soils. In: Proceedings of the dryland-saline-seep control, Edmonton, Canada, June 1978, pp 6–27

    Google Scholar 

  • Aghaee A, Moradi F, Zare-Maivan H, Zarinkamar F, Irandoost HP, Sharifi P (2011) Physiological responses of two rice (Oryza sativa L.) genotypes to chilling stress at seedling stage. Afr J Biotechnol 10(39):7617–7621

    Google Scholar 

  • Ahmad I, Mian A, Maathuis FJ (2016) Overexpression of the rice AKT1 potassium channel affects potassium nutrition and rice drought tolerance. J Exp Bot 67(9):2689–2698

    Article  CAS  Google Scholar 

  • Ahsan N, Lee S-H, Lee D-G, Lee H, Lee SW, Bahk JD, Lee B-H (2007a) Physiological and protein profiles alternation of germinating rice seedlings exposed to acute cadmium toxicity. C R Biol 330(10):735–746

    Article  CAS  Google Scholar 

  • Ahsan N, Lee D-G, Lee S-H, Kang KY, Lee JJ, Kim PJ, Yoon H-S, Kim J-S, Lee B-H (2007b) Excess copper induced physiological and proteomic changes in germinating rice seeds. Chemosphere 67(6):1182–1193

    Article  CAS  Google Scholar 

  • Aina R, Labra M, Fumagalli P, Vannini C, Marsoni M, Cucchi U, Citterio S (2007) Thiol-peptide level and proteomic changes in response to cadmium toxicity in Oryza sativa L roots. Environ Exp Bot 59:381–392

    Article  CAS  Google Scholar 

  • Ali MG, Naylor R, Matthews S (2006) Distinguishing the effects of genotype and seed physiological age on low temperature tolerance of rice (Oryza sativa L.). Exp Agric 42:337–349

    Article  Google Scholar 

  • Ali S, Liu Y, Ishaq M, Shah T, Abdullah Ilyas A, Uddin I (2017) Climate change and its impact on the yield of major food crops: evidence from Pakistan. Foods 6:39

    Article  Google Scholar 

  • Allan AC, Fluhr R (1997) Two distinct sources of elicited reactive oxygen species in tobacco epidermal cells. Plant Cell 9:1559–1572

    Article  CAS  Google Scholar 

  • Alvarado R, Hernaiz S (2007) Antecedentesgeneralessobre el arroz en Chile. In: Alvarado R (ed) Arroz Manejo Tecnologico, vol 162 of Bolet’ in INIA. Instituto de Investigaciones Agropecuarias INIA, Centro Regional de Investigacion Quilamapu, Chillan, Chile, p 179

    Google Scholar 

  • Amin USM, Biswas S, Elias SM et al (2016) Enhanced salt tolerance conferred by the complete 2.3 kb cDNA of the rice vacuolar Na+/H+ antiporter gene compared to 1.9 kb coding region with 50 UTR in transgenic lines of rice. Front Plant Sci 7:14

    Article  CAS  Google Scholar 

  • Amirjani MR (2011) Effect of salinity stress on growth, sugar content, pigments and enzyme activity of rice. Int J Bot 7:73–81

    Article  CAS  Google Scholar 

  • Andaya VC, Mackill DJ (2003) Mapping of QTLs associated with cold tolerance during the vegetative stage in rice. J Exp Bot 54:2579–2585

    Article  CAS  Google Scholar 

  • 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  CAS  Google Scholar 

  • Anjum SA, Xie XY, Wang LC et al (2011) Morphological, physiological and biochemical responses of plants to drought stress. Afr J Agric Res 6(9):2026–2032

    Google Scholar 

  • Anjum NA, Hasanuzzaman M, Hossain MA, Thangavel P, Roychoudhury A, Gill SS, Duarte AC (2015) Jacks of metal/metalloid chelation trade in plants—an overview. Front Plant Sci 6:192

    Google Scholar 

  • Apel K, Hirt H (2004) Reactive oxygen species: metabolism, oxidative stress and signal transduction. Annu Rev Plant Biol 55:373–399

    Article  CAS  Google Scholar 

  • Arenhart RA, De Lima JC, Pedron M, Carvalho FE, Da Silveira JAG, Rosa SB, Margis-Pinheiro M (2013) Involvement of ASR genes in aluminium tolerance mechanisms in rice. Plant Cell Environ 36:52–67

    Article  CAS  Google Scholar 

  • Arduini M, Di Tommaso A, Nanni A (1997) Brittle failure in FRP plate and sheet bonded beams. ACI Struct J 94:363–370

    Google Scholar 

  • Asano T, Hayashi N, Kobayashi M et al (2012) A rice calcium-dependent protein kinase OsCPK12 oppositely modulates salt-stress tolerance and blast disease resistance. Plant J 69(1):26–36

    Article  CAS  Google Scholar 

  • Ashraf M (2001) Relationships between growth and gas exchange characteristics in some salt-tolerant amphidiploids Brassica species in relation to their diploid parents. Environ Exp Bot 45:155–163

    Article  CAS  Google Scholar 

  • Ashraf U, Kanu AS, Mo Z, Hussain S, Anjum SA, Khan I, Tang X (2015) Lead toxicity in rice: effects, mechanisms, and mitigation strategies—a mini review. Environ Sci Pollut Res 22:18318–18332

    Article  CAS  Google Scholar 

  • Baker NR (2008) Chlorophyll fluorescence: a probe of photosynthesis in vivo. Annu Rev Plant Biol 59:89–113

    Article  CAS  Google Scholar 

  • Banerjee A, Roychoudhury A (2018) Abiotic stress, generation of reactive oxygen species, and their consequences: an overview. In: Singh VP, Singh S, Tripathi DK, Prasad SM, Chauhan DK (eds) Reactive oxygen species in plants: boon or bane? Revisiting the role of ROS, 1st edn. Wiley, New York, pp 23–50

    Google Scholar 

  • Banerjee A, Roychoudhury A (2019) Cold stress and photosynthesis. In: Ahmad P, Ahanger MA, Alyemeni MN, Alam P (eds) Photosynthesis, productivity, and environmental stress. Wiley, New York, pp 27–37

    Chapter  Google Scholar 

  • Banerjee A, Roychoudhury A, Krishnamoorthi S (2016) Emerging techniques to decipher microRNAs (miRNAs) and their regulatory role in conferring abiotic stress tolerance of plants. Plant Biotechnol Rep 10:185–205

    Article  Google Scholar 

  • Baruah AR, Ishigo-Oka N, Adachi M (2009) Cold tolerance at the early growth stage in wild and cultivated rice. Euphytica 165:459–470

    Article  Google Scholar 

  • Bartels D, Sunkar R (2005) Drought and salt tolerance in plants. Crit Rev Plant Sci 24(1):23–58

    Article  CAS  Google Scholar 

  • Bassil E, Coku A, Blumwald E (2012) Cellular ion homeostasis: emerging roles of intracellular NHX Na1/H1 antiporters in plant growth and development. J Exp Bot 63(16):5727–5740

    Article  CAS  Google Scholar 

  • Basu S, Roychoudhury A, Saha PP, Sengupta DN (2010a) Differential antioxidative responses of indica rice cultivars to drought stress. Plant Growth Regul 60:51–59

    Article  CAS  Google Scholar 

  • Basu S, Roychoudhury A, Saha PP, Sengupta DN (2010b) Comparative analysis of some biochemical responses of three indica rice varieties during polyethylene glycol-mediated water stress exhibits distinct varietal differences. Acta Physiol Plant 32:551–563

    Article  CAS  Google Scholar 

  • Ben-Saad R, Ben-Ramdhan W, Zouari N, Azaza J, Mieulet D, Guiderdoni E, Hassairi A (2012) Marker-free transgenic durum wheat cv. Karim expressing the AlSAP gene exhibits a high level of tolerance to salinity and dehydration stresses. Mol Breed 30:521–533

    Article  CAS  Google Scholar 

  • Blumwald E, Grover A, Good AG (2004) Breeding for abiotic stress resistance: challenges and opportunities. In: New directions for a diverse planet. Proceedings of the 4th International Crop Science Congress, Brisbane, Australia, 1–15

    Google Scholar 

  • Bonnecarrère V, Borsani O, Díaz P, Capdevielle F, Blanco P, Monza J (2011) Response to photoxidative stress induced by cold in japonica rice is genotype dependent. Plant Sci 180:726–732

    Article  CAS  Google Scholar 

  • Bonnecarrere V, Quero G, Monteverde E, Rosas J, De Vida FP, Cruz M, Borsani O (2015) Candidate gene markers associated with cold tolerance in vegetative stage of rice (Oryzasativa L). Euphytica 203:385–398

    Article  CAS  Google Scholar 

  • Burzynski M (1987) Influence of lead and cadmium on the absorption and distribution of potassium, calcium, magnesium and iron in cucumber seedlings. Acta Physiol Plant 9:229–238

    CAS  Google Scholar 

  • Campo S, Baldrich P, Messeguer J et al (2014) Overexpression of a calcium-dependent protein kinase confers salt and drought tolerance in rice by preventing membrane lipid peroxidation. Plant Physiol 165(2):688–704

    Article  CAS  Google Scholar 

  • Carillo P, Annunziata MG, Pontecorvo G et al (2011) Salinity stress and salt tolerance. In: Shanker A (ed) Abiotic stress in plants: mechanisms and adaptations. InTech, Rijeka, Croatia, pp 2–35

    Google Scholar 

  • Chatterjee C, Dube BK, Sinha P, Srivastava P (2004) Detrimental effects of lead phytotoxicity on growth, yield, and metabolism of rice. Commun Soil Sci Plant Anal 35:255–265

    Article  CAS  Google Scholar 

  • Chen L, Lou QJ, Sun ZX, Xing YZ, Yu XQ, Luo LJ (2006) QTL mapping of low temperature on germination rate of rice. Rice Sci 13:93–98

    Google Scholar 

  • Chen NA, Xu Y, Wang XIN, Du C, Du J, Yuan M, 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  CAS  Google Scholar 

  • Chen LJ, Wuriyanghan H, Zhang YQ et al (2013) An S-domain receptor-like kinase, OsSIK2, confers abiotic stress tolerance and delays dark-induced leaf senescence in rice. Plant Physiol 163(4):1752–1765

    Article  CAS  Google Scholar 

  • Chen HD, Xie WB, He H et al (2014) A high-density SNP genotyping array for rice biology and molecular breeding. Mol Plant 7(3):541–553

    Article  CAS  Google Scholar 

  • Chen G, Hu Q, Luo LE et al (2015) Rice potassium transporter OsHAK1 is essential for maintaining potassium-mediated growth and functions in salt tolerance over low and high potassium concentration ranges. Plant Cell Environ 38(12):2747–2765

    Article  CAS  Google Scholar 

  • Chinnusamy V, Zhu J, Zhu JK (2006) Gene regulation during cold acclimation in plants. Physiol Plant 126(1):52–61

    Article  CAS  Google Scholar 

  • Cotsaftis O, Plett D, Shirley N et al (2012) A two-staged model of Na1 exclusion in rice explained by 3D modeling of HKT transporters and alternative splicing. PLoS One 7(7):e39865. https://doi.org/10.1371/journal.pone.0039865

    Article  CAS  Google Scholar 

  • Cramer GR, Nowak RS (1992) Supplemental manganese improves the relative growth, net assimilation and photosynthetic rates of salt-stressed barley. Physiol Plant 84:600–605

    Article  CAS  Google Scholar 

  • Cushman JC, Bohnert HJ (2000) Genomic approaches to plant stress tolerance. Curr Opin Plant Biol 3:117–124

    Article  CAS  Google Scholar 

  • da Cruz RP, Sperotto RA, Cargnelutti D et al (2013) Avoiding damage and achieving cold tolerance in rice plants. Food Energy Security 22:96–119

    Article  Google Scholar 

  • Dai X, Xu Y, Xu MQ et al (2007) Overexpression of an R1R2R3 MYB gene, OsMYB3R-2, increases tolerance to freezing, drought, and salt stress in transgenic Arabidopsis. Plant Physiol 143(4):1739–1751

    Article  CAS  Google Scholar 

  • DalCorso G, Farinati S, Maistri S, Furini A (2008) How plants cope with cadmium: staking all on metabolism and gene expression. J Integr Plant Biol 50:1268–1280

    Article  CAS  Google Scholar 

  • Das P, Mishra M, Lakra N, Singla-Pareek SL, Pareek A (2014) Mutation breeding: a powerful approach for obtaining abiotic stress tolerant crops and upgrading food security for human nutrition. Mutagen: Exploring Nov Genes Pathw:15–36

    Google Scholar 

  • Dey A, Samanta MK, Gayen S et al (2017) Correction: Enhanced gene expression rather than natural polymorphism in coding sequence of the OsbZIP23 determines drought tolerance and yield improvement in rice genotypes. PLoS One 12:e0187172

    Article  Google Scholar 

  • Dickin E, Wright D (2008) The effects of winter waterlogging and summer drought on the growth and yield of winter wheat (Triticum aestivum L.). Eur J Agron 28(3):234–244

    Article  Google Scholar 

  • Diedhiou CJ, Golldack D (2006) Salt-dependent regulation of chloride channel transcripts in rice. Plant Sci 170:793–800

    Article  CAS  Google Scholar 

  • Diedhiou CJ, Popova OV, Dietz KJ (2008) The SNF1-type serine-threonine protein kinase SAPK4 regulates stress-responsive gene expression in rice. BMC Plant Biol 8:49

    Article  CAS  Google Scholar 

  • Ding Z, Hu X, Wan Y, Wang S, Gao B (2016) Removal of lead, copper, cadmium, zinc, and nickel from aqueous solutions by alkali-modified biochar: batch and column tests. J Ind Eng Chem 33:239–245

    Article  CAS  Google Scholar 

  • Dionisiosese ML, Tobita J (1998) Antioxidant response of seedlings to salinity stress. Plant Sci 135:1–9

    Article  CAS  Google Scholar 

  • Dixit S, Singh A, Sta Cruz MT et al (2014) Multiple major QTL lead to stable yield performance of rice cultivars across varying drought intensities. BMC Genet 15:16

    Article  Google Scholar 

  • Dixit S, Singh A, Sandhu N (2017) Combining drought and submergence tolerance in rice: marker-assisted breeding and QTL combination effects. Mol Breed 37(12):143

    Article  Google Scholar 

  • Dong J, Wu F, Zhang G (2006) Influence of cadmium on antioxidant capacity and four microelement concentrations in tomato seedlings (Lycopersicon esculentum). Chemosphere 64:1659–1666

    Article  CAS  Google Scholar 

  • Du H, Huang F, Wu N et al (2018) Integrative regulation of drought escape through ABA-dependent and-independent pathways in rice. Mol Plant 11:584–587

    Article  CAS  Google Scholar 

  • Dubouzet JG, Sakuma Y, Ito Y et al (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(4):751–763

    Article  CAS  Google Scholar 

  • Dufey I, Draye X, Lutts S, Lorieux M, Martinez C, Bertin P (2015) Novel QTLs in an interspecific backcross Oryza sativa × Oryza glaberrima for resistance to iron toxicity in rice. Euphytica 204:609–625

    Article  CAS  Google Scholar 

  • El-Esawi MA, Alayafi AA (2019) Overexpression of rice Rab7 gene improves drought and heat tolerance and increases grain yield in rice (Oryza sativa L.). Genes 10:56

    Article  CAS  Google Scholar 

  • Ensminger I, Busch F, Huner NP (2006) Photostasis and cold acclimation: sensing low temperature through photosynthesis. Physiol Plant 126(1):28–44

    Article  CAS  Google Scholar 

  • Fahad S, Bajwa AA, Nazir U et al (2017) Crop production under drought and heat stress: plant responses and management options. Front Plant Sci 8:1147

    Article  Google Scholar 

  • Fahad S, Hussain S, Saud S, Hassan S, Ihsan Z, Shah AN, Wu C, Yousaf M, Nasim W, Alharby H, Alghabari F, Huang J (2016a) Exogenously applied plant growth regulators enhance the morpho-physiological growth and yield of rice under high temperature. Front Plant Sci 7:1250

    Article  Google Scholar 

  • Fahad S, Hussain S, Saud S, Khan F, Hassan S, Amanullah W, Nasim M, Arif F, Wang JH (2016b) Exogenously applied plant growth regulators affect heat-stressed rice pollens. J Agron Crop Sci 202(2):139–150

    Article  CAS  Google Scholar 

  • Fahad S, Hussain S, Saud S, Hassan S, Chauhan BS, Khan F, Ihsan MZ, Ullah A, Wu C, Bajwa AA, Alharby H, Amanullah WN, Shahzad B, Tanveer M, Huang J, Feltus FA (2016c) Responses of rapid viscoanalyzer profile and other rice grain qualities to exogenously applied plant growth regulators under high day and high night temperatures. PLoS One 11(7):e0159590

    Article  CAS  Google Scholar 

  • Fahad S, Hussain S, Saud S, Hassan S, Tanveer M, Ihsan MZ, Shah AN, Ullah A, Nasrullah FK, Ullah S, Alharby H, Nasim W, Wu C, Huang J (2016d) A combined application of biochar and phosphorus alleviates heat-induced adversities on physiological, agronomical and quality attributes of rice. Plant Physiol Biochem 103:191–198

    Article  CAS  Google Scholar 

  • Fahad S, Yu H, Wang L, Haroon M, Ullah RS, Nazir A, Khan A (2019) Recent progress in the synthesis of silver nanowires and their role as conducting materials. J Mater Sci 54:997–1035

    Article  CAS  Google Scholar 

  • Faisal ARM, Biswas S, Zerin T, Rahman T, Seraj ZI (2017) Downregulation of the DST transcription factor using artificial microRNA to increase yield, salt and drought tolerance in rice. Am J Plant Sci 8(09):2219

    Article  CAS  Google Scholar 

  • Fan Y, Zhu T, Li M (2017) Heavy metal contamination in soil and brown rice and human health risk assessment near three mining areas in central China. J Healthc Engine 2017:4124302

    Google Scholar 

  • Farooq M, Aziz T, Basra SMA et al (2008) Chilling tolerance in hybrid maize induced by seed priming with salicylic acid. J Agron Crop Sci 194:161–168

    Article  CAS  Google Scholar 

  • Farooq M, Wahid A, Kobayashi N et al (2009a) Plant drought stress: effects, mechanisms and management. In: Sustainable agriculture. Springer, Dordrecht, pp 153–188

    Chapter  Google Scholar 

  • Farooq M, Wahid A, Kobayashi N et al (2009b) Plant drought stress: effects, mechanisms and management. Agron Sustain Dev 29:185–212

    Article  Google Scholar 

  • Farrell TC, Fox KM, Williams RL (2006) Minimising cold damage during reproductive development among temperate rice genotypes. II. Genotypic variation and flowering traits related to cold tolerance screening. Aust J Agr Res 57:89–100

    Article  Google Scholar 

  • Flowers TJ, Flowers SA (2005) Why does salinity pose such a difficult problem for plant breeders? Agric Water Manag 78:15–24

    Article  Google Scholar 

  • Flowers TJ, Yeo AR (1989) Effects of salinity on plant growth and crop yield. In: Cherry JH (ed) Environmental stress in plants. Springer Verlag, Berlin, pp 101–119

    Chapter  Google Scholar 

  • Food and Agricultural Organization (FAO) (2017) Global report on food crises. Food Security and Information Network 2017

    Google Scholar 

  • Food and Agricultural Organization (FAO) (2018) Global report on food crises. Food Security and Information Network 2018

    Google Scholar 

  • Foyer C, Noctor G (2003) Redox sensing and signalling associated with reactive oxygen in chloroplasts, peroxisomes and mitochondria. Physiol Plant 119:355–364

    Article  CAS  Google Scholar 

  • Foyer CH, Noctor G (2009) Redox regulation in photosynthetic organisms: signaling, acclimation and practical implications. Antioxid Redox Signal 11:861–905

    Article  CAS  Google Scholar 

  • Fraiture MA, Roosens NH, Taverniers I, De Loose M, Deforce D, Herman P (2016) Biotech rice: current developments and future detection challenges in food and feed chain. Trends Food Sci Technol 52:66–79

    Article  CAS  Google Scholar 

  • Fu J, Wu H, Ma S, Xiang D (2017) OsJAZ1 attenuates drought resistance by regulating JA and ABA signaling in rice. Front Plant Sci 8:2108

    Article  Google Scholar 

  • Fuchs I, Stolzle S, Ivashikina N (2005) Rice K+ uptake channel OsAKT1 is sensitive to salt stress. Planta 221:212–221

    Article  CAS  Google Scholar 

  • Fujino K, Sekiguchi H, Sato T et al (2004) Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Theor Appl Genet 108:794–799

    Article  CAS  Google Scholar 

  • 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. PNAS 105:12623–12628

    Article  CAS  Google Scholar 

  • Gain P, Mannan MA, Pal PS et al (2004) Effect of salinity on some yield attributes of rice. Pak J Biol Sci 7:760–762

    Article  Google Scholar 

  • Ganguly M, Datta K, Roychoudhury A, Gayen D, Sengupta DN, Datta SK (2012) Overexpression of Rab16A gene in indica rice variety for generating enhanced salt tolerance. Plant Signal Behav 7:502–509

    Article  CAS  Google Scholar 

  • Gao JP, Chao DY, Lin HX (2007) Understanding abiotic stress tolerance mechanisms: recent studies on stress response in rice. J Integr Plant Biol 49:742–750

    Article  CAS  Google Scholar 

  • Gao F, Wang K, Liu Y, Chen Y, Chen P, Shi Z et al (2015) Blocking miR396 increases rice yield by shaping inflorescence architecture. Nat Plants 2(1):1–9

    CAS  Google Scholar 

  • Ghneim-Herrera T, Selvaraj MG, Meynard D et al (2017) Expression of the Aeluropus littoralis AlSAP gene enhances rice yield under field drought at the reproductive stage. Front. Plant Sci 8:994

    Google Scholar 

  • Ghosh B, Ali MN, Saikat G (2016) Response of rice under salinity stress: a review update. J Rice Res 4:167

    Article  Google Scholar 

  • Gill SS, Tuteja N (2010) Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants. Plant Physiol Biochem 48(12):909–930

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Grattan SR, Zeng L, Shannon MC et al (2002) Rice is more sensitive to salinity than previously thought. Calif Agric 56:189–195

    Article  Google Scholar 

  • Guan Q, Takano T, Liu S (2012) Genetic transformation and analysis of rice OsAPX2 gene in Medicago sativa. PLoS One 7(7):e41233

    Article  CAS  Google Scholar 

  • Habibi F, Normohammadi G, Heidarisharif-Abad H, Eivazi A, Majidi-Heravan E, Ghanbari-Malidarreh A (2011) Effect of sowing date on wheat (Triticum Aestivum L.): cold stress on grain yield and yield components at west Azerbaijan of Iran. Adv Environ Biol:3518–3524

    Google Scholar 

  • Hoa PQ, Thanh ND (2017) Analysis of DNA methylation status of the OsSOS1 gene under salt stress in rice. VNU J Sci Nat Sci Technol 32(1S):253–257

    Google Scholar 

  • Hong YB, Zhang HJ, Huang L (2016) Over expression of a stress-responsive NAC transcription factor gene ONAC022 improves drought and salt tolerance in rice. Front Plant Sci 7:4

    Article  Google Scholar 

  • Hossain MA, Cho JI, Han M et al (2010) The ABRE-binding bZIP transcription factor OsABF2 is a positive regulator of abiotic stress and ABA signaling in rice. J Plant Physiol 167(17):1512–1520

    Article  CAS  Google Scholar 

  • Hu H, Dai M, Yao J et al (2006) Over expressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proc Natl Acad Sci U S A 103(35):12987–12992

    Article  CAS  Google Scholar 

  • 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  CAS  Google Scholar 

  • Huang XY, Chao DY, Gao JP et al (2009) A previously unknown zinc finger protein, DST, regulates drought and salt tolerance in rice via stomatal aperture control. Genes Dev 23(15):1805–1817

    Article  CAS  Google Scholar 

  • Huang J, Sun S, Xu D, Lan H, Sun H, Wang Z, Zhang H (2012) A TFIIIA-type zinc finger protein confers multiple abiotic stress tolerances in transgenic rice (Oryza sativa L). Plant Mol Biol 80:337–350

    Article  CAS  Google Scholar 

  • Huang L, Wang Y, Wang W et al (2018) Characterization of transcription factor gene OsDRAP1 conferring drought tolerance in rice. Front. Plant Sci 9:94

    Google Scholar 

  • Islam MM, Khalekuzzaman M (2015) Development of transgenic rice (Oryza sativa L) plant using cadmium tolerance gene (YCFI) through agrobacterium mediated transformation for phytoremediation. Asian J Agric Res 9:139–154

    CAS  Google Scholar 

  • Ito Y, Katsura K, Maruyama K, Taji T, Kobayashi M, Seki M, 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  CAS  Google Scholar 

  • Iyengar E, Reddy M (1996) Photosynthesis in highly salt-tolerant plants. In: Pessarakli M (ed) Handbook of photosynthesis. CRC, Boca Raton, FL, pp 897–909

    Google Scholar 

  • Jain M, Tiwary S, Gadre R (2010) Sorbitol-induced changes in various growth and biochemical parameters in maize. Plant Soil Environ 56:263–267

    Article  CAS  Google Scholar 

  • Jaleel CA, Gopi R, Panneerselvam R (2008) Growth and photosynthetic pigments responses of two varieties of Catharanthus roseus to triadimefon treatment. C R Biol 331:272–277

    Article  CAS  Google Scholar 

  • Jan A, Maruyama K, Todaka D et al (2013) OsTZF1, a CCCH-tandem zinc finger protein, confers delayed senescence and stress tolerance in rice by regulating stress-related genes. Plant Physiol 161(3):1202–1216

    Article  CAS  Google Scholar 

  • Jangam AP, Pathak RR, Raghuram N (2016) Microarray analysis of rice d1 (RGA1) mutant reveals the potential role of G-protein alpha subunit in regulating multiple abiotic stresses such as drought, salinity, heat, and cold. Front Plant Sci 7:11

    Article  Google Scholar 

  • Jeong MJ, Lee SK, Kim BG et al (2006) A rice (Oryza sativa L.) MAP kinase gene, OsMAPK44, is involved in response to abiotic stresses. Plant Cell Tiss Org Cult 85(2):151–160

    Article  CAS  Google Scholar 

  • Jeong JS, Kim YS, Baek KH et al (2010) Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought conditions. Plant Physiol 153(1):185–197

    Article  CAS  Google Scholar 

  • Jeong JS, Kim YS, Redillas MC et al (2013) OsNAC5 over expression enlarges root diameter in rice plants leading to enhanced drought tolerance and increased grain yield in the field. Plant Biotechnol J 11(1):101–114

    Article  CAS  Google Scholar 

  • Jiang L, Liu S, Hou M, Tang J, Chen L, Zhai H, Wan J (2006) Analysis of QTLs for seed low temperature germinability and anoxia germinability in rice (Oryza sativa L). Field Crops Res 98:68–75

    Article  Google Scholar 

  • Ji SL, Jiang L, Wang YH, Liu SJ, Liu X, Zhai HQ, Atsushi Y, Wan JM (2008) QTL and epistasis for low temperature germinability in rice. Acta Agron Sin 34:551–556

    CAS  Google Scholar 

  • Ji X, Dong B, Shiran B, Talbot MJ, Edlington JE, Hughes T, Dolferus R (2011) Control of abscisic acid catabolism and abscisic acid homeostasis is important for reproductive stage stress tolerance in cereals. Plant Physiol 156:647–662

    Article  CAS  Google Scholar 

  • Jonak C, Nakagami H, Hirt H (2004) Heavy metal stress activation of distinct mitogen-activated protein kinase pathways by copper and cadmium. Plant Physiol 136:3276–3283

    Article  CAS  Google Scholar 

  • Kadam N, Tamilselvan A, Lawas LMF et al (2017) Genetic control of plasticity in root morphology and anatomy of rice in response to water-deficit. Plant Physiol 174:2302–2315

    Article  CAS  Google Scholar 

  • 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(5):445–462

    Article  CAS  Google Scholar 

  • Kathuria H, Giri J, Tyagi H, Tyagi AK (2007) Advances in transgenic rice biotechnology. Crit Rev Plant Sci 26:65–103

    Article  CAS  Google Scholar 

  • Katsuhara M, Koshio K, Shibasaka M (2003) Over-expression of a barley aquaporin increased the shoot/root ratio and raised salt sensitivity in transgenic rice plants. Plant Cell Physiol 44(12):1378–1383

    Article  CAS  Google Scholar 

  • Kaveh H, Nemati H, Farsi M (2011) How salinity affect germination and emergence of tomato lines. J Biol Environ Sci 5:159–163

    Google Scholar 

  • 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  CAS  Google Scholar 

  • Kawasaki S, Borchert C, Deyholos M (2001) Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 13:889–905

    Article  CAS  Google Scholar 

  • Khan MA (2012) Current status of genomic based approaches to enhance drought tolerance in rice (Oryza sativa L.), an over view. Mol Plant Breed 3(1):1–10

    Google Scholar 

  • Kibria MG, Hossain M, Murata Y (2017) Antioxidant defense mechanisms of salinity tolerance in rice genotypes. Ric Sci 24:155–162

    Article  Google Scholar 

  • Kim JA, Agrawal GK, Rakwal R et al (2003) Molecular cloning and mRNA expression analysis of a novel rice (Oryza sativa L.) MAPK kinase, OsEDR1, an ortholog of Arabidopsis AtEDR1, reveal its role in defense/stress signalling pathways and development. Biochem Biophys Res Commun 300(4):868–876

    Article  CAS  Google Scholar 

  • Kim SJ, Lee SC, Hong SK, An K, An G, Kim SR (2009) Ectopic expression of a cold-responsive OsAsr1cDNA gives enhanced cold tolerance in transgenic rice plants. Mol Cells 27(4):449–458

    Article  CAS  Google Scholar 

  • Kim S-I, Tai TH (2011) Evaluation of seedling cold tolerance in rice cultivars: a comparison of visual ratings and quantitative indicators of physiological changes. Euphytica 178(3):437–447

    Article  Google Scholar 

  • Kim SH, Choi HS, Cho YC, Kim SR (2011) Cold-responsive regulation of a flower-preferential class III peroxidase gene, OsPOX1, in rice (Oryza sativa L.). J Plant Biol 55(2):123–131

    Article  CAS  Google Scholar 

  • Kim ST, Kim SG, Agrawal GK et al (2014) Rice proteomics: a model system for crop improvement and food security. Proteomics 14:593–610

    Article  CAS  Google Scholar 

  • 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 Gen Genomics 284:45–54

    Article  CAS  Google Scholar 

  • Koh S, Lee SC, Kim MK et al (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(4):453–466

    Article  CAS  Google Scholar 

  • Kong J, Gong JM, Zhang ZG (2003) A new AOX homologous gene OsIM1 from rice (Oryza sativa L.) with an alternative splicing mechanism under salt stress. Theor Appl Genet 107(2):326–331

    Article  CAS  Google Scholar 

  • Kumar K, Sinha AK (2013) Over expression of constitutively active mitogen activated protein kinase 6 enhances tolerance to salt stress in rice. Rice 6(1):25

    Article  Google Scholar 

  • Kumar K, Kumar M, Kim SR et al (2013) Insights into genomics of salt stress response in rice. Rice 6(1):27

    Article  Google Scholar 

  • Kuramata M, Masuya S, Takahashi Y, Kitagawa E, Inoue C, Ishikawa S, Kusano T (2009) Novel cysteine-rich peptides from Digitaria ciliaris and Oryza sativa enhance tolerance to cadmium by limiting its cellular accumulation. Plant Cell Physiol 50:106–117

    Article  CAS  Google Scholar 

  • Kurokawa Y, Noda T, Yamagata Y (2016) Construction of a versatile SNP array for pyramiding useful genes of rice. Plant Sci 242:131–139

    Article  CAS  Google Scholar 

  • Lafitte HR, Price AH, Courtois B (2004) Yield response to water deficit in an upland rice mapping population: associations among traits and genetic markers. Theor Appl Genet 109(6):1237–1246

    Article  CAS  Google Scholar 

  • Lafitte H, Li ZK, Vijayakumar C et al (2006) Improvement of rice drought tolerance through backcross breeding: evaluation of donors and selection in drought nurseries. Field Crops R 97:77–96

    Article  Google Scholar 

  • Larcher W (1980) Physiological plant ecology, 2nd edn. Springer-Verlag, Berlin

    Book  Google Scholar 

  • Le TTT, Williams B, Mundree SG (2018) An osmotin from the resurrection plant Tripogon loliiformis (TlOsm) confers tolerance to multiple abiotic stresses in transgenic rice. Physiol Plant 162:13–34

    Article  CAS  Google Scholar 

  • Lee KS, Choi WY, Ko JC (2003) Salinity tolerance of japonica and indica rice (Oryza sativa L.) at the seedling stage. Planta 216:1043–1046

    Article  CAS  Google Scholar 

  • Lee S-C, Kim J-Y, Kim S-H, Kim S-J, Lee K, Han S-K, Choi H-S, Jeong D-H, An G, Kim S-R (2004a) Trapping and characterization of cold-responsive genes from T-DNA tagging lines in rice. Plant Sci 166(1):69–79

    Article  CAS  Google Scholar 

  • Lee SC, Huh KW, An K, An G, Kim SR (2004b) Ectopic expression of a cold-inducible transcription factor, CBF1/DREB1b, in transgenic rice (Oryza sativa L). Mol Cells (Springer Science & Business Media BV) 18

    Google Scholar 

  • Lee S, An G (2009) Over-expression of OsIRT1 leads to increased iron and zinc accumulations in rice. Plant Cell Environ 32(4):408–416

    Article  CAS  Google Scholar 

  • Lee DG, Ahsan N, Lee SH, Lee JJ, Bahk JD, Kang KY, Lee BH (2009) Chilling stress-induced proteomic changes in rice roots. J Plant Physiol 166:1–11

    Article  CAS  Google Scholar 

  • Lee DH, Kim YS, Lee CB (2011a) The inductive responses of the antioxidant enzymes by salt stress in the rice (Oryza sativa L.). J Plant Physiol 158:737–745

    Article  Google Scholar 

  • Lee SK, Kim BG, Kwon TR et al (2011b) Over expression of the mitogen-activated protein kinase gene OsMAPK33 enhances sensitivity to salt stress in rice (Oryza sativa L.). J Biosci 36(1):139–151

    Article  CAS  Google Scholar 

  • Lee HJ, Abdula SE, Jang DW, Park SH, Yoon UH, Jung YJ, Cho YG (2013) Overexpression of the glutamine synthetase gene modulates oxidative stress response in rice after exposure to cadmium stress. Plant Cell Rep 32:1521–1529

    Article  CAS  Google Scholar 

  • Li S, Li F, Wang J, Zhang WEN, Meng Q, Chen TH, Yang X (2011) Glycinebetaine enhances the tolerance of tomato plants to high temperature during germination of seeds and growth of seedlings. Plant Cell Environ 34:1931–1943

    Article  CAS  Google Scholar 

  • Li H, Li X, Zhang D, Liu H, Guan K (2013) Effects of drought stress on the seed germination and early seedling growth of the endemic desert plant Eremosparton songoricum (Fabaceae). EXCLI J 12:89

    Google Scholar 

  • Li M, Guo LJ, Guo CM (2016) Over-expression of a DUF1644 protein gene, SIDP361, enhances tolerance to salt stress in transgenic rice. J Plant Biol 59(1):62–73

    Article  CAS  Google Scholar 

  • Li J, Li Y, Yin Z et al (2017) OsASR5 enhances drought tolerance through a stomatal closure pathway associated with ABA and H2O2 signalling in rice. Plant Biotechnol J 15:183–196

    Article  CAS  Google Scholar 

  • Li J, Wang XX, Zhao GX et al (2018a) Metal-organic framework-based materials: superior adsorbents for the capture of toxic and radioactive metal ions. Chem Soc Rev 47:2322–2356

    Article  CAS  Google Scholar 

  • Li Y, Xiao J, Chen L et al (2018b) Rice functional genomics research: past decade and future. Mol Plant 11:359–380

    Article  CAS  Google Scholar 

  • Liang C, Wang Y, Zhu Y et al (2014) OsNAP connects abscisic acid and leaf senescence by fine-tuning abscisic acid biosynthesis and directly targeting senescence-associated genes in rice. Proc Natl Acad Sci U S A 111(27):10013–10018

    Article  CAS  Google Scholar 

  • Liao YD, Lin KH, Chen CC et al (2016) Oryza sativa protein phosphatase 1a (OsPP1a) involved in salt stress tolerance in transgenic rice. Mol Breed 36:22

    Article  CAS  Google Scholar 

  • Liao Y, Liu S, Jiang Y, Hu C, Zhang X, Cao X, Chen R (2017) Genome-wide analysis and environmental response profiling of dirigent family genes in rice (Oryza sativa). Genes Genomics 39:47–62

    Article  CAS  Google Scholar 

  • Liu J, Qian M, Cai G, Yang J, Zhu Q (2007) Uptake and translocation of Cd in different rice cultivars and the relation with Cd accumulation in rice grain. J Hazard Mater 143:443–447

    Article  CAS  Google Scholar 

  • Liu D, Chen X, Liu J et al (2012) The rice ERF transcription factor OsERF922 negatively regulates resistance to Magnaporthe oryzae and salt tolerance. J Exp Bot 63(10):3899–3911

    Article  CAS  Google Scholar 

  • Liu X, Li X, Dai C et al (2017) Improved short-term drought response of transgenic rice over-expressing maize C4 phosphoenolpyruvate carboxylase via calcium signal cascade. J Plant Physiol 218:206–221

    Article  CAS  Google Scholar 

  • Lou Q, Chen L, Sun Z, Xing Y, Li J, Xu X, Luo L (2007) A major QTL associated with cold tolerance at seedling stage in rice (Oryza sativa L). Euphytica 158:87–94

    Article  CAS  Google Scholar 

  • Ma X, Zhang Q, Zhu Q, Liu W, Chen Y, Qiu R, Xie Y (2015) A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Mol Plant 8:1274–1284

    Article  CAS  Google Scholar 

  • Ma Q, Dai X, Xu Y, Guo J, Liu Y, Chen N, 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  CAS  Google Scholar 

  • Ma XL, Wang YJ, Xie SL, Wang C, Wang W (2007) Glycinebetaine application ameliorates negative effects of drought stress in tobacco. Russ J Plant Physiol 54:472

    Article  CAS  Google Scholar 

  • Maclean J, Hardy B, Hettel G (2013) Rice Almanac: source book for one of the most important economic activities on earth. IRRI, Los Baños, Philippines

    Google Scholar 

  • Madoka Y, Kashiwagi T, Hirotsu N (2008) Indian rice ‘Kasalath’ contains genes that improve traits of Japanese premium rice ‘Koshihikari’. Theor Appl Genet 116:603–612

    Article  CAS  Google Scholar 

  • Mallikarjuna G, Mallikarjuna K, Reddy MK et al (2011) Expression of OsDREB2A transcription factor confers enhanced dehydration and salt stress tolerance in rice (Oryza sativa L.). Biotechnol Lett 33(8):1689–1697

    Article  CAS  Google Scholar 

  • Miller GA, Suzuki N, Ciftci-Yilmaz SU et al (2010) Reactive oxygen species homeostasis and signalling during drought and salinity stresses. Plant Cell Environ 33(4):453–467

    Article  CAS  Google Scholar 

  • Mishra P, Bhoomika K, Dubey RS (2013) Differential responses of antioxidative defense system to prolonged salinity stress in salt-tolerant and salt-sensitive Indica rice (Oryza sativa L) seedlings. Protoplasma 250:3–19

    Article  CAS  Google Scholar 

  • Mishra S, Singh B, Panda K et al (2016) Association of SNP haplotypes of HKT family genes with salt tolerance in Indian wild rice germplasm. Rice 9(1):15

    Article  Google Scholar 

  • Mithöfer A, Schulze B, Boland W (2004) Biotic and heavy metal stress response in plants: evidence for common signals. FEBS Lett 566:1–5

    Article  CAS  Google Scholar 

  • Miura A, Yonebayashi S, Watanabe K, Toyama T, Shimada H, Kakutani T (2001) Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411(6834):212–214

    Article  CAS  Google Scholar 

  • Miyadate H, Adachi S, Hiraizumi A, Tezuka K, Nakazawa N, Kawamoto T, Satoh-Nagasawa N (2011) OsHMA3, a P1B-type of ATPase affects root-to-shoot cadmium translocation in rice by mediating efflux into vacuoles. New Phytol 189:190–199

    Article  CAS  Google Scholar 

  • Mohabbati F, Paknejad F, Vazan S, Habibi D, Tookallo MR, Moradi F (2013) Protective effect of exogenous PGRs on chlorophyll fluorescence and membrane integrity of rice seedlings under chilling stress. Res J Appl Sci Eng Technol 5(1):146–153

    Article  CAS  Google Scholar 

  • Molla KA, Debnath AB, Ganie SA et al (2015) Identification and analysis of novel salt responsive candidate gene based SSRs (cgSSRs) from rice (Oryza sativa L.). BMC Plant Biol 15:122

    Article  CAS  Google Scholar 

  • Morsy MR, Jouve L, Hausman JF, Hoffmann L, Stewart JM (2007) Alteration of oxidative and carbohydrate metabolism under abiotic stress in two rice (Oryza sativa L.) genotypes contrasting in chilling tolerance. J Plant Physiol 164(2):157–167

    Article  CAS  Google Scholar 

  • 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(16):6309–6314

    Article  CAS  Google Scholar 

  • Munns R (2002) Comparative physiology of salt and water stress. Plant Cell Environ 25:239–250

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Munns R, James RA, Lauchli A (2006) Approaches to increasing the salt tolerance of wheat and other cereals. J Exp Bot 57:1025–1043

    Article  CAS  Google Scholar 

  • Muthurajan R, Shobbar ZS, Jagadish SVK, Bruskiewich R, Ismail A, Leung H, Bennett J (2011) Physiological and proteomic responses of rice peduncles to drought stress. Mol Biotechnol 48(2):173–182

    Article  CAS  Google Scholar 

  • Nahar K, Hasanuzzaman M, Rahman A et al (2016a) Polyamines confer salt tolerance in mung bean (Vigna radiata L.) by reducing sodium uptake, improving nutrient homeostasis, antioxidant defense, and methyl glyoxal detoxification systems. Front. Plant Sci 7:1104

    Google Scholar 

  • Nahar S, Kalita J, Sahoo L et al (2016b) Morphophysiological and molecular effects of drought stress in rice. Ann Plant Sci 5:1409–1416

    Article  Google Scholar 

  • Naik KP, Krishnamurthy N, Ramachandra C (2015) Effect of nutrient sources on grain yield, methane emission and water productivity of rice (Oryza sativa) under different methods of cultivation. Indian J Agron 60(2):249–254

    CAS  Google Scholar 

  • Nakashima K, Tran LSP, Nguyen V et al (2007) Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice. Plant J 51(4):617–630

    Article  CAS  Google Scholar 

  • Nakashima K, Takasaki H, Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K (2012) NAC transcription factors in plant abiotic stress responses. Biochim Biophys Acta Gene Regul Mech 1819(2):97–103

    Article  CAS  Google Scholar 

  • Nagao M, Minami A, Arakawa K, Fujikawa S, Takezawa D (2005) Rapid degradation of starch in chloroplasts and concomitant accumulation of soluble sugars associated with ABA-induced freezing tolerance in the moss Physcomitrella patens. J Plant Physiol 162(2):169–180

    Article  CAS  Google Scholar 

  • Nath M, Yadav S, Sahoo RK et al (2016) PDH45 transgenic rice maintain cell viability through lower accumulation of Na+, ROS and calcium homeostasis in roots under salinity stress. J Plant Physiol 191:1–11

    Article  CAS  Google Scholar 

  • Niu X, Xiong F, Liu J et al (2014) Co-expression of ApGSMT and ApDMT promotes biosynthesis of glycine betaine in rice (Oryza sativa L.) and enhances salt and cold tolerance. Environ Exp Bot 104:16–25

    Article  CAS  Google Scholar 

  • Oda K, Otani M, Uraguchi S, Akihiro T, Fujiwara T (2011) Rice ABCG43 is Cd inducible and confers Cd tolerance on yeast. Biosci Biotech Bioch 75:1211–1213

    Article  CAS  Google Scholar 

  • Osakabe Y, Osakabe K, Shinozaki K et al (2014) Response of plants to water stress. Front Plant Sci 5:86

    Article  Google Scholar 

  • Pandey V, Shukla A (2015) Acclimation and tolerance strategies of rice under drought stress. Ric Sci 22:147–161

    Article  Google Scholar 

  • Parihar P, Singh S, Singh R et al (2014) Effect of salinity stress on plants and its tolerance strategies: a review. Environ Sci Pollut Res 22:4056–4075

    Article  CAS  Google Scholar 

  • Paul S, Roychoudhury A (2019) Comparative analysis of the expression of candidate genes governing salt tolerance and yield attributes in two contrasting rice genotypes, encountering salt stress during grain development. J Plant Growth Regul 38:539–556

    Article  CAS  Google Scholar 

  • Peyman S, Hashem A (2010) Evaluation eighteen rice genotypes in cold tolerant at germination stage. World Appl Sci J 11:1476–1480

    Google Scholar 

  • Platten JD, Egdane JA, Ismail AM (2013) Salinity tolerance, Na + exclusion and allele mining of HKT1;5 in Oryza sativa and O. glaberrima: many sources, many genes, one mechanism? BMC Plant Biol 13:32

    Article  CAS  Google Scholar 

  • Qiu D, Xiao J, Xie W et al (2008) Rice gene network inferred from expression profiling of plants overexpressing OsWRKY13, a positive regulator of disease resistance. Mol Plant 1(3):538–551

    CAS  Google Scholar 

  • Quadir MZ, Duggan BJ (2004) Deformation banding and recrystallization of α fibre components in heavily rolled IF steel. Acta Mater 52:4011–4021

    Article  CAS  Google Scholar 

  • Rahman A, Hossain MS, Mahmud J-A et al (2016) Manganese-induced salt stress tolerance in rice seedlings: regulation of ion homeostasis, antioxidant defense and glyoxalase systems. Physiol Mol Biol Plants 22:291–306

    Article  CAS  Google Scholar 

  • Rajendran K, Tester M, Roy SJ et al (2009) Quantifying the three main components of salinity tolerance in cereals. Plant Cell Environ 23:237–249

    Article  CAS  Google Scholar 

  • Ravikumar G, Manimaran P, Voleti SR et al (2014) Stress-inducible expression of AtDREB1A transcription factor greatly improves drought stress tolerance in transgenic indica rice. Transgenic Res 23(3):421–439

    Article  CAS  Google Scholar 

  • Razmjoo K, Heydarizadeh P, Sabzalian MR (2008) Effect of salinity and drought stresses on growth parameters and essential oil content of Matricaria chamomile. Int J Agric Biol 10:451–454

    Google Scholar 

  • Reddy INBL, Kim B, Yoon I et al (2017) Salt tolerance in rice: focus on mechanisms and approaches. Ric Sci 24:123–144

    Article  Google Scholar 

  • Redillas MC, Jeong JS, Kim YS et al (2012) The over expressioen of OsNAC9 alters the root architecture of rice plants enhancing drought resistance and grain yield under field conditions. Plant Biotechnol J 10(7):792–805

    Article  CAS  Google Scholar 

  • Ren ZH, Gao JP, Li LG et al (2005) A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat Genet 37:1141–1146

    Article  CAS  Google Scholar 

  • Riaz M, Arif MS, Ashraf MA et al (2019) A comprehensive review on rice responses and tolerance to salt stress. In: Mirza H (ed) Advances in rice research for abiotic stress tolerance. Woodhead Publishing, Cambridge, pp 133–158

    Chapter  Google Scholar 

  • Romero-Aranda R, Soria T, Cuartero J (2001) Tomato plant-water uptake and plant-water relationships under saline growth conditions. Plant Sci 160:265–272

    Article  CAS  Google Scholar 

  • Rai A, Bhardwaj A, Misra P, Bag SK, Adhikari B, Tripathi RD, Chakrabarty D (2015) Comparative transcriptional profiling of contrasting rice genotypes shows expression differences during arsenic stress. Plant Genome 8:1–14

    Article  CAS  Google Scholar 

  • Ros R, Cook DT, Martinez-Cortina CARMEN, Picazo I (1992) Nickel and cadmium-related changes in growth, plasma membrane lipid composition, ATPase hydrolytic activity and proton-pumping of rice (Oryza sativa L cv Bahia) shoots. J Exp Bot 43:1475–1481

    Article  CAS  Google Scholar 

  • Roychoudhury A, Chakraborty M (2013) Biochemical and molecular basis of varietal difference in plant salt tolerance. Annu Rev Res Biol 3:422–454

    CAS  Google Scholar 

  • Roychoudhury A, Basu S, Sarkar SN, Sengupta DN (2008) Comparative physiological and molecular responses of a common aromatic indica rice cultivar to high salinity with non-aromatic indica rice cultivars. Plant Cell Rep 27:1395–1410

    Article  CAS  Google Scholar 

  • Roychoudhury A, Basu S, Sengupta DN (2012) Antioxidants and stress-related metabolites in the seedlings of two indica rice varieties exposed to cadmium chloride toxicity. Acta Physiol Plant 34:835–847

    Article  CAS  Google Scholar 

  • Roychoudhury A, Paul S, Basu S (2013) Cross-talk between abscisic acid-dependent and abscisic acid-independent pathways during abiotic stress. Plant Cell Rep 32:985–1006

    Article  CAS  Google Scholar 

  • Saeng-ngam S, Takpirom W, Buaboocha T et al (2012) The role of the OsCam1-1 salt stress sensor in ABA accumulation and salt tolerance in rice. J Plant Biol 55(3):198–208

    Article  CAS  Google Scholar 

  • Sahoo RK, Ansari MW, Tuteja R (2014) OsSUV3 transgenic rice maintains higher endogenous levels of plant hormones that mitigates adverse effects of salinity and sustains crop productivity. Rice 7(1):17

    Article  Google Scholar 

  • Sahoo RK, Tuteja N (2014) OsSUV3 functions in cadmium and zinc stress tolerance in rice (Oryza sativa L cv IR64). Plant Signal Behav 9:115–127

    Google Scholar 

  • Saito K, Miura K, Nagano K, Hayano-Saito Y, Saiito A, Araki H, Kato A (1995) Chromosomal location of quantitative trait loci for cool tolerance at the booting stage in rice variety'Norin-PL8'. Jpn J Breed 45:337–340

    Article  Google Scholar 

  • Saito K, Miura K, Nagano K, Hayano-Saito Y, Araki H, Kato A (2001) Identification of two closely linked quantitative trait loci for cold tolerance on chromosome 4 of rice and their association with anther length. Theor Appl Genet 103:862–868

    Article  CAS  Google Scholar 

  • Saito K, Hayano-Saito Y, Kuroki M, Sato Y (2010) Map-based cloning of the rice cold tolerance gene Ctb1. Plant Sci 179:97–102

    Article  CAS  Google Scholar 

  • Sakurai J, Ahamed A, Murai M et al (2008) Tissue and cell-specific localization of rice aquaporins and their water transport activities. Plant Cell Physiol 49(1):30–39

    Article  CAS  Google Scholar 

  • Samantaray S, Rout GR, Das P (1997) Tolerance of rice to nickel in nutrient solution. Biol Plant 40:295–298

    Article  CAS  Google Scholar 

  • Sangwan V, Örvar BL, Beyerly J, Hirt H, Dhindsa RS (2002) Opposite changes in membrane fluidity mimic cold and heat stress activation of distinct plant MAP kinase pathways. Plant J 31(5):629–638

    Article  CAS  Google Scholar 

  • Satake T, Hayase H (1976) Male sterility caused by cooling treatment at the young microspore stage in rice plants. v. estimation of pollen developmental stage and the most sensitive stage to coolness. Proc Crop Sci Soc Jpn 39:468–473

    Article  Google Scholar 

  • 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(3):399–406

    Article  CAS  Google Scholar 

  • Satoh T, Tezuka K, Kawamoto T, Matsumoto S, Satoh-Nagasawa N, Ueda K, Akagi H (2016) Identification of QTLs controlling low-temperature germination of the east European rice (Oryza sativa L) variety Maratteli. Euphytica 207:245–254

    Article  Google Scholar 

  • Schaeffer HJ, Weber MJ (1999) Mitogen-activated protein kinases: specific messages from ubiquitous messengers. Mol Cell Biol 19:2435–2444

    Article  CAS  Google Scholar 

  • Schmidt R, Mieulet D, Hubberten HM et al (2013) SALTRESPONSIVE ERF1 regulates reactive oxygen species-dependent signaling during the initial response to salt stress in rice. Plant Cell 25(6):2115–2131

    Article  CAS  Google Scholar 

  • Selvaraj MG, Ishizaki T, Valencia M et al (2017) Over expression of an Arabidopsis thaliana galactinol synthase gene improves drought tolerance in transgenic rice and increased grain yield in the field. Plant Biotechnol J 15:1465–1477

    Article  CAS  Google Scholar 

  • Sethy SK, Ghosh S (2013) Effect of heavy metals on germination of seeds. J Nat Sci Biol Med 4:272

    Article  CAS  Google Scholar 

  • Sevanthi AM, Prakash C, Shanmugavadivel PS (2019) Recent progress in rice varietal development for abiotic stress tolerance. In: Advance in rice research abiotic stress tolerance, pp 47–68

    Chapter  Google Scholar 

  • Shamsudin NA, Swamy BM, Ratnam W et al (2016) Marker assisted pyramiding of drought yield QTLs into a popular Malaysian rice cultivar, MR219. BMC Genet 17(1):30

    Article  CAS  Google Scholar 

  • Shah K, Dubey RS (1997) Effect of cadmium on proline accumulation and ribonuclease activity in rice seedlings: role of proline as a possible enzyme protectant. Biol Plant 40(1):121–130

    Article  CAS  Google Scholar 

  • Shao HB, Guo QJ, Chu LY, Zhao XN, Su ZL, Hu YC, Cheng JF (2007) Understanding molecular mechanism of higher plant plasticity under abiotic stress. Colloids Surf B: Biointerfaces 54(1):37–45

    Article  CAS  Google Scholar 

  • Shahzad B, Tanveer M, Rehman A, Cheema SA, Fahad S, Rehman S, Sharma A (2018) Nickel; whether toxic or essential for plants and environment-A review. Plant Physiol Biochem 132:641–651

    Article  CAS  Google Scholar 

  • Shen Y, Shen L, Shen Z et al (2015) The potassium transporter OsHAK21functions in the maintenance of ion homeostasis and tolerance to salt stress in rice. Plant Cell Environ 38(12):2766–2779

    Article  CAS  Google Scholar 

  • Sheng M, Sala C (2001) PDZ domains and the organization of supramolecular complexes. Annu Rev Neurosci 24:1–29

    Article  CAS  Google Scholar 

  • Shi B, Ni L, Zhang A et al (2012) OsDMI3 is a novel component of abscisic acid signaling in the induction of antioxidant defense in leaves of rice. Mol Plant 5(6):1359–1374

    Article  CAS  Google Scholar 

  • Shim JS, Oh N, Chung PJ et al (2018) Over expression of OsNAC14 improves drought tolerance in rice. Front Plant Sci 9:310

    Article  Google Scholar 

  • Shimo H, Ishimaru Y, An G, Yamakawa T, Nakanishi H, Nishizawa NK (2011) Low cadmium (LCD), a novel gene related to cadmium tolerance and accumulation in rice. J Exp Bot 62:5727–5734

    Article  CAS  Google Scholar 

  • Shimono H, Hasegawa T, Iwama K (2002) Response of growth and grain yield in paddy rice to cool water at different growth stages. Field Crop Res 73:67–79

    Article  Google Scholar 

  • Shimono H, Okada M, Kanda E et al (2007) Low temperature induced sterility in rice: evidence for the effects of temperature before panicle initiation. Field Crop Res 101:221–231

    Article  Google Scholar 

  • Silva MLDS, Vitti GC, Trevizam AR (2014) Heavy metal toxicity in rice and soybean plants cultivated in contaminated soil. Rev Ceres 61:248–254

    Article  CAS  Google Scholar 

  • Singh G, Joyce EM, Beddow J et al (2012) Evaluation of antibacterial activity of ZnO nanoparticles coated sonochemically onto textile fabrics. World J Microbiol Biotechnol 2(1):106

    CAS  Google Scholar 

  • Singh R, Singh Y, Xalaxo S et al (2016) From QTL to variety harnessing the benefits of QTLs for drought, flood and salt tolerance in mega rice varieties of India through a multi-institutional network. Plant Sci 242:278–287

    Article  CAS  Google Scholar 

  • Siraul XRR, Richard AJ, Robert TF (2009) A new screening method for osmotic component of salinity tolerance in cereals using infrared thermography. Funct Plant Biol 36:970–977

    Article  CAS  Google Scholar 

  • Soda N, Gupta BK, Anwar K et al (2018) Publisher correction: rice intermediate filament, OsIF, stabilizes photosynthetic machinery and yield under salinity and heat stress. Sci Rep 8:40–72

    Article  CAS  Google Scholar 

  • Song SY, Chen Y, Chen J et al (2011) Physiological mechanisms underlying OsNAC5-dependent tolerance of rice plants to abiotic stress. Planta 234(2):331–345

    Article  CAS  Google Scholar 

  • Sridevi V, Chellamuthu V (2015) Impact of weather on rice—a review. Int J Appl Res 1:825–831

    Google Scholar 

  • Srivastava RK, Pandey P, Rajpoot R, Rani A, Dubey RS (2014) Cadmium and lead interactive effects on oxidative stress and antioxidative responses in rice seedlings. Protoplasma 251:1047–1065

    Article  CAS  Google Scholar 

  • Stefanov K, Seizova K, Popova I, Petkov V, Kimenov G, Popov S (1995) Effect of lead ions on the phospholipid composition in leaves of Zea mays and Phaseolus vulgaris. J Plant Physiol 147:243–246

    Article  CAS  Google Scholar 

  • Su J, Wu R (2004) Stress-inducible synthesis of proline in transgenic rice confers faster growth under stress conditions than that with constitutive synthesis. Plant Sci 166(4):941–948

    Article  CAS  Google Scholar 

  • 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  CAS  Google Scholar 

  • Suzuki T, Yamagiwa N, Matsuo Y, Sakamoto S, Yamaguchi K, Shibasaki M, Noyori R (2001) Catalytic asymmetric aldol reaction of ketones and aldehydes using chiral calcium alkoxides. Tetrahedron Lett 42:4669–4671

    Article  CAS  Google Scholar 

  • Suzuki N, Miller G, Morales J et al (2011) Respiratory burst oxidases: the engines of ROS signaling. Curr Opin Plant Biol 14(6):691–699

    Article  CAS  Google Scholar 

  • Suzuki K, Yamaji N, Costa A et al (2016) OsHKT1; 4-mediated Na1 transport in stems contributes to Na1 exclusion from leaf blades of rice at the reproductive growth stage upon salt stress. BMC Plant Biol 16(1):22

    Article  CAS  Google Scholar 

  • Tak HI, Ahmad F, Babalola OO (2013) Advances in the application of plant growth-promoting rhizobacteria in phytoremediation of heavy metals. Rev Environ Contam Toxicol 22:33–52

    Google Scholar 

  • Takagi H, Tamiru M, Abe A et al (2015) MutMap accelerates breeding of a salt-tolerant rice cultivar. Nat Biotechnol 33(5):445–449

    Article  CAS  Google Scholar 

  • Takahashi R, Ishimaru Y, Senoura T, Shimo H, Ishikawa S, Arao T, Nishizawa NK (2011) The OsNRAMP1 iron transporter is involved in Cd accumulation in rice. J Exp Bot 62:4843–4850

    Article  CAS  Google Scholar 

  • Takeda S, Matsuoka M (2008) Genetic approaches to crop improvement: responding to environmental and population changes. Nat Rev Genet 9:444–457

    Article  CAS  Google Scholar 

  • Takesawa T, Ito M, Kanzaki H, Kameya N, Nakamura I (2002) Over-expression of ζ glutathione S-transferase in transgenic rice enhances germination and growth at low temperature. Mol Breed 9:93–101

    Article  CAS  Google Scholar 

  • Takasaki H, Maruyama K, Kidokoro S et al (2010) The abiotic stress-responsive NAC-type transcription factor OsNAC5 regulates stress-inducible genes and stress tolerance in rice. Mol Genet Genomics 284(3):173–183

    Article  CAS  Google Scholar 

  • Thomson MJ, de Ocampo M, Egdane J, Rahman MA, Sajise AG, Adorada DL et al (2010) Characterizing the Saltol quantitative trait locus for salinity tolerance in rice. Rice 3(2–3):148–160

    Article  Google Scholar 

  • Tian Y, Zhang H, Pan X et al (2011) Over expression of ethylene response factor TERF2 confers cold tolerance in rice seedlings. Transgenic Res 20:857–866

    Article  CAS  Google Scholar 

  • Tiwari S, Krishnamurthy SL, Kumar V et al (2016) Mapping QTLs for salt tolerance in rice (Oryza sativa L.) by bulked segregant analysis of recombinant inbred lines using 50 K SNP chip. PLoS One 11(4):e0153610

    Article  CAS  Google Scholar 

  • Todaka D, Zhao Y, Yoshida T et al (2017) Temporal and spatial changes in gene expression, metabolite accumulation and phytohormone content in rice seedlings grown under drought stress conditions. Plant J 90:61–78

    Article  CAS  Google Scholar 

  • Türkan I, Bor M, Özdemir F, Koca H (2005) Differential responses of lipid peroxidation and antioxidants in the leaves of drought-tolerant P acutifolius Gray and drought-sensitive P vulgaris L subjected to polyethylene glycol mediated water stress. Plant Sci 168:223–231

    Article  CAS  Google Scholar 

  • Ueno D, Yamaji N, Kono I, Huang CF, Ando T, Yano M, Ma JF (2010) Gene limiting cadmium accumulation in rice. PNAS 107:16500–16505

    Article  CAS  Google Scholar 

  • Uga Y, Sugimoto K, Ogawa S et al (2013) Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions. Nat Genet 45:1097–1102

    Article  CAS  Google Scholar 

  • Ujiie K, Ishimaru K (2013) Identification of chromosome regions affecting leaf area with rice chromosome segment substitution lines. Plant Prod Sci 16:31–36

    Article  Google Scholar 

  • Ujiie K, Ishimaru K (2014) Alleles affecting 30 traits for productivity between 2 japonica rice varieties, Koshihikari and Nipponbare (Oryza sativa L.). Plant Prod Sci 17:47–65

    Article  Google Scholar 

  • Ujiie K, Kashiwagi T, Ishimaru K (2012) Identification and functional analysis of alleles for productivity in two sets of chromosome segment substitution lines of rice. Euphytica 187:325–337

    Article  CAS  Google Scholar 

  • Ujiie K, Yamamoto T, Yano M et al (2015) Genetic factors determining varietal differences in characters affecting yield between two rice (Oryza sativa L.) varieties, Koshihikari and IR64. Genet Resour Crop Evol 63:97–123. https://doi.org/10.1007/s10722-015-0237-3

    Article  Google Scholar 

  • United Nations (2017) United Nations Population Division. World Population Prospects 2017

    Google Scholar 

  • Uraguchi S, Mori S, Kuramata M, Kawasaki A, Arao T, Ishikawa S (2009) Root-to-shoot Cd translocation via the xylem is the major process determining shoot and grain cadmium accumulation in rice. J Exp Bot 60:2677–2688

    Article  CAS  Google Scholar 

  • Venkataramaiah N, Ramakrishna SV, Sreevathsa R (2011) Overexpression of phytochelatin synthase (AtPCS) in rice for tolerance to cadmium stress. Biologia 66:1060–1073

    Article  CAS  Google Scholar 

  • Walia H, Wilson C, Condamine P et al (2005) Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage. Plant Physiol 139(2):822–835

    Article  CAS  Google Scholar 

  • Walia H, Wilson C, Zeng L et al (2007) Genome-wide transcriptional analysis of salinity stressed japonica and indica rice genotypes during panicle initiation stage. Plant Mol Biol 63(5):609–623

    Article  CAS  Google Scholar 

  • Wang Q, Guan Y, Wu Y et al (2008) Over expression of a rice OsDREB1F gene increases salt, drought, and low temperature tolerance in both Arabidopsis and rice. Plant Mol Biol 67(6):589–602

    Article  CAS  Google Scholar 

  • Wang D, Pan Y, Zhao X et al (2011) Genome-wide temporal-spatial gene expression profiling of drought responsiveness in rice. BMC Genomics 12:149

    Article  CAS  Google Scholar 

  • Wang H, Zhang M, Guo R et al (2012) Effects of salt stress on ion balance and nitrogen metabolism of old and young leaves in rice (Oryza sativa L.). BMC Plant Biol 12(1):194

    Article  CAS  Google Scholar 

  • Wang M, Mao Y, Lu Y, Wang Z, Tao X, Zhu JK (2018) Multiplex gene editing in rice with simplified CRISPR-Cpf1 and CRISPR-Cas9 systems. J Integr Plant Biol 60:626–631

    Article  CAS  Google Scholar 

  • Wassmann R, Jagadish SVK, Sumfleth K et al (2009) Regional vulnerability of climate change impacts on Asian rice production and scope for adaptation. Adv Agron 102:91–133

    Article  Google Scholar 

  • Wei H, Chen C, Ma X, Zhang Y, Han J, Mei H, Yu S (2017) Comparative analysis of expression profiles of panicle development among tolerant and sensitive rice in response to drought stress. Front Plant Sci 8:437

    Google Scholar 

  • Widmann C, Gibson S, Jarpe MB, Johnson GL (1999) Mitogen-activated protein kinase: conservation of a three-kinase module from yeast to human. Physiol Rev 79:143–180

    Article  CAS  Google Scholar 

  • Wojtaszek P (1997) Mechanisms for the generation of reactive oxygen species in plant defence response. Acta Physiol Plant 19:581–589

    Article  CAS  Google Scholar 

  • Wutipraditkul N, Boonkomrat S, Buaboocha T (2011) Cloning and characterization of catalases from rice, Oryza sativa L. Biosci Biotechnol Biochem 75(10):1900–1906

    Article  CAS  Google Scholar 

  • Xia K, Wang R, Ou X, Fang Z, Tian C, Duan J et al (2012) OsTIR1 and OsAFB2 downregulation via OsmiR393 overexpression leads to more tillers, early flowering and less tolerance to salt and drought in rice. PLoS One 7(1):e30039

    Article  CAS  Google Scholar 

  • Xiang Y, Tang N, Du H et al (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(4):1938–1952

    Article  CAS  Google Scholar 

  • Xie G, Kato H, Sasaki K, Imai R (2009) A cold-induced thioredoxin h of rice, OsTrx23, negatively regulates kinase activities of OsMPK3 and OsMPK6 in vitro. FEBS Lett 583(17):2734–2738

    Article  CAS  Google Scholar 

  • Xie G, Kato H, Imai R (2012) Biochemical identification of the OsMKK6–OsMPK3 signalling pathway for chilling stress tolerance in rice. Biochem J 443(1):95–102

    Article  CAS  Google Scholar 

  • Xie L, Tan Z, Zhou Y, Xu R, Feng L, Xing Y, Qi X (2014) Identification and fine mapping of quantitative trait loci for seed vigor in germination and seedling establishment in rice. J Integr Plant Biol 56(8):749–759

    Article  CAS  Google Scholar 

  • Xin Z, Browse J (2001) Cold comfort farm: the acclimation of plants to freezing temperatures. Plant Cell Environ 23:893–902

    Article  Google Scholar 

  • Xiong L, Zhu JK (2002) Molecular and genetic aspects of plant responses to osmotic stress. Plant Cell Environ 25:131–139

    Article  CAS  Google Scholar 

  • 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  CAS  Google Scholar 

  • Xu LM, Zhou L, Zeng YW et al (2008) Identification and mapping of quantitative trait loci for cold tolerance at the booting stage in a japonica rice near-isogenic line. Plant Sci 174(3):340–347

    Article  CAS  Google Scholar 

  • Xu M, Li L, Fan Y, Wan J, Wang L (2011) ZmCBF3 overexpression improves tolerance to abiotic stress in transgenic rice (Oryza sativa) without yield penalty. Plant Cell Rep 30:1949

    Article  CAS  Google Scholar 

  • Xu Z, Jiang Y, Zhou G (2015) Response and adaptation of photosynthesis, respiration, and antioxidant systems to elevated CO2 with environmental stress in plants. Front Plant Sci 6:701

    Google Scholar 

  • Xue Y, Jiang L, Su N, Wang JK, Deng P, Ma JF et al (2007) The genetic basic and fine-mapping of a stable quantitative-trait loci for aluminium tolerance in rice. Planta 227(1):255–262

    Article  CAS  Google Scholar 

  • Yaish MW, El-kereamy A, Zhu T et al (2010) The APETALA-2-like transcription factor OsAP2–39 controls key interactions between abscisic acid and gibberellin in rice. PLoS Genet 6(9):e1001098

    Article  CAS  Google Scholar 

  • Yamaguchi-Shinozaki K, Shinozaki K (2006) Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annu Rev Plant Biol 57:781–803

    Article  CAS  Google Scholar 

  • Yang T, Poovaiah BW (2003) Calcium/calmodulin-mediated signal network in plants. Trends Plant Sci 8:505–512

    Article  CAS  Google Scholar 

  • Yang A, Dai X, Zhang WH (2012) A R2R3-type MYB gene, OsMYB2, is involved in salt, cold, and dehydration tolerance in rice. J Exp Bot 63:2541–2556

    Article  CAS  Google Scholar 

  • Yang C, Zhang T, Wang H et al (2012) Heritable alteration in salt-tolerance in rice induced by introgression from wild rice (Zizania latifolia). Rice 5(1):36

    Google Scholar 

  • Yang T, Zhang S, Hu Y et al (2014) The role of a potassium transporter OsHAK5 in potassium acquisition and transport from roots to shoots in rice at low potassium supply levels. Plant Physiol 166(2):945–959

    Article  CAS  Google Scholar 

  • Yang LM, Liu HL, Lei L, Zhao HW, Wang JG, Li N et al (2018) Identification of QTLs controlling low-temperature germinability and cold tolerance at the seedling stage in rice (Oryza Sativa L.). Euphytica 214(1):13

    Article  CAS  Google Scholar 

  • Ye H, Du H, Tang N et al (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  CAS  Google Scholar 

  • Yoshida S (1981) Climatic environment and its influence. In: Yoshida S (ed) Fundamentals of rice crop science. International Rice Research Institute, Los Baños, pp 65–110

    Google Scholar 

  • Yoshida T, Mogami J, Yamaguchi-Shinozaki K (2014) ABA-dependent and ABA-independent signaling in response to osmotic stress in plants. Curr Opin Plant Biol 21:133–139

    Article  CAS  Google Scholar 

  • Yousaf M, Li J, Lu J et al (2017) Effects of fertilization on crop production and nutrient-supplying capacity under rice-oilseed rape rotation system. Sci Rep 7:1270

    Article  CAS  Google Scholar 

  • Yuan L, Yang S, Liu B, Zhang M, Wu K (2012) Molecular characterization of a rice metal tolerance protein, OsMTP1. Plant Cell Rep 31:67–79

    Article  CAS  Google Scholar 

  • Yuanyuan M, Yali Z, Jiang L, Hongbo S (2009) Roles of plant soluble sugars and their responses to plant cold stress. Afr J Biotechnol 8(10)

    Google Scholar 

  • Yuet Ping K, Darah I, Chen Y, Sreeramanan S, Sasidharan S (2013) Acute and subchronic toxicity study of Euphorbia hirta L methanol extract in rats. Biomed Res Int, 2013

    Google Scholar 

  • Zaher-Ara T, Boroomand N, Sadat-Hosseini M (2016) Physiological and morphological response to drought stress in seedlings of ten citrus. Trees 30(3):985–993

    Article  CAS  Google Scholar 

  • Zhang M, Liu B (2017) Identification of a rice metal tolerance protein OsMTP11 as a manganese transporter. PLoS One 12:e0174987

    Article  CAS  Google Scholar 

  • Zhang ZS, Xiao YH, Luo M, Li XB, Luo XY, Hou L, Pei Y (2005) Construction of a genetic linkage map and QTL analysis of fiber-related traits in upland cotton (Gossypium hirsutum L). Euphytica 144:91–99

    Article  CAS  Google Scholar 

  • Zhang J, Li J, Wang X et al (2011) OVP1, a vacuolar H+-translocating inorganic pyrophosphatase (V-PPase), over expression improved rice cold tolerance. Plant Physiol Biochem 49:33–38

    Article  CAS  Google Scholar 

  • Zhang T, Qian N, Zhu X, Chen H, Wang S, Mei H, Zhang Y (2013) Variations and transmission of QTL alleles for yield and fiber qualities in upland cotton cultivars developed in China. PLoS One 8:e57220

    Article  CAS  Google Scholar 

  • Zhang ZF, Li YY, Xiao BZ (2016) Comparative transcriptome analysis highlights the crucial roles of photosynthetic system in drought stress adaptation in upland rice. Sci Rep 6:19349

    Article  CAS  Google Scholar 

  • Zhang X, Huang C, Wu D, Qiao F, Li W, Duan L, Xiong L (2017) High-throughput phenotyping and QTL mapping reveals the genetic architecture of maize plant growth. Plant Physiol 173:1554–1564

    Article  CAS  Google Scholar 

  • Zhao J, Wu C, Yuan S et al (2013) Kinase activity of OsBRI1 is essential for brassinosteroids to regulate rice growth and development. Plant Sci 199:113–120

    Article  CAS  Google Scholar 

  • Zheng X, Chen B, Lu G et al (2009) Over expression of a NAC transcription factor enhances rice drought and salt tolerance. Biochem Biophys Res Commun 379(4):985–989

    Article  CAS  Google Scholar 

  • 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(15):4157–4168

    Article  CAS  Google Scholar 

  • Zhou Y, Zhang C, Lin J et al (2015) Over-expression of a glutamate dehydrogenase gene, MgGDH, from Magnaporthe grisea confers tolerance to dehydration stress in transgenic rice. Planta 241(3):727–740

    Article  CAS  Google Scholar 

  • Zokaee-Khosroshahi E-AM, Ershadi M et al (2014) Morphological changes in response to drought stress in cultivated and wild almond species. Int J Hortic Sci Technol 1(1):79–92

    CAS  Google Scholar 

  • Zou M, Guan Y, Ren H et al (2008) A bZIP transcription factor, OsABI5, is involved in rice fertility and stress tolerance. Plant Mol Biol 66(6):675–683

    Article  CAS  Google Scholar 

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  1. Department of Botany, Centre of Advanced Studies, University of Calcutta, Kolkata, West Bengal, India

    Snehalata Majumdar, Falguni Barman & Rita Kundu

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  1. Department of Biotechnology, St. Xavier’s College (Autonomous), Kolkata, West Bengal, India

    Aryadeep Roychoudhury

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Majumdar, S., Barman, F., Kundu, R. (2020). Genomic Approaches to Understand Varietal Differences in Rice Species and Genotypes with Respect to Stress Response and Quality Traits. In: Roychoudhury, A. (eds) Rice Research for Quality Improvement: Genomics and Genetic Engineering. Springer, Singapore. https://doi.org/10.1007/978-981-15-4120-9_7

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