QTL mapping of physiological traits at the booting stage in rice under low temperature combined with nitrogen fertilization

https://doi.org/10.17221/67/2018-CJGPBCitation:Yang S.M., Zhang F.F., Zhang S.H., Li G.Y., Zeng L.Q., Liu G.S., Yu X.F., Qiu X.L. (2019): QTL mapping of physiological traits at the booting stage in rice under low temperature combined with nitrogen fertilization. Czech J. Genet. Plant Breed., 55: 146-155.
download PDF

Further dissection of physiological molecular mechanisms is indispensable to alleviate rice yield losses resulting from cold injury. By using 105 near-isogenic lines (NILs) derived from a backcross between cv. Lijiangxintuanheigu (LTH) and cv. Towada, we detected quantitative trait loci (QTLs) for physiological traits of the rice flag leaf, based on polymorphic simple sequence repeat (SSR) markers, inclusive composite interval mapping (ICIM), mixed composite interval mapping (MCIM) approaches and phenotypic value subjected to combine with cold-water stress and three nitrogen application rates. By using ICIM, a total of 34 QTLs with additive effects (A-QTLs) were identified on chromosomes 1, 3, 4, 5, 6, 7 and 10, and the phenotypic variation (R2) explained by each QTL ranged from 8.46 to 29.14%. By using MCIM, 20 A-QTLs and 14 pairs of QTLs with epistatic × environment interaction effects (Epistatic QTLs) were detected, the contribution of environment interaction (H2AE) was 0.87 to 7.36%, while the contribution rates of E-QTL were from 0.97 to 3.58%. Fourteen A-QTLs were detected by ICIM and MCIM, which may serve as a basis for fine-mapping and candidate gene studies, and providing strategies for the development of cold-tolerant rice cultivars and nitrogen application to alleviate chilling stress.


Cao X.C., Zhong C., Zhu L.F., Zhang J.H., Sajid H.,Wu L.H., Jin Q.Y. (2017): Glycine increases cold tolerance in rice via the regulation of N uptake, physiological characteristics, and photosynthesis. Plant Physiology and Biochemistry, 112: 251–260. https://doi.org/10.1016/j.plaphy.2017.01.008
Dumont E., Fontaine V., Vuylsteker C., Sellier H., Bodèle S., Voedts N., Devaux R., Frise M., Avia K., Hilbert J.L., Bahrman N., Hanocq E., Lejeune H.I., Delbreil B. (2009): Association of sugar content QTL and PQL with physiological traits relevant to frost damage resistance in pea under weld and controlled conditions. Theoretical and Applied Genetics, 118: 1561–1571. https://doi.org/10.1007/s00122-009-1004-7
Endo T., Chiba B., Wagatsuma K., Saeki K., Ando T., Shomura A., Mizubayashi T., Ueda T., Yamamoto T., Nishio T. (2016): Detection of QTLs for cold tolerance of rice cultivar ‘Kuchum’ and effect of QTL pyramiding. Theoretical and Applied Genetics, 129: 631–640.  https://doi.org/10.1007/s00122-015-2654-2
FAO (2015): FAOSTAT Agriculture Data. Available online at: http://faostat.fao.org/site/339/default.aspx (Accessed Oct 1, 2015).
Faruk H.M., Chandra S.B., Kamaruzzaman M., Abdul H.M., Najim U.M., Siddique M.A. (2015): Physiological investigation of rice landraces in a low temperature area of Bangladesh. Research Journal of Agriculture and Forestry Sciences, 3: 1–6.
Gill S.S., Tuteja N. (2010): Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants. Plant Physiology Biochemistry, 48: 909–930. https://doi.org/10.1016/j.plaphy.2010.08.016
Gunawardena T.A., Fukai S. (2005): The interaction of nitrogen application and temperature during reproductive stage on spikelet sterility in field-grown rice. Australia Journal Agricultural Research, 56: 625–636. https://doi.org/10.1071/AR04099
Gutiérrez R.A. (2012): Systems biology for enhanced plant nitrogen nutrition. Science, 336: 1673–1675. https://doi.org/10.1126/science.1217620
IPCC (2013): Climate Change 2013: The Physical Science Basis. Cambridge, New York, Cambridge University Press.
Li H.S., Sun Q., Zhao S.J., Zhang W.H. (2000): The Experiment Principle and Technique on Plant Physiology and Biochemistry. Beijing, Higher Education Press. (in Chinese)
McCouch S.R. (2008): Gene nomenclature system for rice. Rice, 1: 72–84. https://doi.org/10.1007/s12284-008-9004-9
Meng L., Li H.H., Zhang L.Y., Wang J.K. (2015): QTLs IciMapping: integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. The Crop Journal, 3: 269–283. https://doi.org/10.1016/j.cj.2015.01.001
Mitchell J.H., Zulkafli S.L., Bosse J., Campbell B., Snell P., Mace E.S., Godwin I.D., Fukai S. (2016): Rice-cold tolerance across reproductive stages. Crop and Pasture Science, 67: 823–833. https://doi.org/10.1071/CP15331
Morsy M.R., Jouve L., Hausman J.F., Hoffmann L., Stewart J.M. (2007): Alteration of oxidative and carbohydrate metabolism under abiotic stress in two rice (Oryza sativa L.) genotypes contrasting in chilling tolerance. Journal Plant Physiology, 164: 157–167. https://doi.org/10.1016/j.jplph.2005.12.004
Nasholm T., Kielland K., Ganeteg U. (2009): Uptake of organic nitrogen by plants. New Phytologist, 182: 31–48. https://doi.org/10.1111/j.1469-8137.2008.02751.x
Oliver S.N., Van Dongen J.T., Alfred S.C., Mamun E.A., Zhao X., Saini H.S., Fernandes S.F., Blanchard C.L., Sutton B.G., Geigenberger P., Dennis E.S., Dolferus R. (2005): Cold-induced repression of the rice anther-specific cell wall invertase expression gene OSINV4 is correlated with sucrose accumulation and pollen sterility. Plant Cell and Environment, 28: 1534–1551. https://doi.org/10.1111/j.1365-3040.2005.01390.x
Popović B.M., Štajner D., Pavlović R.Ž., Tari I., Csiszár J., Gallé A., Poór P., Galović V., Trudić B., Orlović S. (2017): Biochemical response of hybrid black poplar tissue culture (Populus × canadensis) on water stress. Journal Plant Research, 130: 559–570. https://doi.org/10.1007/s10265-017-0918-4
Rihan Z.H., AL-Issawi M., Fuller P.M. (2017): Advances in physiological and molecular aspects of plant cold tolerance. Journal of Plant Interactions, 12: 143–157. https://doi.org/10.1080/17429145.2017.1308568
Rogers S.O., Bendich A.J. (1989): Extraction of DNA from plant tissues. In: Gelvin S.B., Schilperoort R.A., Verma D.P.S. (eds.): Plant Molecular Biology Manual. Dordrecht, Kluwer Academic Publishers: 73–83.
Shimono H., Abe A., Aoki N., Koumoto T., Sato M, Yokoi S., Kuroda E., Endo T., Saeki K.I., Nagano K. (2016): Combining mapping of physiological quantitative trait loci and transcriptome for cold tolerance for counteracting male sterility induced by low temperatures during reproductive stage in rice. Physiologia Plantarum, 157: 175–192. https://doi.org/10.1111/ppl.12410
Shirasawa S., Endo T., Nakagomi K., Yamaguchi M., Nishio T. (2012): Delimitation of QTL region controlling cold tolerance at booting stage of a cultivar, ‘Lijiangxintuanheigu’, in rice, Oryza sativa L. Theoretical and Applied Genetics, 124: 937–946. https://doi.org/10.1007/s00122-011-1758-6
Song S.Y., Chen Y., Chen J., Dai X.Y., Zhang W.H. (2011): Physiological mechanisms underlying OsNAC5-dependent tolerance of rice plants to abiotic stress. Planta, 234: 331–345. https://doi.org/10.1007/s00425-011-1403-2
Szabados L., Savoure A. (2010): Proline: a multifunctional amino acid. Trends Plant Science, 15: 89–97. https://doi.org/10.1016/j.tplants.2009.11.009
Theocharis A., Clement C., Barka E.A. (2012): Physiological and molecular changes in plants at low temperatures. Planta, 235: 1091–1105. https://doi.org/10.1007/s00425-012-1641-y
Ulziibat B., Ohta H., Fukushima A., Shirasawa S., Kitashiba H., Nishio T. (2016): Examination of candidates for the gene of cold tolerance at the booting stage in a delimited QTL region in rice cultivar ‘Lijiangxintuanheigu’. Euphytica, 211: 331–341. https://doi.org/10.1007/s10681-016-1742-y
Waraich E.A., Ahmad R., Halim A., Aziz T. (2012): Alleviation of temperature stress by nutrient management in crop plants: a review. Journal Soil Science and Plant Nutrition, 12: 221–244. https://doi.org/10.4067/S0718-95162012000200003
Xu G.H., Fan X.R., Miller A.J. (2012): Plant nitrogen assimilation and use efficiency. Annual Review of Plant Biology, 63: 153–182. https://doi.org/10.1146/annurev-arplant-042811-105532
Yang A., Dai X.Y., Zhang W.H. (2012): A R2R3-type MYB gene, OsMYB2, is involved in salt, cold, and dehydration tolerance in rice. Journal Experiment Botany, 63: 2541–2556. https://doi.org/10.1093/jxb/err431
Yang J., Zhu J., Williams R.W. (2007): Mapping the genetic architecture of complex traits in experimental populations. Bioinformatics, 23: 1527–1536. https://doi.org/10.1093/bioinformatics/btm143
Yang S.M., Zhang S.H., Yang T., Wang L. (2018): Detection of QTLs for cold tolerance at booting stage in near-isogenic lines derived from rice landrace Lijiangxintuanheigu. Czech Journal Genetic and Plant Breeding, 54: 93–100. https://doi.org/10.17221/98/2017-CJGPB
Zhang H., Liang W.Q., Yang X.J., Luo X., Jiang N., Ma H., Zhang D.B. (2010): Carbon starved anther encodes a MYB domain protein that regulates sugar partitioning required for rice pollen development. The Plant Cell, 22: 672–689. https://doi.org/10.1105/tpc.109.073668
download PDF

© 2019 Czech Academy of Agricultural Sciences