Identification and Expression Analysis of the Rice Lateral Root Development Mutant lrp1

doi:10.16819/j.1001-7216.2026.241211

Abstract

Abstract:

【Objective】This study aims to investigate the function of the OsLRP1 gene (Os01g72490) in rice lateral root development by phenotypic characterization and expression analysis of the lrp1 mutant.【Method】The lrp1 mutant was first identified through PCR amplification and sequencing. Bioinformatics methods were then employed to analyze the protein structure, conserved domains, transmembrane domains, and signal peptides of OsLRP1. Multiple sequence alignment and phylogenetic tree construction were conducted to explore the evolutionary relationship between OsLRP1 and LRP1 proteins from other species. Quantitative real-time PCR (qRT-PCR) was used to detect the expression levels of OsLRP1 in different rice tissues. Confocal laser scanning microscopy was utilized to observe the subcellular localization of the OsLRP1 protein. Finally, an auxin treatment experiment was performed to determine whether the regulation of lateral root development by OsLRP1 is mediated by auxin.【Result】Phenotypic analysis revealed that compared with the wild-type Zhonghua 11, the lrp1 mutant exhibited a 32% reduction in lateral root primordia number and a 21% decrease in lateral root number. At the maturity stage, the panicle length and 100-grain weight of lrp1 were reduced by 12.5% and 7.4%, respectively, compared with the wild-type. Bioinformatics analysis showed that the OsLRP1 gene belongs to the SHI transcription factor family, encoding a protein of 340 amino acids. Conserved domain analysis indicated that it is a member of the DUF (Domain of Unknown Function) family. No signal peptide or transmembrane domain was detected in the OsLRP1 protein. Subcellular localization in tobacco demonstrated that the OsLRP1 protein is localized in the nucleus. qRT-PCR results indicated that OsLRP1 is expressed in roots, stems, and leaves, with the highest expression level in leaves. Two auxin response elements (AuxREs) were identified within the 1-kb promoter region upstream of OsLRP1. The auxin treatment experiment confirmed that lateral root development in the lrp1 mutant is affected by auxin.【Conclusion】In summary, OsLRP1 regulates lateral root development in rice in an auxin signaling dependent manner and is involved in rice growth, development, and stress responses, further elucidating its crucial role in rice lateral root development.

Key words: rice, root development, lateral root primordium, LRP1 protein

摘要：

【目的】本研究旨在通过对水稻OsLRP1(Os01g72490)突变体lrp1的表型鉴定与表达水平分析，探究OsLRP1基因在水稻侧根发育过程中的功能。【方法】首先通过PCR扩增及测序完成lrp1突变体的鉴定。其次，通过生物信息学方法分析OsLRP1蛋白结构、保守结构域、跨膜结构域、信号肽，并通过多序列比对及进化树构建，分析OsLRP1蛋白与其他物种中LRP1蛋白的系统发育关系；通过qRT-PCR技术，检测OsLRP1在水稻不同组织中的表达水平。借助激光共聚焦显微镜，观察OsLRP1蛋白在细胞内的精确定位。然后通过生长素处理实验验证OsLRP1对侧根发育的调控是否受生长素影响。【结果】表型鉴定结果显示，相较于野生型中花11，lrp1侧根原基数目减少32%，侧根数目减少21%；成熟期时，lrp1穗长和百粒重较野生型分别减少12.5%和7.4%；生物信息学分析结果显示OsLRP1基因属于SHI转录因子，编码340个氨基酸。保守结构域分析结果表明，其属于DUF(Domain Of Unknown Function)家族；OsLRP1蛋白无信号肽及跨膜结构。烟草亚细胞定位结果显示OsLRP1蛋白定位于细胞核。qRT-PCR结果显示，OsLRP1在根、茎和叶中均有表达，且在叶中表达量最高。在OsLRP1上游1 kb启动子区域内发现两种生长素响应元件AuxRE，生长素处理实验证实lrp1突变体侧根发育受生长素影响。【结论】综上所述，OsLRP1依赖生长素信号途径调控水稻侧根发育，参与水稻生长发育及抗逆性，进一步揭示了该基因在水稻侧根发育中的关键作用。

关键词: 水稻, 根系发育, 侧根原基, LRP1蛋白

YI Haokun, LUO Yanmu, HUANG Min, DU Hewei, LI Manfei. Identification and Expression Analysis of the Rice Lateral Root Development Mutant lrp1[J]. Chinese Journal OF Rice Science, 2026, 40(3): 302-311.

易浩昆, 罗堰木, 黄敏, 杜何为, 李曼菲. 水稻侧根发育突变体lrp1鉴定及表达分析[J]. 中国水稻科学, 2026, 40(3): 302-311.

Figures/Tables 10

Table 1. Websites used for bioinformatics analysis

名称 Name	网址 URL
TMHMM-2.0	https://services.healthtech.dtu.dk/services/TMHMM-2.0/
Expasy	https://www.expasy.org/
InterPro	https://www.ebi.ac.uk/interpro/
NPS@:SOPMA	https://npsa.lyon.inserm.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_sopma.html
NetPhos-3.1	https://services.healthtech.dtu.dk/services/NetPhos-3.1/
SignalP 6.0 Server	https://services.healthtech.dtu.dk/services/SignalP-6.0/
NCBI	https://www.ncbi.nlm.nih.gov/
WoLF PSORT II	https://wolfpsort.hgc.jp/
iPSORT	https://ipsort.hgc.jp/
New PLACE	https://www.dna.affrc.go.jp/PLACE/

Fig. 1. Phylogenetic tree of the LRP1 protein across different species The scale bar in the figure represents the unit length of the number of differences between sequences

Fig. 2. PCR amplification electrophoresis of mutant lrp1 (A) and information of mutant targets(B) In figure A, the two leftmost bands were amplified using the genomic DNA of Zhonghua 11 as the template, while the two rightmost bands were amplified using the genomic DNA of lrp1 as the template. M, Marker.

Table 2. Growth periods of the lrp1 mutant d

时期 Period	中花11 Zhonghua 11	lrp1	P值 P-value
出芽期Budding stage	2.9±0.4	3.1±0.4	0.1047
幼苗期Seedling stage	10.3±0.4	10.3±0.5	0.7315
分蘖期Tillering stage	40.4±0.5	40.5±0.7	0.5988
拔节期Jointing stage	60.4±0.5	60.5±0.5	0.5309
抽穗期Heading stage	72.2±0.5	72.3±0.6	0.7699
扬花期Anthesis stage	85.3±0.5	87.1±0.5	6.19×e⁻¹⁵
孕穗期Booting stage	100.3±0.5	102.3±0.5	4.98×e⁻¹⁶
灌浆期Grain filling stage	120.3±0.4	122.4±0.5	8.71×e⁻¹⁷
成熟期Maturity stage	152.3±0.4	154.3±0.4	8.19×e⁻¹⁷

Fig. 3. Prediction of OsLRP1 protein domain

Fig. 4. Analysis of cis-acting elements in the promoter region of OsLRP1

Fig. 5. Root phenotype of lrp1 at the tillering stage and panicle phenotype at the maturity stage A, Whole-plant phenotypes; B, Root system phenotypes; C, Methylene blue staining results (black dots indicate lateral root primordia); D, Panicle phenotypes; E, Statistical graph of lateral root number; F, Statistical graph of lateral root primordia number; G, Statistical graph of panicle length; H, Statistical graph of 100-grain weight. In figure C, Red circles and white arrows indicate the positions of lateral root primordia.

Fig. 6. Results of subcellular localization of OsLRP1 protein In figures A and D, the red dashed lines indicate the cell contours of tobacco cells. In figures B and C, the white dashed lines indicate the cell contours of tobacco cells. DAPI is a specific nuclear dye, and the blue fluorescence signals mark the positions of the nuclei.

Fig. 7. Relative expression level of OsLRP1

Fig. 8. Results of auxin treatment experiments of lrp1 In figure A, WT represents normally grown Zhonghua 11, lrp1control represents normally grown lrp1 mutant, and lrp1IAA represents IAA-treated lrp1 mutant. Each group of three plants corresponds to the labels below, Bar = 2 cm. Figure B is a bar chart of lateral root number, figure C is a bar chart of lateral root length, and figure D is a bar chart of plant height.

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