Identification and Cloning of SG5 in Rice

doi:10.16819/j.1001-7216.2026.250310

Abstract

Abstract:

【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

摘要：

【目的】水稻颖壳发育直接影响稻米产量与品质，挖掘颖壳发育基因并探究其分子功能，可为水稻优质高产遗传改良提供更多的基因资源。【方法】利用EMS诱变徐稻3号获得一个颖壳开裂后不闭合的突变体sg5 (split glume 5)；对其农艺性状和不同开花时间进行浆片表型和细胞学观察；通过图位克隆与BSA-seq相结合的方法鉴定SG5基因；结合野生型各组织表达量检测及GUS转基因株系各组织染色情况，分析SG5组织表达特异性；利用激光共聚焦显微镜观察SG5蛋白在原生质体中的亚细胞定位；通过进化树分析，探讨了SG5在进化过程中的选择情况。【结果】突变体sg5在开花前颖壳发育正常，开花后颖壳保持开裂状态直至成熟。与野生型相比，突变体株高和有效穗数无显著变化，抽穗期显著提前，穗长增加，粒长、粒宽降低，结实率极显著降低。体视显微镜观察结果显示，突变体颖壳开裂是浆片保持膨大状态导致的。SG5基因定位在第5染色体InDel5- 11−InDel5-13区间内，物理间距为3.72 Mb，图位克隆表明sg5突变体中LOC_Os05g50890的第3内含子和第4外显子连接处发生G-A突变导致发生可变剪接，蛋白翻译提前终止。敲除实验证实SG5基因即为目的基因。SG5基因为组成型表达，在根、茎、叶中表达水平较高。SG5蛋白定位在细胞质和细胞核中。SG5在进化过程中发生籼稻、粳稻分化。【结论】本研究鉴定了OsJar1基因一个新的等位突变，发现SG5在自然选择过程中发生了籼、粳分化。本研究为后续深入研究颖壳调控分子机制提供了新的线索，并为水稻设计育种提供新的基因资源。

关键词: 水稻, 颖壳开裂, 浆片, sg5突变体

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.

薛炮, 王友霜, 何弯弯, 黄晨博, 张涵, 丁震乾, 陈秋丽, 范运新, 丁成伟, 孙廉平, 胡婷婷. 水稻颖壳不闭合基因SG5的鉴定与克隆[J]. 中国水稻科学, 2026, 40(2): 210-222.

Figures/Tables 7

Table 1. Primer sequences used in this study

引物名称 Primer name	引物序列（5'‎→3'） Primer sequence (5'→3')	功能 Function
InDel 5-11F	GGAGTTCTGGTGGCTTTCC	基因定位 Gene mapping
InDel 5-11R	CAGTTCCCCATTTCCCTCTA
InDel 5-13F	TGAGTTTCCGGTGTTCCATA
InDel 5-13R	AAGGCAAAGTCGTTCAGCTT
SG5-Cas9-F	ggcaATATTGAGCCCTATATCCAG	基因编辑 Gene editing
SG5- Cas9-R	aaacCTGGATATAGGGCTCAATAT	基因编辑 Gene editing
SG5-1305-GUS-F	catgattacgaattcATCACCTCTGCCCAAAACCA	GUS载体构建 Construction of GUS vector
SG5-1305-GUS-R	tcagatctaccatggTGTAATGGTAGAATCCTGGCTTTACCA	GUS载体构建 Construction of GUS vector
SG5-1305-GFP-F	aagtccggagctagctctagaATGACGATCTGCAGCTGTGAGG	亚细胞定位 Subcellular localization
SG5-1305-GFP-R	ggtcctcgagacgtctctagaAAATCCATAGGCAGTACTGAAATAACTTTGGG	亚细胞定位 Subcellular localization
Hyg-F	ACGGTGTCGTCCATCACAGTTTGCC	潮霉素基因检测 Detection of hygromycin resistance gene
Hyg-R	TTCCGGAAGTGCTTGACATTGGGGA	潮霉素基因检测 Detection of hygromycin resistance gene
Cas9-F	CGTGGAAGATCGGTTCAACGC	阳性株检测 Sequencing of positive plants
Cas9-R	CTGCCGGCCAGATTGGCA	阳性株检测 Sequencing of positive plants
CR-SG5-F	TGATGCCAACTCCTACTGCAC	突变位点检测 Mutation site detection
CR-SG5-R	ACTTGGGCTTTCCGTGTGTT	突变位点检测 Mutation site detection
UBQ10-qPCR-F	TGGTCAGTAATCAGCCAGTTTGG	qRT-PCR
UBQ10-qPCR-R	GCACCACAAATACTTGACGAACAG
SG5-qPCR-F	GATACCTCACCAGTGGTCACTG
SG5-qPCR-R	TCCTAAACGCGTAAGATGTACGG

Fig. 1. Phenotypic characterization of wildtype (Xudao 3, XU3) and sg5 A, Characterization of plant type in wild type and sg5. Scale bar=20 cm. B, Glume morphology and panicle morphology in wild type and sg5. Scale bar=5 cm. C, Comparison of grain size in wild type and sg5. Scale bar=10 mm. D, Comparison of heading date, plant height, panicle number, panicle length, seed setting rate, grain length and grain width in wild type and sg5. Data are given as Mean ± SD (n≥20). Student’s t-test was used to generate P value. *, P < 0.05; **, P < 0.01.

Fig. 2. Developmental morphological changes of glumes and lodicules in wild type (XU3) and sg5 at various time points around flowering A, Characterization of panicle before flowering(A), glume before flowering(B), panicle after flowering(C), glume after flowering(D) in the wild type and sg5(Scale bar=5 cm). E, Florets of consistent early growth from wild type and sg5, showing morphological changes of glumes and lodicules at various time points around flowering. Scale bar = 20 μm. The white boxes indicate the corresponding florets.

Fig. 3. Map-based cloning and functional verification of SG5 A, Map-based cloning of SG5. B, Characterization of DNA and protein sequences in Xudao 3(XU3) and sg5. Underlined nucleotides are the sequence of the ﬁrst half of exons 4 in XU3, others are at the terminal of the intron 3. Red boxes are the splicing site mutation and new splicing sites. Black vertical line, the site of jasmonate. Green vertical line, the site of L-alpha-amino acid. C, Gene editing and homozygous mutant sequences. D, Characterization of plant type in XU3, sg5 mutant, SG5#CR-1, and SG5#CR-2. Scale bar=20 cm. E, Glume morphology of XU3, sg5 mutant, SG5#CR-1, and SG5#CR-2; F, Panicle morphology of wild type, sg5 mutant, SG5#CR-1, and SG5#CR-2. Scale bar=5 cm. G, Number of grains per panicle in XU3, sg5 mutant, and SG5#CR-1; Red dot, Normal seeds. Black dot, Moldy seeds. H, Comparison of heading date, plant height, panicle length, panicle number, and seed setting rate in XU3, SG5#CR-1, and SG5#CR-2. Red dot, Number of plants investigated. Data are given as Mean ± SD (n≥10). Student’s t-test was used to generate P value. * P < 0.05; ** P < 0.01.

Table 2. Summary of differentially expressed genes detected using BSA analysis

差异种类 Category	差异基因数目 Number of differential genes
基因上游 Upstream	638
功能获得型 Stop gain	6
功能缺失型 Stop loss	2
5' UTR	10
3' UTR	14
保守结构缺失/插入 Conservative inframe deletion / insertion	4
散乱结构缺失/插入 Disruptive inframe deletion / insertion	3
移码突变 Frameshift variant	23
错义突变 Missense variant	119
同义突变 Synonymous variant	98
剪接受体变异 Splice acceptor variant & intron variant	4
内含子变异 Intronic	60
基因间变异 Intergenic region	72
基因下游 Downstream	212
合计 Total	1265

Fig. 4. Expression pattern analysis of SG5 and subcellular localization A, qRT-PCR analysis of SG5 gene expression in various tissues. Data are given as Mean ± SD (n=3). B, Histochemical analysis of GUS activity in various tissues.( Scale bar=10 mm). C, Subcellular localization of SG5 in rice protoplast. 35S::GFP(scale bar=50 μm). 35S::SG5-GFP(scale bar=5 μm).

Fig. 5. Phylogenetic tree and multiple sequence alignment analysis of SG5 in rice A, Phylogenetic tree analysis of SG5 in rice. Red frame, Rice resources with the GH3-5 domain. Red arrow, SG5 protein. B, Multiple sequence alignment of SG5 in rice. Gray frame, The domain of GH3-5. Green frame, The site of jasmonate. Blue frame, The site of L-alpha-amino acid.

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