<i>PALEA AND GRAIN SHRUNKEN</i> encoding OsMADS15 determines palea identity to affect rice grain yield and quality

Di Jin; Chao-yue Yang; Xiao Liu; Jin-song Lan; Tao Jiang; Hao Chen; Jia-ying Zhang; Yu-tong Jiang; Bo-ran Peng; Liu-jing Wang; Guang-hua He; Nan Wang; Yun-feng Li; Hui Zhuang

doi:10.1016/j.jgg.2026.04.019

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PALEA AND GRAIN SHRUNKEN encoding OsMADS15 determines palea identity to affect rice grain yield and quality

doi: 10.1016/j.jgg.2026.04.019

a. Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China;
b. Yibin Academy of Southwest University, Yibin, Sichuan 644005, China

Funds:

This study was supported by the Agricultural Science and Technology R&

D Program of Chongqing (NW-CSTB2025NYKJGGXM-DPJSLXMX0002), the National Natural Science Foundation of China (32172044, 32100287), the Natural Science Foundation of Chongqing, China (CSTB2025NSCQ-GPX0550), the Chongqing Modern Agricultural Industry Technology System (CQMAITS202301), the Fundamental Research Funds for the Central Universities (SWU-KR25020, SWU-XDJH202315), the Sichuan Science and Technology Program (2024NSFSC0321, 2024NSFJQ0031), and the National Key Research and Development Program of China (2024YFD1200904).

Received Date: 2025-11-06
Accepted Date: 2026-04-24
Rev Recd Date: 2026-04-22

Available Online: 2026-04-30

Abstract

Abstract

The hull, composed of the lemma and palea, defines rice grain morphology and influences endosperm filling and quality. However, how palea development affects grain filling and quality remains poorly understood. Here, we identify a rice mutant, palea and grain shrunken 1 (pgs1), which exhibits a markedly reduced palea and elongated sterile lemmas. MutMap-based cloning reveals that PGS1 encodes the MADS-box transcription factor OsMADS15. The pgs1 mutant shows smaller but denser grains with substantially reduced chalkiness, and the expression of several palea identity genes, including G1, OsMADS1, and SL1, is significantly decreased. PGS1 is expressed in multiple floral organs, localizes to the nucleus, and lacks intrinsic transcriptional activation activity. Protein interaction assays show that PGS1 physically interacts with the histone demethylase JMJ706, and JMJ706 knockout lines exhibit floral and grain phenotypes similar to those of pgs1. Together, these results support a functional association between PGS1 and JMJ706 in the regulation of palea development and further suggest that defective palea development affects grain filling and grain quality in rice.
- Rice,
- Floral organ development,
- Grain size,
- Grain quality,
- MADS-box transcription factor,
- JMJ706

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References

Agrawal, G.K., Abe, K., Yamazaki, M., Miyao, A., Hirochika, H., 2005. Conservation of the E-function for floral organ identity in rice revealed by the analysis of tissue culture-induced loss-of-function mutants of the OsMADS1 gene. Plant Mol. Biol. 59, 125-135.

Bahrami, F., Arzani, A., Rahimmalek, M., 2021. Tolerance to high temperature at reproductive stage: Trade-offs between phenology, grain yield and yield-related traits in wild and cultivated barleys. Plant Breeding 140, 812-826.

Bowman, J.L., Smyth, D.R., Meyerowitz, E.M., 1991. Genetic interactions among floral homeotic genes of Arabidopsis. Development 112, 1-20.

Bowman, J.L., Smyth, D.R., Meyerowitz, E.M., 2012. The ABC model of flower development: then and now. Development 139, 4095-4098.

Callens, C., Tucker, M.R., Zhang, D., Wilson, Z.A., 2018. Dissecting the role of MADS-box genes in monocot floral development and diversity. J. Exp. Bot. 69, 2435-2459.

Causier, B., Schwarz-Sommer, Z., Davies, B., 2010. Floral organ identity: 20 years of ABCs. Semin Cell Dev. Biol. 21, 73-79.

Coen, E.S., Meyerowitz, E.M., 1991. The war of the whorls: Genetic interactions controlling flower development. Nature 353, 31-37.

Ditta, G., Pinyopich, A., Robles, P., Pelaz, S., Yanofsky, M.F., 2004. The SEP4 gene of Arabidopsis thaliana functions in floral organ and meristem identity. Curr. Biol. 14, 1935-1940.

Duan, Q., Kita, D., Li, C., Cheung, A.Y., Wu, H.M., 2010. FERONIA receptor-like kinase regulates RHO GTPase signaling of root hair development. Proc. Natl. Acad. Sci. U. S. A. 107, 17821-17826.

Ebenezer, G., Amirthalingam, M., Ponsamuel, J., Dayanandan, P., 1990. Role of palea and lemma in the development of rice caryopsis. J. Indian Bot. Soc. 69, 245-250.

Feng, T., Wang, L., Li, L., Liu, Y., Chong, K., Theissen, G., Meng, Z., 2022. OsMADS14 and NF-YB1 cooperate in the direct activation of OsAGPL2 and Waxy during starch synthesis in rice endosperm. New Phytol. 234, 77-92.

Fornara, F., Parenicova, L., Falasca, G., Pelucchi, N., Masiero, S., Ciannamea, S., Lopez-Dee, Z., Altamura, M.M., Colombo, L., Kater, M.M., 2004. Functional characterization of OsMADS18, a member of the AP1/SQUA subfamily of MADS Box genes. Plant Physiol. 135, 2207-2219.

Horigome, A., Nagasawa, N., Ikeda, K., Ito, M., Itoh, J.I., Nagato, Y., 2009. Rice open beak is a negative regulator of class 1 knox genes and a positive regulator of class B floral homeotic gene. Plant J. 58, 724-736.

Hu, Y., Liang, W., Yin, C., Yang, X., Ping, B., Li, A., Jia, R., Chen, M., Luo, Z., Cai, Q., 2015. Interactions of OsMADS1 with floral homeotic genes in rice flower development. Mol. Plant. 8, 1366-1384.

Huang, R., Jiang, L., Zheng, J., Wang, T., Wang, H., Huang, Y., Hong, Z., 2013. Genetic bases of rice grain shape: So many genes, so little known. Trends Plant Sci. 18, 218-226.

Itoh, J.I., Nonomura, K.I., Ikeda, K., Yamaki, S., Inukai, Y., Yamagishi, H., Kitano, H., Nagato, Y., 2005. Rice plant development: From zygote to spikelet. Plant Cell Physiol. 46, 23-47.

Jeon, J.S., Lee, S., An, G., 2008. Intragenic control of expression of a rice MADS box gene OsMADS1. Mol. Cells 26, 474-480.

Jin, Y., Luo, Q., Tong, H., Wang, A., Cheng, Z., Tang, J., Li, D., Zhao, X., Li, X., Wan, J., 2011. An AT-hook gene is required for palea formation and floral organ number control in rice. Dev. Biol. 359, 277-288.

Jongkaewwattana, S., Geng, S., 2001. Inter-relationships amongst grain characteristics, grain-filling parameters and rice (Oryza sativa L.) milling quality. J. Agron. Crop Sci. 187, 223-229.

Li, A., Zhang, Y., Wu, X., Tang, W., Wu, R., Dai, Z., Liu, G., Zhang, H., Wu, C., Chen, G., et al., 2008. DH1, a LOB domain-like protein required for glume formation in rice. Plant Mol. Biol. 66, 491-502.

Li, H., Liang, W., Jia, R., Yin, C., Zong, J., Kong, H., Zhang, D., 2010. The AGL6-like gene OsMADS6 regulates floral organ and meristem identities in rice. Cell Res. 20, 299-313.

Li, X., Sun, L., Tan, L., Liu, F., Zhu, Z., Fu, Y., Sun, X., Sun, X., Xie, D., Sun, C., 2012. TH1, a DUF640 domain-like gene controls lemma and palea development in rice. Plant Mol. Biol. 78, 351-359.

Liu, E., Zhu, S., Du, M., Lyu, H., Zeng, S., Liu, Q., Wu, G., Jiang, J., Dang, X., Dong, Z., 2023. LAX1, functioning with MADS-box genes, determines normal palea development in rice. Gene 883, 147635.

Liu, R., Zhao, D., Li, P., Xia, D., Feng, Q., Wang, L., Wang, Y., Shi, H., Zhou, Y., Chen, F., et al., 2025. Natural variation in OsMADS1 transcript splicing affects rice grain thickness and quality by influencing monosaccharide loading to the endosperm. Plant Commun. 6, 101178.

Lu, S.J., Wei, H., Wang, Y., Wang, H.M., Yang, R.F., Zhang, X.B., Tu, J.M., 2012. Overexpression of a transcription factor OsMADS15 modifies plant architecture and flowering time in rice (Oryza sativa L.). Plant Mol. Biol. 30, 1461-1469.

Luo, Q., Zhou, K., Zhao, X., Zeng, Q., Xia, H., Zhai, W., Xu, J., Wu, X., Yang, H., Zhu, L., 2005. Identification and fine mapping of a mutant gene for palealess spikelet in rice. Planta 221, 222-230.

Ohmori, S., Kimizu, M., Sugita, M., Miyao, A., Hirochika, H., Uchida, E., Nagato, Y., Yoshida, H., 2009. MOSAIC FLORAL ORGANS1, an AGL6-like MADS box gene, regulates floral organ identity and meristem fate in rice. Plant Cell. 21, 3008-3025.

Pelaz, S., Ditta, G.S., Baumann, E., Wisman, E., Yanofsky, M.F., 2000. B and C floral organ identity functions require SEPALLATA MADS-box genes. Nature 405, 200-203.

Prasad, K., Parameswaran, S., Vijayraghavan, U., 2005. OsMADS1, a rice MADS-box factor, controls differentiation of specific cell types in the lemma and palea and is an early-acting regulator of inner floral organs. Plant J. 43, 915-928.

Pu, C.X., Ma, Y., Wang, J., Zhang, Y.C., Jiao, X.W., Hu, Y.H., Wang, L.L., Zhu, Z.G., Sun, D., Sun, Y., 2012. Crinkly4 receptor-like kinase is required to maintain the interlocking of the palea and lemma, and fertility in rice, by promoting epidermal cell differentiation. Plant J. 70, 940-953.

Ren, D., Li, Y., Zhao, F., Sang, X., Shi, J., Wang, N., Guo, S., Ling, Y., Zhang, C., Yang, Z., et al., 2013. MULTI-FLORET SPIKELET1, which encodes an AP2/ERF protein, determines spikelet meristem fate and sterile lemma identity in rice. Plant Physiol. 162, 872-884.

Sang, X., Li, Y., Luo, Z., Ren, D., Fang, L., Wang, N., Zhao, F., Ling, Y., Yang, Z., Liu, Y., 2012. CHIMERIC FLORAL ORGANS1, encoding a monocot-specific MADS box protein, regulates floral organ identity in rice. Plant Physiol. 160, 788-807.

Sun, Q., Zhou, D.X., 2008. Rice jmjC domain-containing gene JMJ706 encodes H3K9 demethylase required for floral organ development. Proc. Natl. Acad. Sci. U. S. A. 105, 13679-13684.

Theissen, G., Melzer, R., Rumpler, F., 2016. MADS-domain transcription factors and the floral quartet model of flower development: Linking plant development and evolution. Development 143, 3259-3271.

Theissen, G., Saedler, H., 2001. Floral quartets. Nature 409, 469-471.

Wang, C., Tang, S., Zhan, Q., Hou, Q., Zhao, Y., Zhao, Q., Feng, Q., Zhou, C., Lyu, D., Cui, L., et al., 2019. Dissecting a heterotic gene through GradedPool-Seq mapping informs a rice-improvement strategy. Nat. Commun. 10, 2982.

Wang, K., Tang, D., Hong, L., Xu, W., Huang, J., Li, M., Gu, M., Xue, Y., Cheng, Z., 2010. DEP and AFO regulate reproductive habit in rice. PLoS Genet. 6, e1000818.

Wu, F., Shi, X., Lin, X., Liu, Y., Chong, K., Theissen, G., Meng, Z., 2017. The ABCs of flower development: Mutational analysis of AP1/FUL-like genes in rice provides evidence for a homeotic (A)-function in grasses. Plant J. 89, 310-324.

Xiao, H., Tang, J., Li, Y., Wang, W., Li, X., Jin, L., Xie, R., Luo, H., Zhao, X., Meng, Z., 2009. STAMENLESS 1, encoding a single C2H2 zinc finger protein, regulates floral organ identity in rice. Plant J. 59, 789-801.

Xiao, N., Pan, C., Li, Y., Wu, Y., Cai, Y., Lu, Y., Wang, R., Yu, L., Shi, W., Kang, H., 2021. Genomic insight into balancing high yield, good quality, and blast resistance of japonica rice. Genome Biol. 22, 283.

Xing, Y., Zhang, Q., 2010. Genetic and molecular bases of rice yield. Annu. Rev. Plant Biol. 61, 421-442.

Yamaguchi, T., Hirano, H.-Y., 2006. Function and diversification of MADS-box genes in rice. World Journal TS. 6, 1923-1932.

Yoshida, A., Suzaki, T., Tanaka, W., Hirano, H.Y., 2009. The homeotic gene long sterile lemma (G1) specifies sterile lemma identity in the rice spikelet. Proc. Natl. Acad. Sci. U. S. A. 106, 20103-20108.

Yoshida, H., Nagato, Y., 2011. Flower development in rice. J. Exp. Bot. 62, 4719-4730.

Yuan, Z., Gao, S., Xue, D.W., Luo, D., Li, L.T., Ding, S.Y., Yao, X., Wilson, Z.A., Qian, Q., Zhang, D. B., 2009. RETARDED PALEA1 controls palea development and floral zygomorphy in rice. Plant Physiol. 149, 235-244.

Zhang, X., Cai, Q., Li, L., Wang, L., Hu, Y., Chen, X., Zhang, D., Persson, S., Yuan, Z., 2024. OsMADS6-OsMADS32 and REP1 control palea cellular heterogeneity and morphogenesis in rice. Dev. Cell 59, 1379-1395.

Zheng, M., Wang, Y., Wang, Y., Wang, C., Ren, Y., Lv, J., Peng, C., Wu, T., Liu, K., Zhao, S., et al., 2015. DEFORMED FLORAL ORGAN1 (DFO1) regulates floral organ identity by epigenetically repressing the expression of OsMADS58 in rice (Oryza sativa). New Phytol. 206, 1476-1490.

Zhuang, H., Wang, H.L., Zhang, T., Zeng, X.Q., Chen, H., Wang, Z.W., Zhang, J., Zheng, H., Tang, J., Ling, Y.H., 2020. NONSTOP GLUMES1 encodes a C2H2 zinc finger protein that regulates spikelet development in rice. Plant Cell 32, 392-413.

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