Evaluating the phenotypic responses of CRISPR/Cas9-edited Mentik Wangi rice mutants T1 focusing on GA20ox2 and OsCKX2 gene knockout
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TILMIIDZAH SALMA FATHIN
https://orcid.org/0009-0007-6398-5061
ATMITRI SISHARMINI
https://orcid.org/0000-0002-1652-6539
ANIVERASRI APRIANA
TRI JOKO SANTOSO
AHMAD YUNUS
♥
https://orcid.org/0000-0001-6483-9671
Abstract
Abstract. Fathin TS, Sisharmini A, Apriana A, Santoso TJ, Yunus A. 2024. Evaluating the phenotypic responses of CRISPR/Cas9-edited Mentik Wangi rice mutants T1 focusing on GA20ox2 and OsCKX2 gene knockout. Biodiversitas 25: 2783-2790. Mentik Wangi is a local Indonesian rice variety with tall plant stature, making it susceptible to lodging and yield loss, necessitating trait improvements to overcome these weaknesses. Gene editing of GA20ox2 and OsCKX2 using CRISPR/Cas9 was conducted to improve the characteristics of Mentik Wangi. This study aimed to evaluate the phenotypic responses of T1 Mentik Wangi mutant lines generated through gene editing using the CRISPR/Cas9 system. Eighty-five mutant lines and wild-type plants were grown and observed in a greenhouse. Phenotypic traits were observed as quantitative traits, such as plant height, panicle length, total number of tillers, number of productive tillers, total number of grains, 1000-grain weight, heading date, and harvesting age; and qualitative traits, such as panicle type and panicle exsertion type. The results showed a decrease in plant height and panicle length in Mentik Wangi rice mutant lines. Several lines exhibited improvements in total tiller number, productive tiller number, total grain number, and 1000-grain weight. Mutant lines required longer to reach the generative phase and displayed differences in panicle type and panicle exsertion type. This study reported that the T1 mutant lines demonstrated distinct phenotypic responses indicating improvements in the desired traits.
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References
Ashikari, M., Sakakibara, H., Lin, S., Yamamoto, T., Takashi, T., Nishimura, A., Angeles, E. R., Qian, Q., Kitano, H., & Matsuoka, M. (2005). Cytokinin oxidase regulates rice grain production. Science (New York, N.Y.), 309(5735), 741–745. https://doi.org/10.1126/science.1113373
Biswas, S., Tian, J., Rong, L., Chen, X., Luo, Z., Chen, M., Zhao, X., Zhang, D., Persson, S., Yuan, Z., & Shi, J. (2020). Investigation of CRISPR/Cas9-induced SD1 rice mutants highlights the importance of molecular characterization in plant molecular breeding. Journal of Genetics and Genomics, 47. https://doi.org/10.1016/j.jgg.2020.04.004
Cheikh, N., & Jones, R. J. (1994). Disruption of Maize Kernel Growth and Development by Heat Stress (Role of Cytokinin/Abscisic Acid Balance). Plant Physiology, 106(1), 45–51. https://doi.org/10.1104/pp.106.1.45
Cortleven, A., Leuendorf, J. E., Frank, M., Pezzetta, D., Bolt, S., & Schmülling, T. (2019). Cytokinin action in response to abiotic and biotic stresses in plants. Plant, Cell & Environment, 42(3), 998–1018. https://doi.org/10.1111/pce.13494
Cortleven, A., & Schmülling, T. (2015). Regulation of chloroplast development and function by cytokinin. Journal of Experimental Botany, 66(16), 4999–5013. https://doi.org/10.1093/jxb/erv132
Das, T., Ghorai, M., Pandey, D., Radha, R., Thakur, M., Rathour, S., Al Tawaha, A. R., Bursal, E., Kumar, V., Nongdam, P., Shekhawat, M., Batiha, G., Ghosh, A., Dwivedi, P., Kumar, M., & Dey, A. (2022). CRISPR/Cas Genome Editing in Engineering Plant Secondary Metabolites of Therapeutic Benefits (pp. 187–208). https://doi.org/10.1007/978-981-16-7262-0_8
Dou, Z., Tang, S., Li, G., Liu, Z. H., Ding, C., Chen, L., Wang, S., & Ding, Y. (2017). Application of Nitrogen Fertilizer at Heading Stage Improves Rice Quality under Elevated Temperature during Grain-Filling Stage. Crop Science, 57. https://doi.org/10.2135/cropsci2016.05.0350
Hambali, A., & Lubis, I. (2017). Evaluasi Produktivitas Beberapa Varietas Padi. Buletin Agrohorti, 3, 137. https://doi.org/10.29244/agrob.3.2.137-145
Huang, L., Zhang, R., Huang, G., Li, Y., Melaku, G., Zhang, S., Chen, H., Zhao, Y., Zhang, J., Zhang, Y., & Hu, F. (2018). Developing superior alleles of yield genes in rice by artificial mutagenesis using the CRISPR/Cas9 system. The Crop Journal, 6(5), 475–481. https://doi.org/10.1016/j.cj.2018.05.005
Jung, Y., Lee, H., Bae, S., Kim, J., Kim, D., Kim, H., Nam, K., Nogoy, F. M., Cho, Y.-G., & Kang, K. (2019). Acquisition of seed dormancy breaking in rice (Oryza sativa L.) via CRISPR/Cas9-targeted mutagenesis of OsVP1 gene. Plant Biotechnology Reports, 13. https://doi.org/10.1007/s11816-019-00580-x
Kurakawa, T., Ueda, N., Maekawa, M., Kobayashi, K., Kojima, M., Nagato, Y., Sakakibara, H., & Kyozuka, J. (2007). Direct control of shoot meristem activity by a cytokinin-activating enzyme. Nature, 445(7128), 652–655. https://doi.org/10.1038/nature05504
Lan, D., Cao, L., Liu, M., Ma, F., Yan, P., Zhang, X., Hu, J., Niu, F., He, S., Cui, J., Yuan, X., Yang, J., Wang, Y., & Luo, X. (2023). The identification and characterization of a plant height and grain length related gene hfr131 in rice. Frontiers in Plant Science, 14, 1152196. https://doi.org/10.3389/fpls.2023.1152196
Li, M., Zhou, J., Gong, L., Zhang, R., Wang, Y., Wang, C., Du, X., Luo, Y., Zhang, Y., Wang, X., & Tang, H. (2022). Identification and Expression Analysis of CKX Gene Family in Brassica juncea var. Tumida and Their Functional Analysis in Stem Development. Horticulturae, 8(8), Article 8. https://doi.org/10.3390/horticulturae8080705
Liao, Z., Yu, H., Duan, J., Yuan, K., Yu, C., Meng, X., Kou, L., Chen, M., Jing, Y., Liu, G., Smith, S. M., & Li, J. (2019). SLR1 inhibits MOC1 degradation to coordinate tiller number and plant height in rice. Nature Communications, 10(1), 2738. https://doi.org/10.1038/s41467-019-10667-2
Manghwar, H., Lindsey, K., Zhang, X., & Jin, S. (2019). CRISPR/Cas System: Recent Advances and Future Prospects for Genome Editing. Trends in Plant Science, 24(12), 1102–1125. https://doi.org/10.1016/j.tplants.2019.09.006
Martignago, D., Siemiatkowska, B., Lombardi, A., & Conti, L. (2020). Abscisic Acid and Flowering Regulation: Many Targets, Different Places. International Journal of Molecular Sciences, 21(24), 9700. https://doi.org/10.3390/ijms21249700
Miki, D., Zhang, W., Zeng, W., Feng, Z., & Zhu, J.-K. (2018). CRISPR/Cas9-mediated gene targeting in Arabidopsis using sequential transformation. Nature Communications, 9(1), 1967. https://doi.org/10.1038/s41467-018-04416-0
Murai, M., Komazaki, T., & Sato, S. (2004). Effects of sd1 and Ur1 (Undulate rachis -1) on Lodging Resistance and Related Traits in Rice. Breeding Science, 54(4), 333–340. https://doi.org/10.1270/jsbbs.54.333
Nawaz, G., Usman, B., Zhao, N., Han, Y., Li, Z., Wang, X., Liu, Y., & Li, R. (2020). CRISPR/Cas9 Directed Mutagenesis of OsGA20ox2 in High Yielding Basmati Rice (Oryza sativa L.) Line and Comparative Proteome Profiling of Unveiled Changes Triggered by Mutations. International Journal of Molecular Sciences, 21(17), Article 17. https://doi.org/10.3390/ijms21176170
Nurhayati, N., Ardie, S. W., Santoso, T. J., & Sudarsono, S. (2021). CRISPR/Cas9-mediated genome editing in rice cv. IPB3S results in a semi-dwarf phenotypic mutant. Biodiversitas Journal of Biological Diversity, 22(9), Article 9. https://doi.org/10.13057/biodiv/d220924
Rong, C., Liu, Y., Chang, Z., Liu, Z., Ding, Y., & Ding, C. (2022). Cytokinin oxidase/dehydrogenase family genes exhibit functional divergence and overlap in rice growth and development, especially in control of tillering. Journal of Experimental Botany, 73(11), 3552–3568. https://doi.org/10.1093/jxb/erac088
Ruzyati, M. (2022). Introduksi Konstruk CRISPR/CAS9 dalam Pengeditan Gen OSGA20ox2 dan OSCKX2 pada Padi Mentik Wangi untuk Memperbaiki Karakter Tinggi Tanaman dan Meningkatkan Hasil Panen [Thesis, UNS (Sebelas Maret University)]. https://digilib.uns.ac.id/dokumen/88942/Introduksi-Konstruk-CRISPRCAS9-dalam-Pengeditan-Gen-OSGA20ox2-dan-OSCKX2-pada-Padi-Mentik-Wangi-untuk-Memperbaiki-Karakter-Tinggi-Tanaman-dan-Meningkatkan-Hasil-Panen
Ruzyati, M., Sisharmini, A., Apriana, A., Santoso, T. J., Purwanto, E., Samanhudi, S., & Yunus, A. (2022). Construction of CRISPR/Cas9_gRNA-OsCKX2 module cassette and its introduction into rice cv. Mentik Wangi mediated by Agrobacterium tumefaciens. Biodiversitas Journal of Biological Diversity, 23(5), Article 5. https://doi.org/10.13057/biodiv/d230552
Santoso, T. J., Trijatmiko, K. R., Char, S. N., Yang, B., & Wang, K. (2020). Targeted mutation of GA20ox-2 gene using CRISPR/Cas9 system generated semi-dwarf phenotype in rice. IOP Conference Series: Earth and Environmental Science, 482(1), 012027. https://doi.org/10.1088/1755-1315/482/1/012027
Sasaki, A., Ashikari, M., Ueguchi-Tanaka, M., Itoh, H., Nishimura, A., Swapan, D., Ishiyama, K., Saito, T., Kobayashi, M., Khush, G. S., Kitano, H., & Matsuoka, M. (2002). A mutant gibberellin-synthesis gene in rice. Nature, 416(6882), Article 6882. https://doi.org/10.1038/416701a
Singh, V., Agrawal, K., Kumhar, B. L., & Patel, R. (2020). LODGING: EFFECT ON CROP PRODUCTION AND ITS MANAGEMENT. Krishi Sci, 01(02), 3.
Sitaresmi, T., Willy, S., Rumanti, I., Ardie, S., & Aswidinnoor, H. (2019). Parameters and Secondary Characters for Selection of Tolerance Rice Varieties under Stagnant Flooding Condition. AGRIVITA Journal of Agricultural Science, 41. https://doi.org/10.17503/agrivita.v41i2.957
Sitoe, H. M., Zhang, Y., Chen, S., Li, Y., Ali, M., Sowadan, O., Karikari, B., Liu, E., Dang, X., Qian, H., & Hong, D. (2022). Detection of QTLs for Plant Height Architecture Traits in Rice (Oryza sativa L.) by Association Mapping and the RSTEP-LRT Method. Plants, 11(7), 999. https://doi.org/10.3390/plants11070999
Spielmeyer, W., Ellis, M. H., & Chandler, P. M. (2002). Semidwarf (sd-1), “green revolution” rice, contains a defective gibberellin 20-oxidase gene. Proceedings of the National Academy of Sciences, 99(13), 9043–9048. https://doi.org/10.1073/pnas.132266399
Sudrajat, I. S. (2020). Analysis Study of Mentik Wangi Cultivar’s Effect on Technical, Allocative, and Economic Efficiency of Organic Rice Farming in Mojosongo District, Boyolali Regency, Indonesia. Canadian Journal of Agriculture and Crops, 5(2), Article 2. https://doi.org/10.20448/803.5.2.108.123
Tanaka, W., Yamauchi, T., & Tsuda, K. (2023). Genetic basis controlling rice plant architecture and its modification for breeding. Breeding Science, 73(1), 3–45. https://doi.org/10.1270/jsbbs.22088
Tsai, Y.-C., Weir, N. R., Hill, K., Zhang, W., Kim, H. J., Shiu, S.-H., Schaller, G. E., & Kieber, J. J. (2012). Characterization of genes involved in cytokinin signaling and metabolism from rice. Plant Physiology, 158(4), 1666–1684. https://doi.org/10.1104/pp.111.192765
Tsuji, H. (2017). Molecular function of florigen. Breeding Science, 67(4), 327–332. https://doi.org/10.1270/jsbbs.17026
Vankova, R. (2014). Cytokinin Regulation of Plant Growth and Stress Responses. In L.-S. P. Tran & S. Pal (Eds.), Phytohormones: A Window to Metabolism, Signaling and Biotechnological Applications (pp. 55–79). Springer. https://doi.org/10.1007/978-1-4939-0491-4_3
Wang, Q., Gao, H., Liu, K., Wang, H., Zhang, F., Wei, L., Lu, K., Li, M., Shi, Y., Zhao, J., Zhou, W., Peng, B., & Yuan, H. (2024). CRISPR/Cas9-mediated enhancement of semi-dwarf glutinous traits in elite Xiangdaowan rice (Oryza sativa L.): Targeting SD1 and Wx genes for yield and quality improvement. Frontiers in Plant Science, 15. https://doi.org/10.3389/fpls.2024.1333191
Yamaguchi, S. (2008). Gibberellin Metabolism and its Regulation. Annual Review of Plant Biology, 59(1), 225–251. https://doi.org/10.1146/annurev.arplant.59.032607.092804
Yeh, S.-Y., Chen, H.-W., Ng, C.-Y., Lin, C.-Y., Tseng, T.-H., Li, W.-H., & Ku, M. S. B. (2015). Down-Regulation of Cytokinin Oxidase 2 Expression Increases Tiller Number and Improves Rice Yield. Rice, 8(1), Article 1. https://doi.org/10.1186/s12284-015-0070-5
Yunus, A., Mulyawati, R., & Parjanto, P. (2021). Yield of the Mutant (M6) Short Stem of Mentik Wangi Rice Varieties Resulting from Gamma Ray Irradiation 300 Gray. Journal of Biodiversity and Biotechnology, 1(2), Article 2. https://doi.org/10.20961/jbb.v1i2.56437
Zegeye, W. A., Chen, D., Islam, M., Wang, H., Riaz, A., Rani, M. H., Hussain, K., Liu, Q., Zhan, X., Cheng, S., Cao, L., & Zhang, Y. (2022). OsFBK4, a novel GA insensitive gene positively regulates plant height in rice (Oryza Sativa L.). Ecological Genetics and Genomics, 23, 100115. https://doi.org/10.1016/j.egg.2022.100115
Zhan, C., Hu, J., Pang, Q., Yang, B., Cheng, Y., Xu, E., Zhu, P., Li, Y., Zhang, H., & Cheng, J. (2019). Genome-wide association analysis of panicle exsertion and uppermost internode in rice (Oryza sativa L.). Rice, 12(1), 72. https://doi.org/10.1186/s12284-019-0330-x
Zhang, N., Roberts, H. M., Van Eck, J., & Martin, G. B. (2020). Generation and Molecular Characterization of CRISPR/Cas9-Induced Mutations in 63 Immunity-Associated Genes in Tomato Reveals Specificity and a Range of Gene Modifications. Frontiers in Plant Science, 11. https://doi.org/doi: 10.3389/fpls.2020.00010
Zhang, W., Peng, K., Cui, F., Wang, D., Zhao, J., Zhang, Y., Yu, N., Wang, Y., Zeng, D., Wang, Y., Cheng, Z., & Zhang, K. (2021). Cytokinin oxidase/dehydrogenase OsCKX11 coordinates source and sink relationship in rice by simultaneous regulation of leaf senescence and grain number. Plant Biotechnology Journal, 19(2), 335–350. https://doi.org/10.1111/pbi.13467
Zheng, X., Zhang, S., Liang, Y., Zhang, R., Liu, L., Qin, P., Zhang, Z., Wang, Y., Zhou, J., Tang, X., & Zhang, Y. (2023). Loss-function mutants of OsCKX gene family based on CRISPR-Cas systems revealed their diversified roles in rice. The Plant Genome, 16(2), e20283. https://doi.org/10.1002/tpg2.20283
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