Genetics, Physiological Mechanism and Breeding for Tolerance against Submergence, Salinity, and Saline-Submergence Stress in Rice (Oryza sativa L.)
DOI:
https://doi.org/10.14719/pst.2536Keywords:
Flood, Marker-assisted selection, Saltol, Sub1, Quantitative trait lociAbstract
Rice is a staple food and one of the most crucial crops globally, providing sustenance for more than half of the world's population. Climate change has a crucial impact on the agricultural sector, particularly rice cultivation, due to the increase in abiotic stress incidences. Salinity is one of the most severe abiotic stresses on rice production globally. Salt stress significantly reduces growth performance, affecting various metabolic and physiological processes in rice. Submergence is another type of abiotic stress affecting rice growth and yield. Recently, a newly emerged abiotic stress called saline submergence may also jeopardize rice production. Seawater intrusion into rice fields located nearby coastal areas may cause saline flash floods, especially during monsoon season. Rice cultivated in coastal areas is prone to saline-submergence stress, leading to a significantly lower yield. Although Sub1 and Saltol QTLs are widely used in developing rice cultivars with submergence and salinity tolerance, there is a lack of studies conducted to explore the potential performance of breeding lines with Sub1 and Saltol QTLs under saline-submergence stress. It has been hypothesized that the introgression of Sub1 and Saltol QTLs into elite rice cultivars might result in potentially tolerant breeding lines to saline-submergence stress. Further breeding projects, however, need to be conducted to prove this postulation. The present mini-review deals with genetics, physiological mechanisms, and breeding achievements for submergence and salinity-tolerant rice while at the same time highlighting saline-submergence as an emerging type of abiotic stress in rice cultivation.
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References
IPCC. Summary for Policymakers. In: Climate Change 2023: Synthesis Report. A Report of the Intergovernmental Panel on Climate Change. Contribution of Working Groups I, II, and III to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change. [Core Writing Team, Lee H and Romero J (eds.)] 2023, IPCC, Geneva, Switzerland, 36 pages.
Hunt JD, Byers E. Reducing sea level rise with submerged barriers and dams in Greenland. Mitigation and Adaptation Strategies for Global Change. 2019;24(5):779–94. https://doi.org/10.1007/s11027-018-9831-y.
Septiningsih EM, Pamplona AM, Sanchez DL, Neeraja CN, Vergara G V., Heuer S, et al. Development of submergence-tolerant rice cultivars: The Sub1 locus and beyond. Ann Bot. 2009;103(2):151–60. https://doi.org/10.1093/aob/mcn206.
Kamarudin K, Said SM. Climate change putting national rice security at risk. 2021 Oct 20. Bernama. https://www.bernama.com/en/b_focus/news.php?id=2014949.
Rojas M, Lambert F, Ramirez-Villegas J, Challinor AJ. Emergence of robust precipitation changes across crop production areas in the 21st century. Proc Nat Acad Sci. 2019;116(14):6673–78. https://doi.org/10.1073/pnas.1811463116
Kurniasih B, Tarigan I, Firmansyah E, Indradewa D. Rice growth in a combined submergence and salinity stresses. IOP Conf Ser Earth Environ Sci. 2021;752(1):012012. https://doi.org/10.1088/1755-1315/752/1/012012
Chakraborty K, Ray S, Vijayan J, Molla KA, Nagar R, Jena P, et al. Preformed aerenchyma determines the differential tolerance response under partial submergence imposed by fresh and saline water flooding in rice. Physiol Plant. 2021;173(4):1597–615. https://doi.org/10.1111/ppl.13536
Azid A, Che Hasnam CN, Juahir H, Amran MA, Toriman ME, Kamarudin MKA, et al. Coastal erosion measurement along Tanjung Lumpur to Cherok Paloh, Pahang during the northeast monsoon season. J Teknol. 2015;74(1):27–34.
Nasrudin N, Kurniasih B. The agro-physiological characteristics of three rice varieties affected by water depth in the coastal agricultural land of Yogyakarta, Indonesia. Biodiversitas. 2021;22(9). https://doi.org/10.13057/biodiv/d220907
Syafiqah Alia Sazali, Mohd Shukor Nordin, Noraziyah Abd. Aziz Shamsudin, Rozilawati Shahari, Mohd Rafii Yusop, Mohd Shahril Firdaus Ab Razak, et al. Susceptibility of Malaysian Rice (Oryza sativa L.) Cultivar to Saline Water Submergence Based on the Morphological Traits. J Agrobiotechnol. 2021;12(2):47–55. https://doi.org/10.37231/jab.2021.12.2.257
Kumar P, Sharma PK. Soil Salinity and Food Security in India. Front Sustain Food Syst. 2020;4. https://doi.org/10.3389/fsufs.2020.533781
Fukagawa NK, Ziska LH. Rice: Importance for Global Nutrition. J Nutr Sci Vitaminol (Tokyo). 2019 ;65:S2-S3. https://doi.org/10.3177/jnsv.65.S2
Salleh MS, Malek RA, Shahari R, Nordin MS. Screening rice (Oryza sativa L.) genotypes for resistance against drought. Water Conservation and Management. 2020;4(2):68–72. https://doi.org/10.14719/pst.2023
Iftekharuddaula KM, Amin A, Shalahuddin AKM, Halder T, Yasmeen R, Hossain MA, et al. Current Scenarios, Progress, and Prospects of Developing Technologies for Flood-Tolerant Rice in Bangladesh. Advances in Rice Research for Abiotic Stress Tolerance. Elsevier Inc.; 2019. 265–279p. https://doi.org/10.1016/B978-0-12-814332-2.00012-5
Septiningsih EM, Pamplona AM, Sanchez DL, Iftekharuddaula K, Masuduzzaman ASM, Vergara G V, et al. The Sub1 Gene and Its Implications in Developing Submergence-Tolerant Rice Cultivars. Metro Manilla; 2008.
Oladosu Y, Rafii MY, Arolu F, Chukwu SC, Muhammad I, Kareem I, et al. Submergence Tolerance in Rice?: Review of Mechanism, Breeding and, Future Prospects. Sustainability. 2020;12(4), 163:1–16. https://doi.org/10.3390/su12041632
Kumar A, Nayak AK, Hanjagi PS, Kumari K, S V, Mohanty S, et al. Submergence stress in rice: Adaptive mechanisms, coping strategies, and future research needs. Environ Exp Bot. 2021;186:104448. https://doi.org/10.1016/j.envexpbot.2021.104448
Mohd Ikmal A, Noraziyah AAS, Wickneswari R, Amira I, Puteri Dinie Ellina Z. Interéaction of submergence tolerance and drought yield QTLs (Sub1 and qDTYs) enhances morpho?physiological traits and survival of rice (Oryza sativa L.) under submergence. Annals of Applied Biology. 2021;178(2):355–66. https://doi.org/10.1111/aab.12664
Luo FL, Nagel KA, Scharr H, Zeng B, Schurr U, Matsubara S. Recovery dynamics of growth, photosynthesis and carbohydrate accumulation after de-submergence: a comparison between two wetland plants showing escape and quiescence strategies. Ann Bot. 2011;107(1):49–63. https://doi.org/10.1093/aob/mcq212
Tahir MA, Ibrahim M, Sarwar G, Iftikhar Y, Ha SK, Han KH, et al. Impact of Indigenous Industrial Compost on The Growth of Coarse and Fine Rice Varieties under Saline Environment. Pertanika J Trop Agric Sci. 2013;36(1):61–70.
Singh RK. Salt tolerance in rice: seedling and reproductive stage QTL mapping come of age. 2021;1–25. https://doi.org/10.1007/s00122-021-03890-3
Kaur N, Kaur G, Pati PK. Deciphering Strategies for Salt Stress Tolerance in Rice in the Context of Climate Change. In: Advances in Rice Research for Abiotic Stress Tolerance. Elsevier; 2019. 113–32p. https://doi.org/10.1016/B978-0-12-814332-2.00006-X
Yao D, Wu J, Luo Q, Zhang D, Zhuang W, Xiao G, et al. Effects of Salinity Stress at Reproductive Growth Stage on Rice (Oryza sativa L.) Composition, Starch Structure, and Physicochemical Properties. Front Nutr. 2022;9. https://doi.org/10.3389/fnut.2022.926217
Fraga TI, Carmona F de C, Anghinoni I, Genro Junior SA, Marcolin E. Flooded rice yield as affected by levels of water salinity in different stages of its cycle. Rev Bras Cienc Solo. 2010;34(1):175–82. https://doi.org/10.1590/S0100-06832010000100018
Che Yah FN, Shamsudin NAA, Ab Razak MSF, Yusop MR, Bhuiyan MAR, Nordin MS, et al. Morphological, Biochemical and Genetic Variation of Rice (Oryza sativa L.) Genotypes to Vegetative Stage Salinity Stress. Plant Science Today. 2023; https://doi.org/10.14719/pst.2023
Chakraborty K, Guru A, Jena P, Ray S, Guhey A, Chattopadhyay K, et al. Rice with SUB1< QTL possesses greater initial leaf gas film thickness leading to delayed perception of submergence stress. Ann Bot. 2021;127(2):251–65. https://doi.org/10.1093/aob/mcaa171
Pattanagul W, Thitisaksakul M. Effect of salinity stress on growth and carbohydrate metabolism in three Rice (Oryza sativa L.) cultivars differing in salinity tolerance. Indian J Exp Biol. 2008;46(10):736–42.
Bailey-Serres J, Fukao T, Ronald P, Ismail A, Heuer S, Mackill D. Submergence Tolerant Rice: SUB1’s Journey from Landrace to Modern Cultivar. Rice. 2010;3(2–3):138–47. https://doi.org/10.1007/s12284-010-9048-5
Xu K, Mackill DJ. A major locus for submergence tolerance mapped on rice chromosome 9. Molecular Breeding. 1996;2(3):219–24. https://doi.org/10.1007/BF00564199
Iftekharuddaula KM, Newaz MA, Salam MA, Ahmed HU, Mahbub MAA, Septiningsih EM, et al. Rapid and high-precision marker-assisted backcrossing to introgress the SUB1 QTL into BR11, the rainfed lowland rice mega variety of Bangladesh. Euphytica. 2011;178(1):83–97. https://doi.org/10.1007/s10681-010-0272-2
Xu K, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, et al. Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature. 2006;442(7103):705–8. https://doi.org/10.1038/nature04920
Emerick K, Ronald PC. Sub1 Rice: Engineering Rice for Climate Change. Cold Spring Harb Perspect Biol. 2019;11(12):a034637. https://doi.org/10.1101/cshperspect.a034637
Sarkar RK, Reddy JN, Sharma SG, Ismail AM. Physiological basis of submergence tolerance in rice and implications for crop improvement. Curr Sci. 2006;91(7):899–06.
Singh S, Mackill DJ, Ismail AM. Field Crops Research Responses of SUB1 rice introgression lines to submergence in the field?: Yield and grain quality. Field Crops Res. 2009;113:12–23. https://doi.org/10.1016/j.fcr.2009.04.003
Neeraja CN, Maghirang-Rodriguez R, Pamplona A, Heuer S, Collard BCY, Septiningsih EM, et al. A marker-assisted backcross approach for developing submergence-tolerant rice cultivars. Theoretical and Applied Genetics. 2007;115(6):767–76. https://doi.org/10.1016/j.fcr.2009.04.003
Waziri A, Kumar, Purty R. Saltol QTL and Their Role in Salinity Tolerance in Rice. Austin J Biotechnol Bioeng. 2016;3(3):1067.
Mohammadi-Nejad G, Arzani A, Rezai AM, Singh RK, Gregorio GB. Assessment of rice genotypes for salt tolerance using microsatellite markers associated with the saltol QTL. Afr J Biotechnol. 2008;7(6):730–6.
Bonilla P, Dvorak J, Mackill D, Deal K, Gregorio G. RFLP and SSLP mapping of salinity tolerance genes in chromosome 1 of rice (Oryza sativa L.) using recombinant inbred lines. Philippine Agricultural Scientist. 2002;65(1):68–76.
Kim SH, Bhat PR, Cui X, Walia H, Xu J, Wanamaker S, et al. Detection and validation of single feature polymorphisms using RNA expression data from a rice genome array. BMC Plant Biol. 2009;9:1–10. https://doi.org/10.1186/1471-2229-9-65
Soda N, Kushwaha HR, Soni P, Singla-Pareek SL, Pareek A. A suite of new genes defining salinity stress tolerance in seedlings of contrasting rice genotypes. Funct Integr Genomics. 2013;13(3):351–65. https://doi.org/10.1007/s10142-013-0328-1
Thomson MJ, de Ocampo M, Egdane J, Rahman MA, Sajise AG, Adorada DL, et al. Characterizing the Saltol quantitative trait locus for salinity tolerance in rice. Rice. 2010;3(2–3):148–60. https://doi.org/10.1007/s12284-010-9053-8
Theerawitaya C, Tisarum R, Samphumphuang T, Takabe T, Cha-um S. Expression levels of the Na+/K+ transporter OsHKT2;1 and vacuolar Na+/H+ exchanger OsNHX1, Na enrichment, maintaining the photosynthetic abilities and growth performances of indica rice seedlings under salt stress. Physiology and Molecular Biology of Plants. 2020;26(3):513–23. https://doi.org/10.1007%2Fs12298-020-00769-3
Singh VK, Singh BD, Kumar A, Maurya S, Krishnan SG, Vinod KK, et al. Marker-Assisted Introgression of Saltol QTL Enhances Seedling Stage Salt Tolerance in the Rice Variety Pusa Basmati 1 . Int J Genomics. 2018;1–12. https://doi.org/10.1155/2018/8319879
Qin H, Li Y, Huang R. Advances and Challenges in the Breeding of Salt-Tolerant Rice. 2021;21(21): 8385. https://doi.org/10.3390%2Fijms21218385
Vinod KK, Krishnan SG, Babu NN, Nagarajan M, Singh AK. Improving salt tolerance in rice: looking beyond the conventional. Salt Stress in Plants: Signalling, Omics and Adaptations. 2013. http://dx.doi.org/10.1007/978-1-4614-6108-1_10
Dangendorf S, Marcos M, Wöppelmann G, Conrad CP, Frederikse T, Riva R. Reassessment of 20th-century global mean sea level rise. Proc Nat Acad Sci. 2017;114(23):5946–51. https://doi.org/10.1073/pnas.1616007114
Kulp SA, Strauss BH. New elevation data triple estimates of global vulnerability to sea-level rise and coastal flooding. Nat Commun. 2019;10(1):4844. https://doi.org/10.1038/s41467-019-12808-z
Islam MA, Hoque MA, Ahmed KM, Butler AP. Impact of Climate Change and Land Use on Groundwater Salinization in Southern Bangladesh—Implications for Other Asian Deltas. Environ Manage. 2019;64(5):640–9. https://doi.org/10.1007/s00267-019-01220-4
Das G, Patra JK, Baek KH. Insight into MAS: A Molecular Tool for Development of Stress Resistant and Quality of Rice through Gene Stacking. Front Plant Sci. 2017;8. https://doi.org/10.3389/fpls.2017.00985
Muthu V, Abbai R, Nallathambi J, Rahman H, Sasikala R, Kambale R, et al. Pyramiding QTLs controlling tolerance against drought, salinity, and submergence in rice through marker-assisted breeding. PLoS One. 2020;15(1):1–18. https://doi.org/10.1371/journal.pone.0227421
Nair MM, Shylaraj KS. Introgression of dual abiotic stress tolerance QTLs (Saltol QTL and Sub1 gene) into Rice (Oryza sativa L.) variety Aiswarya through marker-assisted backcross breeding. Physiology and Molecular Biology of Plants. 2021;27(3):497–514. https://doi.org/10.1007/s12298-020-00893-0
Kuanar SR, Molla KA, Chattopadhyay K, Sarkar RK, Mohapatra PK. Introgression of Sub1 (SUB1) QTL in mega rice cultivars increases ethylene production to the detriment of grain-filling under stagnant flooding. Sci Rep. 2019;9(1):18567. https://doi.org/10.1038/s41598-019-54908-2
Wu YP, Wang SM, Chang YC, Ho C, Hsu YC. Submergence Gene Sub1A Transfer into Drought-Tolerant Japonica Rice DT3 Using Marker-Assisted Selection. Int J Mol Sci. 2021;22(24):13365. https://doi.org/10.3390/ijms222413365
Chattopadhyay K, Nayak AK, Marndi BC, Poonam A, Chakraborty K, Sarkar RK. Novel screening protocol for precise phenotyping of salt-tolerance at reproductive stage in rice. Physiology and Molecular Biology of Plants. 2018;24(6):1047–58. https://doi.org/10.1007/s12298-018-0591-7
Lekklar C, Pongpanich M, Suriya-Arunroj D, Chinpongpanich A, Tsai H, Comai L, et al. Genome-wide association study for salinity tolerance at the flowering stage in a panel of rice accessions from Thailand. BMC Genomics. 2019;20(1):1–18. https://doi.org/10.1186/s12864-018-5317-2
Tsai YC, Chen KC, Cheng TS, Lee C, Lin SH, Tung CW. Chlorophyll fluorescence analysis in diverse rice varieties reveals the positive correlation between the seedling's salt tolerance and photosynthetic efficiency. BMC Plant Biol. 2019;19(1):403. https://doi.org/10.1186/s12870-019-1983-8
Uyoh EA, Ntui VO, Umego C, Ita EE, Opara C. Morphological and molecular screening of rice accessions for salt tolerance. Afr J Biotechnol. 2019;18(27):612–21. http://dx.doi.org/10.5897/AJB2019.16801
Rahman MA, Thomson MJ, De Ocampo M, Egdane JA, Salam MA, Shah-E-Alam M, et al. Assessing trait contribution and mapping novel QTL for salinity tolerance using the Bangladeshi rice landrace. Rice. 2019;12(1). https://doi.org/10.1186/
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Copyright (c) 2022 Syafiqah Alia Sazali, Noraziyah Abd Aziz Shamsudin, Mohd Y. Rafii , Mohd Shahril Firdaus Ab Razak, Muhammad Fahmi Yunus, Fatien Najwa Che Yah, Firdaus Ahmad, MOHD SYAHMI SALLEH
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