Molecular insight into drought tolerance of CR Dhan 40: an upland rice line from Eastern India
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Anbazhagan K, Bhatnagar-Mathur P, Vadez V, Dumbala SR, Kavi Kishor PB, Sharma KK (2015) DREB1A overexpression in transgenic chickpea alters key traits influencing plant water budget across water regimes. Plant Cell Rep 34:199–210. https://doi.org/10.1007/s00299-014-1699-z
Benny J, Pisciotta A, Caruso T (2019) Identification of key genes and its chromosome regions linked to drought responses in leaves across different crops through meta-analysis of RNA-Seq data. BMC Plant Biol 19:194. https://doi.org/10.1186/s12870-019-1794-y
Bharath P, Gahir S, Raghavendra AS (2021) Abscisic acid-induced stomatal closure: an important component of plant defense against abiotic and biotic stress. Front Plant Sci 12:615114. https://doi.org/10.3389/fpls.2021.615114
Bhattacharjee A, Khurana P, Jain M (2016) Characterization of rice homeobox genes, OsHOX22 and OsHOX24, and over-expression of OsHOX24 in transgenic arabidopsis suggest their role in abiotic stress response. Front Plant Sci. https://doi.org/10.3389/fpls.2016.00627
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. https://doi.org/10.1093/bioinformatics/btu170
Bouman BAM, Peng S, Castaoeda AR, Visperas RM (2005) Yield and water use of irrigated tropical aerobic rice systems. Agric Water Manag. https://doi.org/10.1016/j.agwat.2004.11.007
Cao X, Liao Y, Rong S, Hu C, Zhang X, Chen R, Xu Z, Gao X, Li L, Zhu J (2016) Identification and characterization of a novel abiotic stress responsive sulphotransferase gene (OsSOT9) from rice. Biotechnol Biotechnol Equip 30:227–235. https://doi.org/10.1080/13102818.2015.1136237
Chatterjee A, Dey T, Galiba G, Kocsy G, Dey N, Kar RK (2021) Effect of combination of light and drought stress on physiology and oxidative metabolism of rice plants. Plant Sci 8:762–777. https://doi.org/10.14719/pst.2021.8.4.124
Chen Y, Zhang B, Li C, Lei C, Kong C, Yang Y, Gong M (2019) A comprehensive expression analysis of the expansin gene family in potato (Solanum tuberosum) discloses stress-responsive expansin-like B genes for drought and heat tolerances. PLoS ONE 14:e0219837. https://doi.org/10.1371/journal.pone.0219837
Cingolani P, Platts A, le Wang L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (austin) 6(2):80–92. https://doi.org/10.4161/fly.19695
Dana MM, Pintor-Toro JA, Cubero B (2006) Transgenic tobacco plants overexpressing chitinases of fungal origin show enhanced resistance to biotic and abiotic stress agents. Plant Physiol 142:722–730. https://doi.org/10.1104/pp.106.086140
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. https://doi.org/10.1007/s11103-011-9830-9
Du Y, Zhao Q, Chen L, Yao X, Zhang W, Zhang B, Xie F (2020) Effect of drought stress on sugar metabolism in leaves and roots of soybean seedlings. Plant Physiol Biochem 146:1–12. https://doi.org/10.1016/j.plaphy.2019.11.003
Duan J, Cai W (2012) OsLEA3-2, an abiotic stress induced gene of rice plays a key role in salt and drought tolerance. PLoS ONE 7:e45117. https://doi.org/10.1371/journal.pone.0045117
Filippou P, Bouchagier P, Skotti E, Fotopoulos V (2014) Proline and reactive oxygen/nitrogen species metabolism is involved in the tolerant response of the invasive plant species Ailanthus altissima to drought and salinity. Environ Exp Bot 97:1–10. https://doi.org/10.1016/j.envexpbot.2013.09.010
Fukagawa NK, Ziska LH (2019) Rice: importance for global nutrition. J Nutr Sci Vitaminol (tokyo) 65(Supplement):S2–S3. https://doi.org/10.3177/jnsv.65.S2
Ganie SA, Ahammed GJ (2021) Dynamics of cell wall structure and related genomic resources for drought tolerance in rice. Plant Cell Rep 40:437–459. https://doi.org/10.1007/s00299-020-02649-2
Gao C, Han B (2009) Evolutionary and expression study of the aldehyde dehydrogenase (ALDH) gene superfamily in rice (Oryza sativa). Gene 431:86–94. https://doi.org/10.1016/j.gene.2008.11.010
Ge SX, Jung D, Yao R (2020) ShinyGO: a graphical gene-set enrichment tool for animals and plants. Bioinformatics 36:2628–2629. https://doi.org/10.1093/bioinformatics/btz931
Gill SS, Tuteja N (2010) Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants. Plant Physiol Biochem 48:909–930. https://doi.org/10.1016/j.plaphy.2010.08.016
Guo C, Ge X, Ma H (2013) The rice OsDIL gene plays a role in drought tolerance at vegetative and reproductive stages. Plant Mol Biol. https://doi.org/10.1007/s11103-013-0057-9
Han Y, Gao S, Muegge K, Zhang W, Zhou B (2015) Advanced applications of RNA sequencing and challenges. Bioinform Biol Insights 15:29–46. https://doi.org/10.4137/BBI.S28991
Hasanuzzaman M, Bhuyan MHMB, Zulfiqar F, Raza A, Mohsin SM, Mahmud JA, Fujita M, Fotopoulos V (2020) Reactive oxygen species and antioxidant defense in plants under abiotic stress: revisiting the crucial role of a universal defense regulator. Antioxidants (basel) 9(8):681. https://doi.org/10.3390/antiox9080681
Hoque MA, Banu MN, Nakamura Y, Shimoishi Y, Murata Y (2008) Proline and glycinebetaine enhance antioxidant defense and methylglyoxal detoxification systems and reduce NaCl-induced damage in cultured tobacco cells. J Plant Physiol 165(8):813–824. https://doi.org/10.1016/j.jplph.2007.07.013
Huang K, Wu T, Ma Z, Li Z, Chen H, Zhang M, Bian M, Bai H, Jiang W, Du X (2021) Rice transcription factor OsWRKY55 is involved in the drought response and regulation of plant growth. Int J Mol Sci 22:4337. https://doi.org/10.3390/ijms22094337
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. https://doi.org/10.1007/s11103-009-9483-0
Jan A, Maruyama K, Todaka D, Kidokoro S, Abo M, Yoshimura E, Shinozaki K, Nakashima K, Yamaguchi-Shinozaki K (2013) OsTZF1, a CCCH-tandem zinc finger protein, confers delayed senescence and stress tolerance in rice by regulating stress-related genes. Plant Physiol 161:1202–1216. https://doi.org/10.1104/pp.112.205385
Janiak A, Wasniewski MK, Sowa M, Gajek K, Żmuda K, Kościelniak J (2018) No time to waste: transcriptome study reveals that drought tolerance in barley may be attributed to stressed-like expression patterns that exist before the occurrence of stress. Front Plant Sci 8:2212. https://doi.org/10.3389/fpls.2017.02212
Jedrzejas MJ, Chander M, Setlow P, Krishnasamy G (2000) Structure and mechanism of action of a novel phosphoglycerate mutase from Bacillus stearothermophilus. EMBO J 19:1419–1431. https://doi.org/10.1093/emboj/19.7.1419
Jiang D, Chen W, Gao J (2019) Overexpression of the trehalose-6-phosphate phosphatase OsTPP3 increases drought tolerance in rice. Plant Biotechnol Rep 13:285–292. https://doi.org/10.1007/s11816-019-00541-4
Jisha V, Dampanaboina L, Vadassery J, Mithöfer A, Kappara S, Ramanan R (2015) Overexpression of an AP2/ERF type transcription factor OsEREBP1 confers biotic and abiotic stress tolerance in rice. PLoS ONE 10:e0127831. https://doi.org/10.1371/journal.pone.0127831
Joshi R, Wani SH, Singh B, Bohra A, Dar ZA, Lone AA, Pareek A, Singla-Pareek SL (2016) Transcription factors and plants response to drought stress: current understanding and future directions. Front Plant Sci 7:1029. https://doi.org/10.3389/fpls.2016.01029
Kim SI, Andaya VC, Tai TH (2011) Cold sensitivity in rice (Oryza sativa L.) is strongly correlated with a naturally occurring I99V mutation in the multifunctional glutathione transferase isoenzyme GSTZ2. Biochem J 435:373–380. https://doi.org/10.1042/BJ20101610
Kumar S, Asif MH, Chakrabarty D, Tripathi RD, Dubey RS, Trivedi PK (2013) Expression of a rice Lambda class of glutathione S-transferase, OsGSTL2, in Arabidopsis provides tolerance to heavy metal and other abiotic stresses. J Hazard Mater 15(248–249):228–237. https://doi.org/10.1016/j.jhazmat.2013.01.004
Lee KO, Jang HH, Jung BG, Chi YH, Lee JY, Choi YO, Lee JR, Lim CO, Cho MJ, Lee SY (2000) Rice 1Cys-peroxiredoxin over-expressed in transgenic tobacco does not maintain dormancy but enhances antioxidant activity. FEBS Lett 486(2):103–106. https://doi.org/10.1016/s0014-5793(00)02230-4
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. https://doi.org/10.1007/s00425-011-1458-0
Liang Y, Tabien RE, Tarpley L, Mohammed AR, Septiningsih EM (2021) Transcriptome profiling of two rice genotypes under mild field drought stress during grain-filling stage. AoB Plants 13:43. https://doi.org/10.1093/aobpla/plab043
Liao Y, Smyth GK, Hi WS (2014) Feature counts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923–930. https://doi.org/10.1093/bioinformatics/btt656
Liu N, Jiang L, Zhang W, Liu L, Zhai H, Wan J (2008) Role of LOX3 gene in alleviating adverse effects of drought and pathogens in rice. Rice Sci 15:276–282. https://doi.org/10.1016/S1672-6308(09)60004-4
Liu Q, Dong GR, Ma YQ, Zhao SM, Liu X, Li XK, Li YJ, Hou BK (2021) Rice glycosyltransferase gene UGT85E1 is involved in drought stress tolerance through enhancing abscisic acid response. Front Plant Sci 12:790195. https://doi.org/10.3389/fpls.2021.790195
Luo Y, Fang B, Wang W, Yang Y, Rao L, Zhang C (2019) Genome-wide analysis of the rice J-protein family: identification, genomic organization, and expression profiles under multiple stresses. 3 Biotech 9:358. https://doi.org/10.1007/s13205-019-1880-8
Mathan J, Singh A, Ranjan A (2021) Sucrose transport in response to drought and salt stress involves ABA-mediated induction of OsSWEET13 and OsSWEET15 in rice. Physiol Plant 17:1620–1637. https://doi.org/10.1111/ppl.13210
McDowell NG, Pockman WT, Allen CD, Breshears DD, Cobb N, Kolb T (2008) Mechanisms of plant survival and mortality during drought: why do some plants survive while others succumb to drought? New Phytol 178:719–739. https://doi.org/10.1111/j.1469-8137.2008.02436.x
Niu Z, Li G, Hu H (2021) A gene that underwent adaptive evolution, LAC2 (LACCASE), in Populus euphratica improves drought tolerance by improving water transport capacity. Hortic Res 8:88. https://doi.org/10.1038/s41438-021-00518-x
Ozturk M, Turkyilmaz BU, García-Caparrós P, Khursheed Gul A, Hasanuzzaman M (2021) Osmoregulation and its actions during the drought stress in plants. Physiol Plant 172:1321–1335. https://doi.org/10.1111/ppl.13297
Pandey P, Irulappan V, Bagavathiannan MV, Senthil-Kumar M (2017) Impact of combined abiotic and biotic stresses on plant growth and avenues for crop improvement by exploiting physio-morphological traits. Front Plant Sci 8:537. https://doi.org/10.3389/fpls.2017.00537
Park SI, Kwon HJ, Cho MH, Song JS, Kim BG, Baek J, Kim SL, Ji H, Kwon TR, Kim KH, Yoon IS (2021) The OsERF115/AP2EREBP110 transcription factor is involved in the multiple stress tolerance to heat and drought in rice plants. Int J Mol Sci 22:7181. https://doi.org/10.3390/ijms22137181
Peleg Z, Blumwald E (2011) Hormone balance and abiotic stress tolerance in crop plants. Curr Opin Plant Biol 14:290–295. https://doi.org/10.1016/j.pbi.2011.02.001
Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL (2016) Transcript-level expression analysis of RNA-seq experiments with HISAT StringTie and Ba llgown. Nat Protoc 11:1650–1667. https://doi.org/10.1038/nprot.2016.095
Rahman F, Hassan M, Rosli R, Almousally I, Hanano A (2018) Evolutionary and genomic analysis of the caleosin/peroxygenase (CLO/PXG) gene/protein families in the Viridiplantae. PLoS ONE 13:e0196669. https://doi.org/10.1371/journal.pone.0196669
Sahid S, Roy C, Paul S, Datta R (2020) Rice lectin protein r40c1 imparts drought tolerance by modulating S-adenosylmethionine synthase 2, stress-associated protein 8 and chromatin-associated proteins. J Exp Bot 71:7331–7346. https://doi.org/10.1093/jxb/eraa400
Salvi P, Manna M, Kaur H, Thakur T, Gandass N, Bhatt D, Muthamilarasan M (2021) Phytohormone signaling and crosstalk in regulating drought stress response in plants. Plant Cell Rep 40:1305–1329. https://doi.org/10.1007/s00299-021-02683-8
Sham A, Moustafa K, Al-Ameri S, Al-Azzawi A, Iratni R, AbuQamar S (2015) Identification of Arabidopsis candidate genes in response to biotic and abiotic stresses using comparative microarrays. PLoS ONE 10:e0125666. https://doi.org/10.1371/journal.pone.0125666
Singh KK, Ghosh S (2013) Regulation of glutamine synthetase isoforms in two differentially drought-tolerant rice (Oryza sativa L.) cultivars under water deficit conditions. Plant Cell Rep 23:183–193. https://doi.org/10.1007/s00299-012-1353-6
Sofo A, Scopa A, Nuzzaci M, Vitti A (2015) Ascorbate peroxidase and catalase activities and their genetic regulation in plants subjected to drought and salinity stresses. Int J Mol Sci 16:13561–13578. https://doi.org/10.3390/ijms160613561
Sun Z, Li S, Chen W, Zhang J, Zhang L, Sun W, Wang Z (2021) Plant dehydrins: expression, regulatory networks, and protective roles in plants challenged by abiotic stress. Int J Mol Sci 22(23):12619. https://doi.org/10.3390/ijms222312619
Tang Y, Bao X, Zhi Y, Wu Q, Guo Y, Yin X, Zeng L, Li J, Zhang J, He W, Liu W, Wang Q, Jia C, Li Z, Liu K (2019) Overexpression of a MYB family gene, OsMYB6, increases drought and salinity stress tolerance in transgenic rice. Front Plant Sci 10:168. https://doi.org/10.3389/fpls.2019.00168
Thomas A, Beena R, Laksmi G, Soni KB, Alex S, Viji MM (2022) Changes in sucrose metabolic enzymes to water stress in contrasting rice genotypes. Plant Stress 5:100088. https://doi.org/10.1016/j.stress.2022.100088
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7:562–578. https://doi.org/10.1038/nprot.2012.016
Wang F, Niu H, Xin D, Long Y, Wang G, Liu Z, Li G, Zhang F, Qi M, Ye Y, Wang Z, Pei B, Hu L, Yuan C, Chen X (2021) OsIAA18 an Aux/IAA transcription factor gene, is involved in salt and drought tolerance in rice. Front Plant Sci 12:738660. https://doi.org/10.3389/fpls.2021.738660
Xiang J, Chen X, Hu W, Xiang Y, Yan M, Wang J (2018) Overexpressing heat-shock protein OsHSP50.2 improves drought tolerance in rice. Plant Cell Rep 37:1585–1595. https://doi.org/10.1007/s00299-018-2331-4
Zhang Z, Zhang Q, Wu J, Zheng X, Zheng S, Sun X, Qiu Q, Lu T (2013) Gene knockout study reveals that cytosolic ascorbate peroxidase 2 (OsAPX2) plays a critical role in growth and reproduction in rice under drought, salt and cold stresses. PLoS ONE 8:e57472. https://doi.org/10.1371/journal.pone.0057472