Abstract
Rice (Oryza sativa L.) is one of the key food crops in ensuring global food security and accounts for nearly one fourth of the world’s total food supply. Rice production is significantly affected by abiotic stresses. Cytokinins (CKs) play a pivotal role in the regulation of the plant growth, development and abiotic stress responses. In present study, genome-wise analysis led to the identification of 10 Isopentenyl transferase (IPT) gene family members, encoding rate-limiting enzymes in CK biosynthesis pathway in rice. Phylogenetic analysis categorized IPTs into four subfamilies that are structurally and functionally conserved across species with similar gene structures, motifs, domains, cis-acting elements were identified. We performed a genome-wide identification of IPT family members from the rice genome, identified their chromosomal location, gene structure, protein properties, cis-element and phylogeny. Further, Real-time PCR analysis was carried out to understand the spatio-temporal and stress responsive expression of IPT gene family members. OsIPT1, OsIPT2, OsIPT4, OsIPT7, OsIPT8 and OsIPT10 showed similar expression level in both root and shoot of seedling or more expression in root, while OsIPT3, OsIPT5, OsIPT6 and OsIPT9 showed higher expression in shoot as compared with root in seedlings. Abiotic stress responsive expression analysis showed that abiotic stresses reduced the expression of all family members except IPT6. Analysis of expression of IPTs in rice cv. Kitaake (low biomass and low yielding) and Taipei (high biomass and high yielding) showed that expression of IPTs were higher in different tissues in Taipei. Present study has also elaborately described the tissue and stage specific expression and for further analysis of IPT in the regulation of biotic and abiotic stress resistance, growth, and development in rice, and provides a comprehensive analysis of the OsIPT gene family, including structures and functions.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Bailey, T. L., Boden, M., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., Ren, J., Li, W. W., & Noble, W. S. (2009). MEME SUITE: tools for motif discovery and searching. Nucleic Acids Research, 37, W202–W208. https://doi.org/10.1093/nar/gkp335
Barciszewski, J., Siboska, G. E., Rattan, S. I., & Clark, B. F. (2000). Occurrence, biosynthesis and properties of kinetin (N6-furfuryladenine). Plant Growth Regulation, 32, 257–265. https://doi.org/10.1023/A:1010772421545
Belintani, N. G., Guerzoni, J. T. S., Moreira, R. M. P., & Vieira, L. G. E. (2012). Improving low-temperature tolerance in sugarcane by expressing the ipt gene under a cold inducible promoter. Biologia Plantarum, 56(1), 71–77. https://doi.org/10.1007/s10535-012-0018-1
Beznec, A., Faccio, P., Miralles, D. J., Abeledo, L. G., Oneto, C. D., Garibotto, M. B., et al. (2021). Stress-induced expression of IPT gene in transgenic wheat reduces grain yield penalty under drought. Journal, Genetic Engineering & Biotechnology, 19(1), 67. https://doi.org/10.1186/s43141-021-00171-w
Brugière, N., Humbert, S., Rizzo, N. W., Bohn, J. A., & Habben, J. E. (2008). A member of the maize isopentenyl transferase gene family, Zea mays isopentenyl transferase 2 (ZmIPT2), encodes a cytokinin biosynthetic enzyme expressed during kernel development. Plant Molecular Biology, 67, 215–229. https://doi.org/10.1007/s11103-008-9312-x
Calderini, O., Bovone, T., Scotti, C., Pupilli, F., Piano, E., & Arcioni, S. (2007). Delay of leaf senescence in Medicago sativa transformed with the ipt gene controlled by the senescence-specific promoter SAG12. Plant Cell Reports, 26(5), 611–615. https://doi.org/10.1007/s00299-006-0262-y
Chen, C., Chen, H., Zhang, Y., Thomas, H. R., Frank, M. H., He, Y., & Xia, R. (2020). TBtools: An integrative toolkit developed for interactive analyses of big biological data. Molecular Plant, 13(8), 1194–1202. https://doi.org/10.1016/j.molp.2020.06.009
Chorev, M., & Carmel, L. (2012). The function of introns. Frontiers in Genetics, 3, 55. https://doi.org/10.3389/fgene.2012.00055
Daskalova, S. M., McCormac, A. C., Scott, N. W., Onckelen, H. A., & Elliott, M. C. (2007). Effect of seed-specific expression of the ipt gene on Nicotiana tabacum L. seed composition. Plant Growth Regulation, 51, 217–229. https://doi.org/10.1007/s10725-006-9162-y
Davies, P. J. (2004). Plant hormones biosynthesis, signal transduction, action. Kluwer Academic Publishers.
Décima Oneto, C., Otegui, M. E., Baroli, I., Beznec, A., Faccio, P., Bossio, E., Blumwald, E., & Lewi, D. (2016). (2016). Water deficit stress tolerance in maize conferred by expression of an isopentenyltransferase (IPT) gene driven by a stress- and maturation-induced promoter. Journal of Biotechnology, 220, 66–77. https://doi.org/10.1016/j.jbiotec.2016.01.014
FAO 2022 (https://www.fao.org/statistics/en/) Accessed on 06/July/2023.
Feng, Y., Lv, J., Peng, M., Li, J., Wu, Y., Gao, M., Wu, X., Wang, Y., Wu, T., Zhang, X., Xu, X., & Han, C. L. (2022). Genome-wide identification and characterization of the IPT family members in nine Rosaceae species and a functional analysis of MdIPT5b in cold resistance. Horticultural Plant Journal, 9(4), 616–630. https://doi.org/10.1016/j.hpj.2022.12.010
Frébortová, J., Greplová, M., Seidl, M. F., Heyl, A., & Frébort, I. (2015). Biochemical characterization of putative adenylate dimethylallyltransferase and cytokinin dehydrogenase from Nostoc sp. PCC 7120. PloS one, 10, e0138468. https://doi.org/10.1371/journal.pone.0138468
Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R. D., & Bairoch, A. (2003). ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Research, 31(13), 3784–3788. https://doi.org/10.1093/nar/gkg563
Ghanem, M. E., Albacete, A., Smigocki, A. C., Frébort, I., Pospísilová, H., Martínez-Andújar, C., Acosta, M., Sánchez-Bravo, J., Lutts, S., Dodd, I. C., & Pérez-Alfocea, F. (2011). Root-synthesized cytokinins improve shoot growth and fruit yield in salinized tomato (Solanum lycopersicum L.) plants. Journal Of Experimental Botany, 62(1), 125–140. https://doi.org/10.1093/jxb/erq266
Ghosh, A., Shah, M. N., Jui, Z. S., Saha, S., Fariha, K. A., & Islam, T. (2018). Evolutionary variation and expression profiling of isopentenyl transferase gene family in Arabidopsis thaliana L. and Oryza sativa L. Plant Gene, 15, 15–27. https://doi.org/10.1016/j.plgene.2018.06.002
Giron, D., Frago, E., Glevarec, G., Pieterse, C. M. J., & Dicke, M. (2013). Cytokinins as key regulators in plant-microbe-insect interactions: Connecting plant growth and defence. Functional Ecology, 27(3), 599–609. https://doi.org/10.1111/1365-2435.12042
Ha, S., Vankova, R., Yamaguchi-Shinozaki, K., Shinozaki, K., & Tran, L. S. P. (2012). Cytokinins: Metabolism and function in plant adaptation to environmental stresses. Trends in Plant Science, 17, 172–179. https://doi.org/10.1016/j.tplants.2011.12.005
Higo, K., Ugawa, Y., Iwamoto, M., & Korenaga, T. (1999). Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Research, 27(1), 297–300. https://doi.org/10.1093/nar/27.1.297
Hirota, O., Oka, M., & Takeda, T. (1990). Sink activity estimation by sink size and dry matter increase during the ripening stage of Barley (Hordeum vulgare) and Rice (Oryza sativa). Annals of Botany, 65, 349–353. https://doi.org/10.1093/oxfordjournals.aob.a087944
Horton, P., Park, K. J., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C. J., & Nakai, K. (2007). WoLF PSORT: protein localization predictor. Nucleic Acids Research, 35, W585–W587. https://doi.org/10.1093/nar/gkm259
Hu, B., Jin, J., Guo, A. Y., Zhang, H., Luo, J., & Gao, G. (2015). GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics, 31(8), 1296–1297. https://doi.org/10.1093/bioinformatics/btu817
Joshi, R., Sahoo, K. K., Tripathi, A. K., Kumar, R., Gupta, B. K., Pareek, A., & Singla-Pareek, S. L. (2018). Knockdown of an inflorescence meristem-specific cytokinin oxidase—OsCKX2 in rice reduces yield penalty under salinity stress condition. Plant, Cell & Environment, 41(5), 936–946. https://doi.org/10.1111/pce.12947
Kant, S., Burch, D., Badenhorst, P., Palanisamy, R., Mason, J., & Spangenberg, G. (2015). Regulated expression of a cytokinin biosynthesis gene IPT delays leaf senescence and improves yield under rainfed and irrigated conditions in canola (Brassica napus L.). PloS One, 10(1), e0116349. https://doi.org/10.1371/journal.pone.0116349
Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N., & Sternberg, M. J. (2015). The Phyre2 web portal for protein modeling, prediction and analysis. Nature Protocols, 10(6), 845–858. https://doi.org/10.1038/nprot.2015.053
Kiba, T., Takei, K., Kojima, M., & Sakakibara, H. (2013). Side-chain modification of cytokinins controls shoot growth in Arabidopsis. Developmental Cell, 27(4), 452–461. https://doi.org/10.1016/j.devcel.2013.10.004
Laskowski, R. A., Jabłońska, J., Pravda, L., Vařeková, R. S., & Thornton, J. M. (2018). PDBsum: Structural summaries of PDB entries. Protein Science: A Publication of the Protein Society, 27(1), 129–134. https://doi.org/10.1002/pro.3289
Lin, Y., Cao, M. L., Xu, C. G., Chen, H., Wei, J., & Zhang, Q. F. (2002). Cultivating rice with delaying leaf-senescence by PSAG12-IPT gene transformation. Acta Botanica Sinica, 44, 1333–1338.
Liu, Y. D., Yin, Z. J., Yu, J. W., Li, J., Wei, H. L., Han, X. L., & Shen, F. F. (2011). Improved salt tolerance and delayed leaf senescence in transgenic cotton expressing the Agrobacterium IPT gene. Biologia Plantarum, 56, 237–246. https://doi.org/10.1007/s10535-012-0082-6
Liu, Z., Lv, Y., Zhang, M., Liu, Y., Kong, L., Zou, M., Lu, G., Cao, J., & Yu, X. (2013). Identification, expression, and comparative genomic analysis of the IPT and CKX gene families in Chinese cabbage (Brassica rapa ssp. pekinensis). BMC Genomics, 14, 594. https://doi.org/10.1186/1471-2164-14-594
Livak, K. J., & Schmittgen, T. D. (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods, 25(4), 402–408. https://doi.org/10.1006/meth.2001.1262
Li, Q., Robson, P. R. H., Bettany, A. J. E., Donnison, I. S., Thomas, H., & Scott, I. M. (2004). Modification of senescence in ryegrass transformed with IPT under the control of a monocot senescence-enhanced promoter. Plant Cell Reports, 22(11), 816–821. https://doi.org/10.1007/s00299-004-0762-6
Mantri, N., Patade, V. Y., Penna, S., Ford, R., & Pang, E. C. (2012). Abiotic stress responses in plants: Present and future. In P. Ahmad & M. Prasad (Eds.), Abiotic Stress Responses in Plants. Springer. https://doi.org/10.1007/978-1-4614-0634-1_1
McCabe, M. S., Garratt, L. C., Schepers, F., Jordi, W. J., Stoopen, G. M., Davelaar, E., et al. (2001). Effects of P(SAG12)-IPT gene expression on development and senescence in transgenic lettuce. Plant Physiology, 127(2), 505–516.
Merewitz, E. B., Du, H., Yu, W., Liu, Y., Gianfagna, T., & Huang, B. (2012). Elevated cytokinin content in ipt transgenic creeping bentgrass promotes drought tolerance through regulating metabolite accumulation. Journal of Experimental Botany, 63(3), 1315–1328. https://doi.org/10.1093/jxb/err372
Mok, D. W., & Mok, M. C. (2001). Cytokinin metabolism and action. Annual Review of Plant Physiology and Plant Molecular Biology, 52, 89–118. https://doi.org/10.1146/annurev.arplant.52.1.89
Nishii, K., Wright, F., Chen, Y. Y., & Möller, M. (2018). Tangled history of a multigene family: The evolution of Isopentenyl transferase genes. PLoS ONE, 13(8), e0201198. https://doi.org/10.1371/journal.pone.0201198
Nishiyama, R., Watanabe, Y., Fujita, Y., Le, D. T., Kojima, M., Werner, T., et al. (2011). Analysis of cytokinin mutants and regulation of cytokinin metabolic genes reveals important regulatory roles of cytokinins in drought, salt and abscisic acid responses, and abscisic acid biosynthesis. The Plant Cell, 23(6), 2169–2183. https://doi.org/10.1105/tpc.111.087395
Pavlíková, D., Pavlík, M., Procházková, D., Zemanová, V., Hnilička, F., & Wilhelmová, N. (2014). Nitrogen metabolism and gas exchange parameters associated with zinc stress in tobacco expressing an ipt gene for cytokinin synthesis. Journal of Plant Physiology, 171(7), 559–564. https://doi.org/10.1016/j.jplph.2013.11.016
Pei, Z., Chengxiang, G., Na, Z., Zujun, Y., Yudong, L., & Fafu, S. (2012). Study on differential expression patterns of senescence-associated genes in transgenic cotton with IPT gene. Molecular Plant Breeding, 10, 324–330. https://doi.org/10.1007/s10535-013-0324-2
Peleg, Z., Reguera, M., Tumimbang, E., Walia, H., & Blumwald, E. (2011). Cytokinin-mediated source/sink modifications improve drought tolerance and increase grain yield in rice under water-stress. Plant Biotechnology Journal, 9(7), 747–758. https://doi.org/10.1111/j.1467-7652.2010.00584.x
Qin, H., Gu, Q., Zhang, J., Sun, L., Kuppu, S., Zhang, Y., et al. (2011). Regulated expression of an Isopentenyl transferase gene (IPT) in peanut significantly improves drought tolerance and increases yield under field conditions. Plant and Cell Physiology, 52(11), 1904–1914. https://doi.org/10.1093/pcp/pcr125
Rivero, R. M., Kojima, M., Gepstein, A., Sakakibara, H., Mittler, R., Gepstein, S., & Blumwald, E. (2007). Delayed leaf senescence induces extreme drought tolerance in a flowering plant. Proceedings of the National Academy of Sciences of the United States of America, 104(49), 19631–19636. https://doi.org/10.1073/pnas.0709453104
Rivero, R. M., Gimeno, J., Van Deynze, A., Walia, H., & Blumwald, E. (2010). Enhanced cytokinin synthesis in tobacco plants expressing PSARK::IPT prevents the degradation of photosynthetic protein complexes during drought. Plant and Cell Physiology, 51(11), 1929–1941. https://doi.org/10.1093/pcp/pcq143
Robson, P. R., Donnison, I. S., Wang, K., Frame, B., Pegg, S. E., Thomas, A., & Thomas, H. (2004). Leaf senescence is delayed in maize expressing the Agrobacterium IPT gene under the control of a novel maize senescence-enhanced promoter. Plant Biotechnology Journal, 2(2), 101–112. https://doi.org/10.1046/j.1467-7652.2004.00054.x
Roitsch, T., & Ehneß, R. (2000). Regulation of source/sink relations by cytokinins. Plant Growth Regulation, 32, 359–367. https://doi.org/10.1023/A:1010781500705
Sakakibara, H. (2006). Cytokinins: Activity, biosynthesis, and translocation. Annual Review of Plant Biology, 57, 431–449. https://doi.org/10.1146/annurev.arplant.57.032905.105231
Sakamoto, T., Sakakibara, H., Kojima, M., Yamamoto, Y., Nagasaki, H., Inukai, Y., et al. (2006). Ectopic expression of KNOTTED1-like homeobox protein induces expression of cytokinin biosynthesis genes in rice. Plant Physiology, 142(1), 54–62. https://doi.org/10.1104/pp.106.085811
Santosh Kumar, V. V., Yadav, S. K., Verma, R. K., Shrivastava, S., Ghimire, O., Pushkar, S., Rao, M. V., Senthil Kumar, T., & Chinnusamy, V. (2021). The abscisic acid receptor OsPYL6 confers drought tolerance to indica rice through dehydration avoidance and tolerance mechanisms. Journal of Experimental Botany, 72(4), 1411–1431. https://doi.org/10.1093/jxb/eraa509
Skalák, J., Černý, M., Jedelský, P., Dobrá, J., Ge, E., Novák, J., Hronková, M., Dobrev, P., Vanková, R., & Brzobohatý, B. (2016). Stimulation of ipt overexpression as a tool to elucidate the role of cytokinins in high temperature responses of Arabidopsis thaliana. Journal of Experimental Botany, 67(9), 2861–2873. https://doi.org/10.1093/jxb/erw129
Snyder, G. W., Sammons, D. J., & Sicher, R. C. (1993). Spike removal effects on dry matter production, assimilate distribution and grain yields of three soft red winter wheat genotypes. Field Crops Research, 33, 1–11. https://doi.org/10.1016/0378-4290(93)90091-Z
Sun, J., Niu, Q. W., Tarkowski, P., Zheng, B., Tarkowska, D., Sandberg, G., Chua, N. H., & Zuo, J. (2003). The Arabidopsis AtIPT8/PGA22 gene encodes an isopentenyl transferase that is involved in de novo cytokinin biosynthesis. Plant physiology, 131(1), 167–176. https://doi.org/10.1104/pp.011494
Takei, K., Sakakibara, H., & Sugiyama, T. (2001). Identification of genes encoding adenylate isopentenyltransferase, a Cytokinin Biosynthesis Enzyme, in Arabidopsis thaliana. The Journal of biological chemistry. 276, 26405–26410. https://doi.org/10.1074/jbc.M102130200
Verma, R. K., Santosh Kumar, V. V., Yadav, S. K., Pushkar, S., Rao, M. V., & Chinnusamy, V. (2019). Overexpression of ABA receptor PYL10 gene confers drought and cold tolerance to indica rice. Frontiers in Plant Science, 10, 1488. https://doi.org/10.3389/fpls.2019.01488
Wang, Y., Shen, W., Chan, Z., & Wu, Y. (2015). Endogenous cytokinin overproduction modulates ROS homeostasis and decreases salt stress resistance in Arabidopsis Thaliana. Frontiers in Plant Science, 6, 1004. https://doi.org/10.3389/fpls.2015.01004
Wang, X., Ding, J., Lin, S., Liu, D., Gu, T., Wu, H., et al. (2020). Evolution and roles of cytokinin genes in angiosperms 2: Do ancient CKXs play housekeeping roles while non-ancient CKXs play regulatory roles? Horticulture Research, 7, 29. https://doi.org/10.1038/s41438-020-0246-z
Wang, Na., Chen, J., Gao, Y., Zhou, Y., Chen, M., Xu, Z., Fang, Z., & Ma, Y. (2022). Genomic analysis of isopentenyl transferase genes and functional characterization of TaIPT8 indicates positive effects of cytokinins on drought tolerance in wheat. The Crop Journal, 11(1), 46–56. https://doi.org/10.1016/j.cj.2022.04.010
Xiao, X. O., Zeng, Y. M., Cao, B. H., Lei, J. J., Chen, Q. H., Meng, C. M., et al. (2017). PSAG12-IPT overexpression in eggplant delays leaf senescence and induces abiotic stress tolerance. The Journal of Horticultural Science and Biotechnology, 92(4), 349–357. https://doi.org/10.1080/14620316.2017.1287529
Xu, Y., Burgess, P., Zhang, X., & Huang, B. (2016). Enhancing cytokinin synthesis by overexpressing IPT alleviated drought inhibition of root growth through activating ROS-scavenging systems in Agrostis stolonifera. Journal of Experimental Botany, 67(6), 1979–1992. https://doi.org/10.1093/jxb/erw019
Xu, Y., & Huang, B. (2017). Transcriptional factors for stress signaling, oxidative protection, and protein modification in IPT-transgenic creeping bentgrass exposed to drought stress. Environmental and Experimental Botany, 144, 49–60. https://doi.org/10.1016/j.envexpbot.2017.10.004
Yadav, S. K., Santosh Kumar, V. V., Verma, R. K., Yadav, P., Saroha, A., Wankhede, D. P., Chaudhary, B., & Chinnusamy, V. (2020). Genome-wide identification and characterization of ABA receptor PYL gene family in rice. BMC Genomics, 21(1), 676. https://doi.org/10.1186/s12864-020-07083-y
Yadav, S. K., Yadav, P., & Chinnusamy, V. (2023). Nutrigenomics in cereals. In R. Deshmukh, A. Nadaf, W. A. Ansari, K. Singh, & H. Sonah (Eds.), Biofortification in Cereals. Springer. https://doi.org/10.1007/978-981-19-4308-9_12
Yadav, P., Santosh Kumar, V. V., Priya, J., Yadav, S. K., Nagar, S., Singh, M., & Chinnusamy, V. (2023a). A versatile protocol for efficient transformation and regeneration in mega indica rice cultivar MTU1010: Optimization through hormonal variables. Methods and Protocols, 6(6), 113. https://doi.org/10.3390/mps6060113
Yi, Z., Peng, Z., Zhao, L., Fangjun, L., & Xiaoli, T. (2019). An isopentyl transferase gene driven by the senescence-inducible SAG12 promoter improves salinity stress tolerance in cotton. Journal of Cotton Research, 2, 15. https://doi.org/10.1186/s42397-019-0032-3
Zhang, P., Wang, W. Q., Zhang, G. L., Kaminek, M., Dobrev, P., Xu, J., & Gruissem, W. (2010). Senescence-inducible expression of isopentenyl transferase extends leaf life, increases drought stress resistance and alters cytokinin metabolism in cassava. Journal of Integrative Plant Biology, 52(7), 653–669. https://doi.org/10.1111/j.1744-7909.2010.00956.x
Zhao, M., Lin, Y., & Chen, H. (2020). Improving nutritional quality of rice for human health. TAG. Theoretical and Applied Genetics, 133(5), 1397–1413. https://doi.org/10.1007/s00122-019-03530-x
Acknowledgements
The authors acknowledge all in kind contributions and the facilities provided by Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi.
Funding
This work was supported by Indian Council of Agricultural Research (ICAR-12th plan scheme) funded project code (21–46). Incentivizing Research in Agriculture on “Towards understanding C3-C4 intermediate pathway in poaceae and functionality C4 genes in rice”.
Author information
Authors and Affiliations
Contributions
VC, conceived the study. PY and SKY contributed to conduct the experiments. PY, MS, MPS contributed to data analysis and draft preparation. VC edited the draft. All authors have read and agreed to the published version of the manuscript.
Corresponding author
Ethics declarations
Conflict of interest
No conflict of interests regarding this publication.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Yadav, P., Yadav, S.K., Singh, M. et al. Genome wide identification and characterization of Isopentenyl transferase (IPT) gene family associated with cytokinin synthesis in rice. Plant Physiol. Rep. (2024). https://doi.org/10.1007/s40502-024-00793-5
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s40502-024-00793-5