Chinese Journal OF Rice Science >
Identification and Cloning of SG5 in Rice
Received date: 2025-03-12
Revised date: 2025-06-05
Online published: 2025-09-25
【Objective】 Rice glume development directly affects both grain yield and quality. Identifying genes that control glume development and characterizing their functions can provide valuable genetic resources for breeding. 【Method】 The split glume 5 (sg5) mutant was isolated from a mutant library generated by ethyl methanesulfonate (EMS) mutagenesis of the rice variety Xudao 3 (XU3). Phenotypic investigation and analysis were performed on both the wild type and the sg5 mutant. SG5 was identified using a combination of map-based cloning and bulked segregant analysis sequencing (BSA-seq). The temporal and spatial expression patterns of SG5 were examined by qRT PCR and GUS staining. Subcellular localization of SG5 was observed in rice protoplasts. An evolutionary tree was constructed to analyze the natural selection of SG5. 【Result】 The mutant exhibited normal glume development before flowering, but the glumes remained split until maturity. Compared with the wild type, the mutant showed earlier heading, longer panicles, reduced grain length and width, and a significantly lower seed-setting rate, while plant height and effective panicle number remained unchanged. Microscopic observation indicated that the split glume phenotype was caused by persistent swelling of the lodicules. SG5 was mapped to a 3.72 Mb physical interval between InDel5-11 and InDel5-13 on chromosome 5. In the sg5 mutant, a G-to-A mutation at the junction of intron 3 and exon 4 of LOC_Os05g50890 led to alternative splicing and premature protein termination. Knockout experiments confirmed that SG5 is the target gene. SG5 is constitutively expressed, with higher transcript levels in roots, stems, and leaves. The SG5 protein localizes to both the cytoplasm and nucleus. Evolutionary analysis revealed that SG5 has undergone differentiation between indica and japonica subspecies during evolution. 【Conclusion】 This study identifies a novel allele of OsJar1 and reveals that SG5 has diverged between indica and japonica under natural selection. These findings provide new clues for further dissection of the molecular regulatory network controlling glume development and offer valuable genetic resources for precision breeding in rice.
Key words： rice; glume cracking; lodicule; sg5 mutant
XUE Pao, WANG Youshuang, HE Wanwan, HUANG Chenbo, ZHANG Han, DING Zhenqian, CHEN Qiuli, FAN Yunxin, DING Chengwei, SUN Lianping, HU Tingting . Identification and Cloning of SG5 in Rice[J]. Chinese Journal OF Rice Science, 2026 , 40(2) : 210 -222 . DOI: 10.16819/j.1001-7216.2026.250310
| [1] | Xing Y Z, Zhang Q F. Genetic and molecular bases of rice yield[J]. Annual Review of Plant Biology, 2010, 61: 421-442. |
| [2] | Ren D Y, Ding C Q, Qian Q. Molecular bases of rice grain size and quality for optimized productivity[J]. Science Bulletin, 2023, 68(3): 314-350. |
| [3] | Theissen G, Melzer R. Molecular mechanisms underlying origin and diversification of the Angiosperm flower[J]. Annals of Botany, 2007, 100(3): 603-619. |
| [4] | Soltis D E, Chanderbali A S, Kim S, Buzgo M, Soltis P S. The ABC model and its applicability to basal angiosperms[J]. Annals of Botany, 2007, 100(2): 155-163. |
| [5] | Maoileidigh D S O, Graciet E, Wellmer F. Gene networks controlling Arabidopsis thaliana flower development[J]. New Phytologist, 2014, 201: 16-30. |
| [6] | Krizek B A, Fletcher J C. Molecular mechanisms of flower development: An armchair guide[J]. Nature Reviews Genetics, 2005, 6(9): 688-698. |
| [7] | Causier B, Schwarz-Sommer Z, Davies B. Floral organ identity: 20 years of ABCs[J]. Seminars in Cell & Developmental Biology, 2010, 21(1): 73-79. |
| [8] | 郭爽, 李云峰, 任德勇, 王增, 杜青, 何光华. 水稻内稃扭曲突变体palea distortion 1 (pd1) 的鉴定与基因定位[J]. 分子植物育种, 2011, 9(3): 256-260. |
| Guo S, Li Y F, Ren D Y, Wang Z, Du Q, He G H. Identification and gene mapping of a palea distortion 1 (pd1) mutant in rice (Oryza sativa L.)[J]. Molecular Plant Breeding, 2011, 9(3): 256-260. (in Chinese with English abstract) | |
| [9] | Jin Y, Luo Q, Tong H N, Wang A J, Cheng Z J, Tang J F, Li D Y, Zhao X F, Li X B, Wan J M, Jiao Y L, Chu C C, Zhu L H. An AT-hook gene is required for palea formation and floral organ number control in rice[J]. Developmental Biology, 2011, 359(2): 277-288. |
| [10] | 陈东, 毛毕刚, 潘银林, 彭彦, 韶也, 吴天昊, 赵炳然. 水稻颖花畸形突变体(gm(t))的遗传分析与基因定位[J]. 分子植物育种, 2019, 17(15): 5026-5031. |
| Chen D, Mao B G, Pan Y L, Peng Y, Shao Y, Wu T H, Zhao B R. Genetic analysis and gene mapping of glume malformation mutant(gm(t)) in rice[J]. Molecular Plant Breeding, 2019, 17(15): 5026-5031. (in Chinese with English abstract) | |
| [11] | 薛大伟. 两个水稻花器官突变体的遗传分析[D]. 北京: 中国农业科学院, 2006. |
| Xue D W. The genetic analysis of two floral organ mutants from rice[D]. Chinese Academy of Agricultural Sciences, 2006. Beijing: Chinese Academy of Agricultural Sciences, 2006. (in Chinese with English abstract) | |
| [12] | Jeon J S, Jang S, Lee S, Nam J, Kim C, Lee S H, Chung Y Y, Kim S R, Lee Y H, Cho Y G, An G. leafy hull sterile1 is a homeotic mutation in a rice MADS box gene affecting rice flower development[J]. The Plant Cell, 2000, 12(6): 871-884. |
| [13] | Agrawal G K, Abe K, Yamazaki M, Miyao A, Hirochika H. 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[J]. Plant Molecular Biology, 2005, 59(1): 125-135. |
| [14] | Prasad K, Parameswaran S, Vijayraghavan U. 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[J]. The Plant Journal, 2005, 43(6): 915-928. |
| [15] | Hu Y, Liang W Q, Yin C S, Yang X L, Ping B Z, Li A X, Jia R, Chen M J, Luo Z J, Cai Q, Zhao X X, Zhang D B, Yuan Z. Interactions of OsMADS1 with floral homeotic genes in rice flower development[J]. Molecular plant, 2015, 8(9): 1366-1384. |
| [16] | Pelucchi N, Fornara F, Favalli C, Masiero S, Lago C, P E M, Colombo L, Kater M M. Comparative analysis of rice MADS-box genes expressed during flower development[J]. Sexual Plant Reproduction, 2002, 15(3): 113-122. |
| [17] | Wang K J, Tang D, Hong L L, Xu W Y, Huang J, Li M, Gu M H, Xue Y B, Cheng Z K. DEP and AFO regulate reproductive habit in rice[J]. PLoS Genetics, 2010, 6(1): e1000818. |
| [18] | Kobayashi K, Yasuno N, Sato Y, Yoda M, Yamazaki R, Kimizu M, Yoshida H, Nagamura Y, Kyozuka J. Inflorescence meristem identity in rice is specified by overlapping functions of three AP1/FUL-like MADS box genes and PAP2 a SEPALLATA MADS box gene[J]. The Plant Cell, 2012, 24(5): 1848-1859. |
| [19] | Yadav S R, Prasad K, Vijayraghavan U. Divergent regulatory OsMADS2 functions control size, shape and differentiation of the highly derived rice floret second-whorl organ[J]. Genetics, 2007, 176(1): 283-294. |
| [20] | Yao S G, Ohmori S, Kimizu M, Yoshida H. Unequal genetic redundancy of rice PISTILLATA orthologs, OsMADS2 and OsMADS4, in lodicule and stamen development[J]. Plant & Cell Physiology, 2008, 49(5): 853-857. |
| [21] | Yu X Q, Xia S S, Xu Q K, Cui Y J, Gong M, Zeng D L, Zhang Q, Shen L, Jiao G A, Gao Z Y, Hu J, Zhang G H, Zhu L, Guo L B, Ren D Y, Qian Q. ABNORMAL FLOWER AND GRAIN 1 encodes OsMADS6 and determines palea identity and affects rice grain yield and quality[J]. Science China Life Sciences, 2020, 63(2): 228-238. |
| [22] | Ohmori S, Kimizu M, Sugita M, Miyao A, Hirochika H, Uchida E, Nagato Y, Yoshida H. MOSAIC FLORAL ORGANS1, an AGL6 -like MADS box gene, regulates floral organ identity and meristem fate in rice[J]. The Plant Cell, 2009, 21(10): 3008-3025. |
| [23] | Zhang J, Nallamilli B R, Mujahid H, Peng Z H. OsMADS6 plays an essential role in endosperm nutrient accumulation and is subject to epigenetic regulation in rice (Oryza sativa)[J]. The Plant Journal, 2010, 64(4): 604-617. |
| [24] | Duan Y L, Xing Z, Diao Z J, Xu W Y, Li S P, Du X Q, Wu G H, Wang C L, Lan T, Meng Z, Liu H Q, Wang F, Wu W R, Xue Y B. Characterization of Osmads6-5, a null allele, reveals that OsMADS6 is a critical regulator for early flower development in rice (Oryza sativa L.)[J]. Plant Molecular Biology, 2012, 80(4-5): 429-442. |
| [25] | Wang H H, Zhang L, Cai Q, Hu Y, Jin Z M, Zhao X X, Fan W, Huang Q M, Luo Z J, Chen M J, Zhang D B, Yuan Z. OsMADS32 interacts with PI-like proteins and regulates rice flower development[J]. Journal of Integrative Plant Biology, 2015, 57(5): 504-513. |
| [26] | Luo Q, Zhou K D, Zhao X F, Zeng Q C, Xia H A, Zhai W X, Xu J C, Wu X J, Yang H S, Zhu L H. Identification and fine mapping of a mutant gene for palealess spikelet in rice[J]. Planta, 2005, 221(2): 222-230. |
| [27] | Xiao H, Tang J F, Li Y F, Wang W M, Li X B, Jin L, Xie R, Luo H F, Zhao X F, Meng Z, He G H, Zhu L H. STAMENLESS 1, encoding a single C2H2 zinc finger protein, regulates floral organ identity in rice[J]. The Plant Journal, 2009, 59(5): 789-801. |
| [28] | Yan D W, Zhang X M, Zhang L, Ye S H, Zeng L J, Liu J Y, Li Q, He Z H. CURVED CHIMERIC PALEA 1 encoding an EMF1-like protein maintains epigenetic repression of OsMADS58in rice palea development[J]. The Plant Journal, 2015, 82(1): 12-24. |
| [29] | Zheng M, Wang Y H, Wang Y L, Wang C M, Ren Y L, Lv J, Peng C, Wu T, Liu K, Zhao S L, Liu X, Guo X P, Jiang L, Terzaghi W, Wan J M. DEFORMED FLORAL ORGAN1 (DFO1) regulates floral organ identity by epigenetically repressing the expression of OsMADS58 in rice (Oryza sativa)[J]. The New Phytologist, 2015, 206(4): 1476-1490. |
| [30] | 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. RETARDED PALEA1 controls palea development and floral zygomorphy in rice[J]. Plant Physiology, 2009, 149(1): 235-244. |
| [31] | Zeng D D, Qin R, Alamin M, Liang R, Yang C C, Jin X L, Shi C H. DBOP specifies palea development by suppressing the expansion of the margin of palea in rice[J]. Genes and Genomics, 2016, 38(11): 1095-1103. |
| [32] | Lee D Y, Lee J, Moon S, Park S Y, An G. The rice heterochronic gene SUPERNUMERARY BRACT regulates the transition from spikelet meristem to floral meristem[J]. The Plant Journal, 2007, 49(1): 64-78. |
| [33] | Ren D Y, Li Y F, Zhao F M, Sang X C, Shi J Q, Wang N, Guo S, Ling Y H, Zhang C W, Yang Z L, He G H. MULTI-FLORET SPIKELET1, which encodes an AP2/ERF protein, determines spikelet meristem fate and sterile lemma identity in rice[J]. Plant Physiology, 2013, 162(2): 872-884. |
| [34] | Ren D Y, Rao Y C, Wu L W, Xu Q K, Li Z Z, Yu H P, Zhang Y, Leng Y J, Hu J, Zhu L, Gao Z Y, Dong G J, Zhang G H, Guo L B, Zeng D L, Qian Q. The pleiotropic ABNORMAL FLOWER AND DWARF1 affects plant height, floral development and grain yield in rice[J]. Journal of Integrative Plant Biology, 2016, 58(6): 529-539. |
| [35] | Yan D W, Zhou Y, Ye S H, Zeng L J, Zhang X M, He Z H. BEAK-SHAPED GRAIN 1/TRIANGULAR HULL 1, a DUF640 gene, is associated with grain shape, size and weight in rice[J]. Science China Life Sciences, 2013, 56(3): 275-283. |
| [36] | Livak K J, Schmittgen T D. Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCTmethod[J]. Methods, 2001, 25(4): 402-408. |
| [37] | 王忠, 顾蕴洁, 高煜珠. 水稻开颖机理的探讨: Ⅲ.浆片的结构及其在开颖过程中内含物的变化[J]. 作物学报, 1991, 17(2): 96-101, 161-162. |
| Wang Z, Gu Y J, Gao Y Z. Studies on the mechanism of the anthesis of rice Ⅲ.Structure of the lodicule and changes of its contents during flowering[J]. Acta Agronomica Sinica, 1991, 17(2): 96-101, 161-162. (in Chinese with English abstract) | |
| [38] | 秦鹏. 水稻颖壳发育基因hzp和ug1的研究[D]. 长沙: 湖南农业大学, 2021. |
| Qin P. The study on genes hzp and ug1 controlling rice glume development[D]. Changsha: Hunan Agricultural University, 2021. (in Chinese with English abstract) | |
| [39] | Terol J, Domingo C, Talón M. The GH3 family in plants: Genome wide analysis in rice and evolutionary history based on EST analysis[J]. Gene, 2006, 371(2): 279-290. |
| [40] | Riemann M, Riemann M, Takano M. Rice JASMONATE RESISTANT 1 is involved in phytochrome and jasmonate signalling[J]. Plant, Cell & Environment, 2008, 31(6): 783-792. |
| [41] | Xiao Y G, Chen Y, Charnikhova T, Mulder P P J, Heijmans J, Hoogenboom A, Agalou A, Michel C, Morel J B, Dreni L, Kater M M, Bouwmeester H, Wang M, Zhu Z, Ouwerkerk P B F. OsJAR1 is required for JA-regulated floret opening and anther dehiscence in rice[J]. Plant Molecular Biology, 2014, 86(1/2): 19-33. |
| [42] | Jain M, Kaur N, Tyagi A K, Khurana J P. The auxin-responsive GH3 gene family in rice (Oryza sativa)[J]. Functional & Integrative Genomics, 2006, 6(1): 36-46. |
| [43] | Zhao S Q, Xiang J J, Xue H W. Studies on the rice LEAF INCLINATION1 (LC1), an IAA-amido synthetase, reveal the effects of auxin in leaf inclination control[J]. Molecular Plant, 2013, 6(1): 174-187. |
| [44] | Du H, Wu N, Fu J, Wang S P, Li X H, Xiao J H, Xiong L Z. A GH3 family member, OsGH3-2, modulates auxin and abscisic acid levels and differentially affects drought and cold tolerance in rice[J]. Journal of Experimental Botany, 2012, 63(18): 6467-6480. |
| [45] | Fu J, Yu H H, Li X H, Xiao J H, Wang S P. Rice GH3 gene family: Regulators of growth and development[J]. Plant Signaling Behavior, 2011, 6(4): 570-574. |
| [46] | Kong W L, Zhong H, Deng X X, Gautam M, Gong Z Y, Zhang Y, Zhao G Q, Liu C, Li Y S. Evolutionary analysis of GH3 genes in six Oryza Species/Subspecies and their expression under salinity stress in Oryza sativa ssp. japonica[J]. Plants, 2019, 8(2): 30. |
| [47] | Mao C J, He J M, Liu L, Deng Q M, Yao X F, Liu C M, Qiao Y L, Li P, Ming F. OsNAC2 integrates auxin and cytokinin pathways to modulate rice root development[J]. Plant Biotechnology Journal, 2020, 18(2): 429-442. |
| [48] | Ding X H, Cao Y L, Huang L L, Zhao J, Xu C G, Li X H, Wang S P. Activation of the Indole-3-Acetic Acid-Amido synthetase GH3-8 suppresses expansin expression and promotes salicylate- and jasmonate-independent basal immunity in rice[J]. The Plant Cell, 2008, 20(1): 228-240. |
| [49] | Yadav S R, Khanday I, Majhi B B, Veluthambi K, Vijayraghavan U. Auxin-responsive OsMGH3, a common downstream target of OsMADS1 and OsMADS6, controls rice floret fertility[J]. Plant and Cell Physiology, 2011, 52(12): 2123-2135. |
| [50] | Fukumoto K, Alamgir K M, Yamashita Y, Mori I C, Matsuura H, Galis I. Response of rice to insect elicitors and the role of OsJAR1 in wound and herbivory-induced JA-Ile accumulation[J]. Journal of Integrative Plant Biology, 2013, 55(8): 775-784. |
| [51] | Song S S, Qi T C, Huang H, Ren Q C, Wu D W, Chang C Q, Peng W, Liu Y, Peng J R, Xie D X. The jasmonate-ZIM domain proteins interact with the R2R3-MYB transcription factors MYB21 and MYB24 to affect jasmonate-regulated stamen development in Arabidopsis[J]. The Plant Cell, 2011, 23(3): 1000-1013. |
| [52] | Wakuta S, Suzuki E, Saburi W, Matsuura H, Nabeta K, Imai R, Matsui H. OsJAR1 and OsJAR2 are jasmonyl-L-isoleucine synthases involved in wound- and pathogen-induced Jasmonic acid signalling[J]. Biochemical and Biophysical Research Communications, 2011, 409: 634-639. |
| [53] | Zhang S N, Wang S K, Xu Y X, Yu C L, Shen C J, Qian Q, Geisler M, Jiang D A, Qi Y H. The auxin response factor, OsARF19, controls rice leaf angles through positively regulating OsGH3-5 and OsBRI1[J]. Plant, Cell and Environment, 2015, 38: 638-654. |
| [54] | Ding W Y, Gou Y J, Li Y J, Li J J, Fang Y D, Liu X P, Zhu X Y, Ye R J, Heng Y Q, Wang H Y, Shen R X. A jasmonate-mediated regulatory network modulates diurnal floret opening time in rice[J]. New phytologist, 2024, 244(1): 176-191. |
| [55] | 王忠, 顾蕴洁, 高煜珠. 水稻开颖机理的探讨: V.不育系与可育系浆片和花丝结构的比较[J]. 作物学报, 1994, 20(1): 13-17, 129-131. |
| Wang Z, Gu Y J, Gao Y Z. Studies on the mechanism of the anthesis of rice V. comparison of lodicule and filament structure between sterile line and fertile line[J]. Acta Agronomica Sinica, 1994, 20(1): 13-17, 129-131. (in Chinese with English abstract) |
/
| 〈 |
|
〉 |