Abstract
The OsSPL16 (SQUAMOSA promoter-binding protein like 16) or GW8 (Grain Width 8) gene is expressed specifically in developing seeds and positively controls grain width and weight by modulating cell proliferation and enlargement in the spikelet hull of rice. OsSPL16 acts as the direct upstream suppressor of GW7 (Grain Width 7), a gene responsible for grain slenderness. The down-regulation of the OsSPL16 gene will effectively disrupt its interaction with the GW7 gene, leading to the development of slender rice grains. In our investigation, we introduced grain slenderness to a bold grain-type rice cultivar, ASD16, by employing the CRISPR/Cas9 system to knock-out the function of the OsSPL16 gene. Molecular analysis of spl16 mutants unveiled the existence of mutations within the first exon of OsSPL16, which included in-frame and frame-shift mutations. Our results demonstrated that inducing frame-shift mutations in the coding sequence of the OsSPL16 gene could effectively impart grain slenderness in bold grain varieties.
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References
Arulganesh, T., Kumam, Y., Kumar, K. K., Arul, L., Kokiladevi, E., Nakeeran, S., Varanavasiappan, S., Manonmani, S., & Sudhakar, D. (2021). Genome editing of elite rice cultivar CO51 for bacterial leaf blight resistance. Electronic Journal of Plant Breeding, 12(4), 1060–1068. https://doi.org/10.37992/2021.1204.147
Aslam, K., Naveed, S. A., Sabar, M., Shabir, G., Shah, S. M., Khan, A. R., Shah, M. M., Fiaz, S., Xu, J., & Arif, M. (2022). Identification of QTLs for rice grain size and weight by high-throughput SNP markers in the IR64 x Sadri population. Frontiers in Genetics. https://doi.org/10.3389/fgene.2022.955347
Calingacion, M., Laborte, A., Nelson, A., Resurreccion, A., Concepcion, J. C., Daygon, V. D., Mumm, R., Reinke, R., Dipti, S., Bassinello, P. Z., et al. (2014). Diversity of global rice markets and the science required for consumer-targeted rice breeding. PLoS ONE, 9(1), e85106. https://doi.org/10.1371/journal.pone.0085106
Custodio, M. C., Cuevas, R. P., Ynion, J., Laborte, A. G., Velasco, M. L., & Demont, M. (2019). Rice quality: How is it defined by consumers, industry, food scientists, and geneticists? Trends in Food Science & Technology, 92, 122–137. https://doi.org/10.1016/j.tifs.2019.07.039
Dehairs, J., Talebi, A., Cherifi, Y., & Swinnen, J. V. (2016). CRISP-ID: Decoding CRISPR mediated indels by Sanger sequencing. Scientific Reports, 6(1), 28973. https://doi.org/10.1038/srep28973
Diana, P. A., Shanthinie, A., Arulganesh, T., Kumam, Y., Kumar, K. K., Arul, L., Kokiladevi, E., Varanavasiappan, S., Manonmani, S., & Sudhakar, D. (2022). Targeted editing of OsSWEET13, a bacterial leaf blight susceptible gene in rice using CRISPR tool. Electronic Journal of Plant Breeding, 13(3), 772–779. https://doi.org/10.37992/2022.1303.139
Hiei, Y., & Komari, T. (2008). Agrobacterium-mediated transformation of rice using immature embryos or calli induced from mature seed. Nature Protocols, 3(5), 824–834. https://doi.org/10.1038/nprot.2008.46
Hu, J., Huang, L., Chen, G., Liu, H., Zhang, Y., Zhang, R., Zhang, S., Liu, J., Hu, Q., Hu, F., Wang, W., & Ding, Y. (2021). The elite alleles of OsSPL4 regulate grain size and increase grain yield in rice. Rice, 14, 1–18. https://doi.org/10.1186/s12284-021-00531-7
Ishizaki, T., Ueda, Y., Takai, T., Maruyama, K., & Tsujimoto, Y. (2023). In-frame mutation in rice TEOSINTE BRANCHED1 (OsTB1) improves productivity under phosphorus deficiency. Plant Science, 330, 111627. https://doi.org/10.1016/j.plantsci.2023.111627
Lee, Y. K., Kim, G. T., Kim, I. J., Park, J., Kwak, S. S., Choi, G., & Chung, W. I. (2006). LONGIFOLIA1 and LONGIFOLIA2, two homologous genes, regulate longitudinal cell elongation in Arabidopsis. https://doi.org/10.1242/dev.02604.
Li, N., & Li, Y. (2016). Signaling pathways of seed size control in plants. Current Opinion in Plant Biology, 33, 23–32. https://doi.org/10.1016/j.pbi.2016.05.008
Li, N., Xu, R., & Li, Y. (2019). Molecular networks of seed size control in plants. Annual Review of Plant Biology, 70, 435–463. https://doi.org/10.1146/annurev-arplant-050718-095851
Liu, H., Ding, Y., Zhou, Y., Jin, W., Xie, K., & Chen, L. L. (2017). CRISPR-P 2.0: an improved CRISPR-cas9 tool for genome editing in plants. Molecular Plant, 10(3), 530–532. https://doi.org/10.1016/j.molp.2017.01.003
Liu, W., Xie, X., Ma, X., Li, J., Chen, J., & Liu, Y. G. (2015). DSDecode: A web-based tool for decoding of sequencing chromatograms for genotyping of targeted mutations. Molecular Plant, 8(9), 1431–1433. https://doi.org/10.1016/j.molp.2015.05.009
Lu, Y., Chuan, M., Wang, H., Chen, R., Tao, T., Zhou, Y., Xu, Y., Li, P., Yao, Y., Xu, C., & Yang, Z. (2022). Genetic and molecular factors in determining grain number per panicle of rice. Frontiers in Plant Science, 13, 964246. https://doi.org/10.3389/fpls.2022.964246
Saravanan, S., Latha, R., & Arumugam Pillai, M. (2020). Studies on relative impact of rice varieties ASD 16 and TPS 5 on farmer’s adoption. International Journal of Current Microbiology and Applied Sciences, 9, 1509–1513. https://doi.org/10.20546/ijcmas.2020.909.191
Schindele, P., Wolter, F., & Puchta, H. (2020). CRISPR guide RNA design guidelines for efficient genome editing. RNA Tagging: Methods and Protocols. https://doi.org/10.1007/978-1-0716-0712-1_19
Si, L., Chen, J., Huang, X., Gong, H., Luo, J., Hou, Q., Zhou, T., Lu, T., Zhu, J., Shangguan, Y., Chen, E., Gong, C., Zhao, Q., Jing, Y., Zhao, Y., Li, Y., Cui, L., Fan, D., Lu, Y., … Han, B. (2016). OsSPL13 controls grain size in cultivated rice. Nature Genetics, 48(4), 447–456. https://doi.org/10.1038/ng.3518
Siddiq, E. A., Vemireddy, L. R., & Nagaraju, J. (2012). Basmati rices: Genetics, breeding and trade. Agricultural Research, 1, 25–36. https://doi.org/10.1007/s40003-011-0011-5
Sultana, S., Faruque, M., & Islam, M. R. (2022). Rice grain quality parameters and determination tools: A review on the current developments and future prospects. International Journal of Food Properties, 25(1), 1063–1078. https://doi.org/10.1080/10942912.2022.2071295
Tang, L., Mao, B., Li, Y., Lv, Q., Zhang, L., Chen, C., He, H., Wang, W., Zeng, X., Shao, Y., Pan, Y., Hu, Y., Peng, Y., Fu, X., Li, H., Xia, S., & Zhao, B. (2017). Knockout of OsNramp5 using the CRISPR/Cas9 system produces low Cd-accumulating indica rice without compromising yield. Scientific Reports, 7(1), 14438. https://doi.org/10.1038/s41598-017-14832-9
Wang, J., Wu, B., Lu, K., Wei, Q., Qian, J., Chen, Y., & Fang, Z. (2019). The amino acid permease 5 (OsAAP5) regulates tiller number and grain yield in rice. Plant Physiology, 180(2), 1031–1045. https://doi.org/10.1104/pp.19.00034
Wang, S., Li, S., Liu, Q., Wu, K., Zhang, J., Wang, S., Wang, Y., Chen, X., Zhang, Y., Gao, C., Wang, F., Huang, H., & Fu, X. (2015). The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality. Nature Genetics, 47(8), 949–954. https://doi.org/10.1038/ng.3352
Wang, S., Wu, K., Yuan, Q., Liu, X., Liu, Z., Lin, X., Zeng, R., Zhu, H., Dong, G., Qian, Q., Zhang, G., & Fu, X. (2012). Control of grain size, shape and quality by OsSPL16 in rice. Nature Genetics, 44(8), 950–954. https://doi.org/10.1038/ng.2327
Xie, K., Minkenberg, B., & Yang, Y. (2015). Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system. Proceedings of the National Academy of Sciences, 112(11), 3570–3575. https://doi.org/10.1073/pnas.1420294112
Xie, X., Ma, X., Zhu, Q., Zeng, D., Li, G., & Liu, Y. G. (2017). CRISPR-GE: A convenient software toolkit for CRISPR-based genome editing. Molecular Plant, 10(9), 1246–1249. https://doi.org/10.1016/j.molp.2017.06.004
Xu, H., Zhao, M., Zhang, Q., Xu, Z., & Xu, Q. (2016). The DENSE ERECT PANICLE 1 (DEP1) gene offering the potential in the breeding of high-yielding rice. Breeding Science, 66(5), 659–667. https://doi.org/10.1270/jsbbs.16120
Yuan, H., Qin, P., Hu, L., Zhan, S., Wang, S., Gao, P., Li, J., Jin, M., Xu, Z., Gao, Q., Du, A., Tu, B., Chen, W., Ma, B., Wang, Y., & Li, S. (2019). OsSPL18 controls grain weight and grain number in rice. Journal of Genetics and Genomics, 46(1), 41–51. https://doi.org/10.1016/j.jgg.2019.01.003
Yuyu, C., Aike, Z., Pao, X., Xiaoxia, W., Yongrun, C., Beifang, W., Yue, Z., Liaqat, S., Shihua, C., Liyong, C., & Yingxin, Z. (2020). Effects of GS3 and GL3 1 for grain size editing by CRISPR/Cas9 in rice. Rice Science, 27(5), 405–413. https://doi.org/10.1016/j.rsci.2019.12.010
Zhang, H., Zhang, J., Wei, P., Zhang, B., Gou, F., Feng, Z., Mao, Y., Yang, L., Zhang, H., Xu, N., & Zhu, J. K. (2014). The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation. Plant Biotechnology Journal, 12(6), 797–807. https://doi.org/10.1111/pbi.12200
Zhang, X. F., Yang, C. Y., Lin, H. X., Wang, J. W., & Xue, H. W. (2021). Rice SPL12 coevolved with GW5 to determine grain shape. Science Bulletin, 66, 2353–2357. https://doi.org/10.1016/j.scib.2021.05.005
Zhao, D., Zhang, C., Li, Q., & Liu, Q. (2022). Genetic control of grain appearance quality in rice. Biotechnology Advances. https://doi.org/10.1016/j.biotechadv.2022.108014
Acknowledgements
The authors thank the Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, for providing facilities. The authors also thank the Department of Rice for facilitating the conduct of agronomic evaluation.
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The authors acknowledge the receipt of funds for conducting this study through the scheme “Establishment of DBT-BUILDER-TNAU interdisciplinary life science platform for advanced research and education” (No. BT/INF/22/SP45584/2022) of the Department of Biotechnology, Government of India.
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Shanthinie, A., Vignesh, P., Kumar, K.K. et al. Enhancing rice grain quality through the knock-out of the OsSPL16 gene. Plant Physiol. Rep. (2024). https://doi.org/10.1007/s40502-024-00790-8
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DOI: https://doi.org/10.1007/s40502-024-00790-8