Natural variation in MORE GRAINS 1 regulates grain number and grain weight in rice

Abstract

Grain yield is determined mainly by grain number and grain weight. In this study, we identified and characterized MORE GRAINS1 (MOG1), a gene associated with grain number and grain weight in rice (Oryza sativa L.), through map-based cloning. Overexpression of MOG1 increased grain yield by 18.6%–22.3% under field conditions. We determined that MOG1, a bHLH transcription factor, interacts with OsbHLH107 and directly activates the expression of LONELY GUY (LOG), which encodes a cytokinin-activating enzyme and the cell expansion gene EXPANSIN-LIKE1 (EXPLA1), positively regulating grain number per panicle and grain weight. Natural variations in the promoter and coding regions of MOG1 between Hap-LNW and Hap-HNW alleles resulted in changes in MOG1 expression level and transcriptional activation, leading to functional differences. Haplotype analysis revealed that Hap-HNW, which results in a greater number and heavier grains, has undergone strong selection but has been poorly utilized in modern lowland rice breeding. In summary, the MOG1–OsbHLH107 complex activates LOG and EXPLA1 expression to promote cell expansion and division of young panicles through the cytokinin pathway, thereby increasing grain number and grain weight. These findings suggest that Hap-HNW could be used in strategies to breed high-yielding temperate japonica lowland rice.

Keywords

grain number / grain weight / MOG1 / natural variation / rice

References

[1] Ashikari, M.,Sakakibara, H.,Lin, S.,Yamamoto, T.,Takashi, T.,Nishimura, A.,Angeles, E.,Qian, Q.,Kitano, H., and Matsuoka, M. (2005). Cytokinin oxidase regulates rice grain production. Science309:741–745.

[2] Chen, T.K.,Luo, L.X.,Zhao, Z.,Wang, H.,Chen, C.,Liu, Y.Z.,Li, X.C.,Guo, T., and Xiao, W.M. (2023). Fine mapping and candidate gene analysis of qGL10 affecting rice grain length. Crop J.11:540–548.

[3] Choi, B.S.,Kim, Y.J.,Markkandan, K.,Koo, Y.J.,Song, J.T., and Seo, H.S. (2018). GW2 functions as an E3 ubiquitin ligase for rice Expansin-Like 1. Int. J. Mol. Sci. 19:1904.

[4] Dong, N.Q.,Sun, Y.,Guo, T.,Shi, C.L.,Zhang, Y.M.,Kan, Y.,Xiang, Y.H.,Zhang, H.,Yang, Y.B.,Li, Y.C., et al. (2020). UDP-glucosyltransferase regulates grain size and abiotic stress tolerance associated with metabolic flux redirection in rice. Nat. Commun.11:2629.

[5] Excoffier, L., and Lischer, H. (2010). Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour.10:564–567.

[6] Fan, C.,Xing, Y.,Mao, H.,Lu, T.,Han, B.,Xu, C.,Li, X., and Zhang, Q. (2006). GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor. Appl. Genet.112:1164–1171.

[7] Fang, N.,Xu, R.,Huang, L.J.,Zhang, B.L.,Duan, P.,Li, N.,Luo, Y.H., and Li, Y.H. (2016). SMALL GRAIN 11 controls grain size, grain number and grain yield in rice. Rice9:64.

[8] Gao, X.Y.,Zhang, J.Q.,Zhang, X.J.,Zhou, J.,Jiang, Z.S.,Huang, P.,Tang, Z.B.,Bao, Y.M.,Cheng, J.P.,Tang, H.J., et al. (2019). Rice qGL3/OsPPKL1 functions with the GSK3/SHAGGY-Like kinase OsGSK3 to modulate Brassinosteroid signaling. Plant Cell31:1077–1093.

[9] Guo, T.,Chen, K.,Dong, N.Q.,Ye, W.W.,Shan, J.X., and Lin, H.X. (2020a). Tillering and small grain 1 dominates the tryptophan aminotransferase family required for local auxin biosynthesis in rice. J. Integr. Plant Biol62:581–600.

[10] Guo, T.,Lu, Z.Q.,Shan, J.X.,Ye, W.W.,Dong, N.Q., and Lin, H.X. (2020b). ERECTA1 acts upstream of the OsMKKK10-OsMKK4-OsMPK6 cascade to control spikelet number by regulating cytokinin metabolism in rice. Plant Cell32:2763–2779.

[11] Heang, D., and Sassa, H. (2012a). Antagonistic actions of HLH/bHLH proteins are involved in grain length and weight in rice. PLoS One7: e31325.

[12] Heang, D., and Sassa, H. (2012b). An atypical bHLH protein encoded by POSITIVE REGULATOR OF GRAIN LENGTH 2 is involved in controlling grain length and weight of rice through interaction with a typical bHLH protein APG. Breed. Sci.62:133–141.

[13] Hori, K., and Sun, J. (2022). Rice grain size and quality. Rice15:33.

[14] Hu, J.,Wang, Y.X.,Fang, Y.X.,Zeng, L.J.,Xu, J.,Yu, H.P.,Shi, Z.Y.,Pan, J.J.,Zhang, D.,Kang, S.J., et al. (2015). A rare allele of GS2 enhances grain size and grain yield in rice. Mol. Plant8:1455–1465.

[15] Huang, J.,Chen, Z.,Lin, J.,Chen, J.,Wei, M.,Liu, L.,Yu, F.,Zhang, Z.,Chen, F.,Jiang, L., et al. (2022a). Natural variation of the BRD2 allele affects plant height and grain size in rice. Planta256:27.

[16] Huang, Y.S.,Dong, H.,Mou, C.L.,Wang, P.,Hao, Q.X.,Zhang, M.,Wu, H.M.,Zhang, F.L.,Ma, T.F.,Miao, R., et al. (2022b). Ribonuclease H-like gene Small Grain2 regulates grain size in rice through brassinosteroids signal pathway. J. Integr. Plant Biol.64:1883–1900.

[17] Ishimaru, K.,Hirotsu, N.,Madoka, Y.,Murakami, N.,Hara, N.,Onodera, H.,Kashiwagi, T.,Ujiie, K.,Shimizu, B.,Onishi, A., et al. (2013). Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield. Nat. Genet.45:707–711.

[18] Ji, X.,Du, Y.X.,Li, F.,Sun, H.Z.,Zhang, J.,Li, J.Z.,Peng, T.,Xin, Z.Y., and Zhao, Q.Z. (2019). The basic helix-loop-helix transcription factor, OsPIL15, regulates grain size via directly targeting a purine permease gene OsPUP7 in rice. Plant Biotechnol. J.17:1527–1537.

[19] Jin, J.,Hua, L.,Zhu, Z.F.,Tan, L.B.,Zhao, X.H.,Zhang, W.F.,Liu, F.X.,Fu, Y.C.,Cai, H.W.,Sun, X.Y., et al. (2016). GAD1 encodes a secreted peptide that regulates grain number, grain length, and awn development in rice domestication. Plant Cell28:2453–2463.

[20] Li, G.L.,Xu, B.X.,Zhang, Y.P.,Xu, Y.W.,Khan, N.U.,Xie, J.Y.,Sun, X.M.,Guo, H.F.,Wu, Z.Y.,Wang, X.Q., et al. (2022). RGN1 controls grain number and shapes panicle architecture in rice. Plant Biotechnol. J.20:158–167.

[21] Li, J.Z.,Han, Y.C.,Liu, L.,Chen, Y.P.,Du, Y.X.,Zhang, J.,Sun, H.Z., and Zhao, Q.Z. (2015). qRT9, a quantitative trait locus controlling root thickness and root length in upland rice. J. Exp. Bot.66:2723–2732.

[22] Li, N.,Xu, R., and Li, Y.H. (2019). Molecular networks of seed size control in plants. Annu. Rev. Plant Biol.70:435–463.

[23] Li, X.X.,Duan, X.P.,Jiang, H.X.,Sun, Y.J.,Tang, Y.P.,Yuan, Z.,Guo, J.K.,Liang, W.Q.,Chen, L.,Yin, J.Y., et al. (2006). Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis. Plant Physiol.141:1167–1184.

[24] Li, Y.B.,Fan, C.C.,Xing, Y.Z.,Jiang, Y.H.,Luo, L.J.,Sun, L.,Shao, D.,Xu, C.J.,Li, X.H.,Xiao, J.H., et al. (2011). Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nat. Genet.43:1266–1269.

[25] Li, Y.J.,Wu, S.,Huang, Y.Y.,Ma, X.,Tan, L.B.,Liu, F.X.,Lv, Q.M.,Zhu, Z.F.,Hu, M.X.,Fu, Y.C., et al. (2023). OsMADS17 simultaneously increases grain number and grain weight in rice. Nat. Commun.14:3098.

[26] Librado, P., and Rozas, J. (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics25:1451–1452.

[27] Lin, S.J.,Liu, Z.P.,Zhang, K.,Yang, W.F.,Zhan, P.L.,Tan, Q.Y.,Gou, Y.J.,Ma, S.P.,Luan, X.,Huang, C.B., et al. (2023). GL9 from Oryza glumaepatula controls grain size and chalkiness in rice. Crop J.11:198–207.

[28] Liu, C.,Ma, T.,Yuan, D.Y.,Zhou, Y.,Long, Y.,Li, Z.W.,Dong, Z.Y.,Duan, M.J.,Yu, D.,Jing, Y.Z., et al. (2022a). The OsEIL1-OsERF115-target gene regulatory module controls grain size and weight in rice. Plant Biotechnol. J.20:1470–1486.

[29] Liu, D.P.,Zhao, H.,Xiao, Y.H.,Zhang, G.X.,Cao, S.Y.,Yin, W.C.,Qian, Y.W.,Yin, Y.H.,Zhang, J.S.,Chen, S.Y., et al. (2022b). A cryptic inhibitor of cytokinin phosphorelay controls rice grain size. Mol. Plant15:293–307.

[30] Liu, L.C.,Tong, H.N.,Xiao, Y.H.,Che, R.H.,Xu, F.,Hu, B.,Liang, C.Z.,Chu, J.F.,Li, J.Y., and Chu, C.C. (2015). Activation of Big Grain 1 significantly improves grain size by regulating auxin transport in rice. Proc. Natl. Acad. Sci. U. S. A.112:11102–11107.

[31] Liu, Q.,Han, R.X.,Wu, K.,Zhang, J.Q.,Ye, Y.F.,Wang, S.S.,Chen, J.F.,Pan, Y.J.,Li, Q.,Xu, X.P., et al. (2018). G-protein βγ subunits determine grain size through interaction with MADS-domain transcription factors in rice. Nat. Commun.9:852.

[32] Livak, K., and Schmittgen, T. (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2^-ΔΔCt method. Methods25:402–408.

[33] Lo, S.F.,Cheng, M.L.,Hsing, Y.C.,Chen, Y.S.,Lee, K.W.,Hong, Y.F.,Hsiao, Y.,Hsiao, A.S.,Chen, P.J.,Wong, L.I., et al. (2020). Rice Big Grain 1 promotes cell division to enhance organ development, stress tolerance and grain yield. Plant Biotechnol. J.18:1969–1983.

[34] Lu, Y.,Chuan, M.L.,Wang, H.Y.,Chen, R.J.,Tao, T.Y.,Zhou, Y.,Xu, Y.,Li, P.C.,Yao, Y.L.,Xu, C.W., et al. (2022). Genetic and molecular factors in determining grain number per panicle of rice. Front. Plant Sci.13:964246.

[35] Ma, Q.B.,Dai, X.Y.,Xu, Y.Y.,Guo, J.,Liu, Y.J.,Chen, N.,Xiao, J.,Zhang, D.J.,Xu, Z.H.,Zhang, X.S., et al. (2009). Enhanced tolerance to chilling stress in OsMYB3R-2 transgenic rice is mediated by alteration in cell cycle and ectopic expression of stress genes. Plant Physiol.150:244–256.

[36] Mao, H.,Sun, S.,Yao, J.,Wang, C.,Yu, S.,Xu, C.,Li, X., and Zhang, Q.F. (2010). Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc. Natl. Acad. Sci. U. S. A.107:19579–19584.

[37] Miao, J.,Yang, Z.F.,Zhang, D.P.,Wang, Y.Z.,Xu, M.B.,Zhou, L.H.,Wang, J.,Wu, S.J.,Yao, Y.L.,Du, X., et al. (2019). Mutation of RGG2, which encodes a type B heterotrimeric G protein γ subunit, increases grain size and yield production in rice. Plant Biotechnol. J.17:650–664.

[38] Qi, P.,Lin, Y.-S.,Song, X.-J.,Shen, J.-B.,Huang, W.,Shan, J.-X.,Zhu, M.-Z.,Jiang, L.,Gao, J.-P., and Lin, H.-X. (2012). The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1;3. Cell Res.22:1666–1680.

[39] Ren, D.Y.,Ding, C.Q., and Qian, Q. (2023). Molecular bases of rice grain size and quality for optimized productivity. Sci. Bull.68:314–350.

[40] Ruan, B.P.,Shang, L.G.,Zhang, B.,Liu, C.L.,Zeng, D.L.,Peng, Y.L.,Guo, L.B.,Zhu, L.,Ren, D.Y.,Hu, J., et al. (2020). Natural variation in the promoter of TGW2 determines grain width and weight in rice. New Phytol.227:629–640.

[41] Sakamoto, T., and Matsuoka, M. (2008). Identifying and exploiting grain yield genes in rice. Curr. Opin. Plant Biol.11:209–214.

[42] Shi, C.L.,Ren, Y.L.,Liu, L.L.,Wang, F.,Zhang, H.,Tian, P.,Pan, T.,Wang, Y.F.,Jing, R.N.,Liu, T.Z., et al. (2019). Ubiquitin specific protease 15 has an important role in regulating grain width and size in rice. Plant Physiol.180:381–391.

[43] Tang, Z.B.,Gao, X.Y.,Zhan, X.Y.,Fang, N.Y.,Wang, R.Q.,Zhan, C.F.,Zhang, J.Q.,Cai, G.,Cheng, J.P.,Bao, Y.M., et al. (2021). Natural variation in OsGASR7 regulates grain length in rice. Plant Biotechnol. J.19:14–16.

[44] Teacher, A., and Griffiths, D. (2011). HapStar: Automated haplotype network layout and visualization. Mol. Ecol. Resour.11:151–153.

[45] Toki, S.,Hara, N.,Ono, K.,Onodera, H.,Tagiri, A.,Oka, S., and Tanaka, H. (2006). Early infection of scutellum tissue with Agrobacterium allows high-speed transformation of rice. Plant J.47:969–976.

[46] Wang, A.H.,Hou, Q.Q.,Si, L.Z.,Huang, X.H.,Luo, J.H.,Lu, D.F.,Zhu, J.J.,Shangguan, Y.Y.,Miao, J.S.,Xie, Y.F., et al. (2019). The PLATZ transcription factor GL6 affects grain length and number in rice. Plant Physiol.180:2077–2090.

[47] Wang, S.K.,Li, S.,Liu, Q.,Wu, K.,Zhang, J.Q.,Wang, S.S.,Wang, Y.,Chen, X.B.,Zhang, Y.,Gao, C.X., et al. (2015a). The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality. Nat. Genet.47:949–954.

[48] Wang, S.K.,Wu, K.,Yuan, Q.B.,Liu, X.Y.,Liu, Z.B.,Lin, X.Y.,Zeng, R.Z.,Zhu, H.T.,Dong, G.J.,Qian, Q., et al. (2012). Control of grain size, shape and quality by OsSPL16 in rice. Nat. Genet.44:950–954.

[49] Wang, Y.L.,Jiang, C.H.,Zhang, X.T.,Yan, H.M.,Yin, Z.G.,Sun, X.M.,Gao, F.H.,Zhao, Y.,Liu, W.,Han, S.C., et al. (2024). Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding. Plant Biotechnol. J.22:662–677.

[50] Wang, Y.X.,Xiong, G.S.,Hu, J.,Jiang, L.,Yu, H.,Xu, J.,Fang, Y.X.,Zeng, L.J.,Xu, E.B.,Xu, J., et al. (2015b). Copy number variation at the GL7 locus contributes to grain size diversity in rice. Nat. Genet.47:944–948.

[51] Wu, B.,Meng, J.H.,Liu, H.B.,Mao, D.H.,Yin, H.R.,Zhang, Z.Y.,Zhou, X.C.,Zhang, B.,Sherif, A.,Liu, H.Y., et al. (2023). Suppressing a phosphohydrolase of cytokinin nucleotide enhances grain yield in rice. Nat. Genet.55:1381–1389.

[52] Wu, H.M.,Xie, D.J.,Tang, Z.S.,Shi, D.Q., and Yang, W.C. (2020). PINOID regulates floral organ development by modulating auxin transport and interacts with MADS16 in rice. Plant Biotechnol. J.18:1778–1795.

[53] Wu, W.G.,Liu, X.Y.,Wang, M.H.,Meyer, R.S.,Luo, X.J.,Ndjiondjop, M.-N.,Tan, L.B.,Zhang, J.W.,Wu, J.Z.,Cai, H.W., et al. (2017). A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication. Nat. Plants3:17064.

[54] Wu, Y.,Wang, Y.,Mi, X.,Shan, J.,Li, X.,Xu, J., and Lin, H. (2016). The QTL GNP1 encodes GA20ox1, which increases grain number and yield by increasing cytokinin activity in rice panicle meristems. PLoS Genet.12: e1006386.

[55] Xia, H.,Luo, Z.,Xiong, J.,Ma, X.S.,Lou, Q.J.,Wei, H.B.,Qiu, J.,Yang, H.,Liu, G.L.,Fan, L.J., et al. (2019). Bi-directional selection in upland rice leads to its adaptive differentiation from lowland rice in drought resistance and productivity. Mol. Plant12:170–184.

[56] Xiao, Y.H.,Liu, D.P.,Zhang, G.X.,Gao, S.P.,Liu, L.H.,Xu, F.,Che, R.H.,Wang, Y.Q.,Tong, H.N., and Chu, C.C. (2019). Big Grain 3, encoding a purine permease, regulates grain size via modulating cytokinin transport in rice. J. Integr. Plant Biol.61:581–597.

[57] Xiong, D.,Wang, R.,Wang, Y.,Li, Y.,Sun, G., and Yao, S. (2023). SLG2 specifically regulates grain width through WOX11-mediated cell expansion control in rice. Plant Biotechnol. J.21:1904–1918.

[58] Xu, R.,Duan, P.,Yu, H.,Zhou, Z.,Zhang, B.,Wang, R.,Li, J.,Zhang, G.,Zhuang, S.,Lyu, J., et al. (2018). Control of grain size and weight by the OsMKKK10-OsMKK4-OsMAPK6 signaling pathway in rice. Mol. Plant11:860–873.

[59] Xu, R.,Li, N., and Li, Y. (2019). Control of grain size by G protein signaling in rice. J. Integr. Plant Biol.61:533–540.

[60] Yang, X.M.,Ren, Y.L.,Cai, Y.,Niu, M.,Feng, Z.M.,Jing, R.N.,Mou, C.L.,Liu, X.,Xiao, L.J.,Zhang, X., et al. (2018). Overexpression of OsbHLH107, a member of the basic helix-loop-helix transcription factor family, enhances grain size in rice (Oryza sativa L.). Rice11:41.

[61] Yang, Y.N.,Ma, X.S.,Xia, H.,Wang, L.,Chen, S.J.,Xu, K.,Yang, F.,Zou, Y.Q.,Wang, Y.L.,Zhu, J.M., et al. (2022). Natural variation of Alfin-like family affects seed size and drought tolerance in rice. Plant J.112:1176–1193.

[62] Zhan, P.L.,Ma, S.P.,Xiao, Z.L.,Li, F.P.,Wei, X.,Lin, S.J.,Wang, X.L.,Ji, Z.,Fu, Y.,Pan, J.H., et al. (2022). Natural variations in grain length 10 (GL10) regulate rice grain size. J. Genet. Genomics49:405–413.

[63] Zhang, Z.Y.,Li, J.J.,Pan, Y.H.,Li, J.L.,zhou, L.,Shi, H.L.,Zeng, Y.W.,Guo, H.F.,Yang, S.M.,Zheng, W.W., et al. (2017). Natural variation in CTB4a enhances rice adaptation to cold habitats. Nat. Commun.8:14788.

[64] Zhang, Z.Y.,Li, J.J.,Tang, Z.S.,Sun, X.M.,Zhang, H.L.,Yu, J.P.,Yao, G.X.,Li, G.L.,Guo, H.F.,Li, J.L., et al. (2018). Gnp4/LAX2, a RAWUL protein, interferes with the OsIAA3-OsARF25 interaction to regulate grain length via the auxin signaling pathway in rice. J. Exp. Bot.69:4723–4737.

[65] Zhao, D.S.,Li, Q.F.,Zhang, C.Q.,Zhang, C.,Yang, Q.Q.,Pan, L.X.,Ren, X.Y.,Lu, J.,Gu, M.H., and Liu, Q.Q. (2018). GS9 acts as a transcriptional activator to regulate rice grain shape and appearance quality. Nat. Commun.9:1240.

[66] Zhou, S.R., and Xue, H.W. (2019). The rice PLATZ protein SHORT GRAIN6 determines grain size by regulating spikelet hull cell division. J. Integr. Plant Biol.62:847–864.

[67] Zhou, Y.,Tao, Y.J.,Zhu, J.Y.,Miao, J.,Liu, J.,Liu, Y.H.,Yi, C.D.,Yang, Z.F.,Gong, Z.Y., and Liang, G.H. (2017). GNS4, a novel allele of DWARF11, regulates grain number and grain size in a high-yield rice variety. Rice10:34.

RIGHTS & PERMISSIONS

2024 The Authors. Journal of Integrative Plant Biology published by John Wiley & Sons Australia, Ltd on behalf of Institute of Botany, Chinese Academy of Sciences.