水稻生长调节因子GRF基因家族的鉴定及生物信息学分析

doi:10.13304/j.nykjdb.2024.0328

摘要/Abstract

摘要：

生长调节因子（growth regulating factor，GRF）作为一种植物特有的转录因子，在植物生长发育过程中发挥重要作用。为鉴定水稻GRF基因家族成员，通过生物信息学方法对其蛋白的理化性质、二级结构、三级结构、亚细胞定位、基因结构、顺式作用元件、染色体定位、进化关系和共线性进行分析。结果表明，共鉴定出12个水稻GRF基因，其蛋白长度为211~456 aa，分子量为22.3~49.3 kD，等电点为4.78~9.85，亚细胞定位主要定位于细胞核；水稻GRF基因含有2~5个外显子，启动子顺式作用元件主要与激素调控、胁迫响应、光响应相关；12个GRF基因不均匀地分布在2、3、4、6、7、11、12号染色体上；水稻GRF基因与玉米亲缘关系较近，与番茄、拟南芥同源性较低；水稻GRF基因不存在串联重复事件，大片段重复是其主要扩张方式。以上研究结果为深入研究水稻GRF基因功能提供了理论依据。

关键词: 水稻, 生长调节因子, GRF基因家族, 生物信息学

Abstract:

As a plant-specific transcription factor， growth regulating factor （GRF） plays an important role in plant growth and development. To identify the members of the rice GRF gene family， protein physicochemical properties， sequence comparison， secondary and tertiary structure prediction， subcellular localisation， gene structure， cis-acting elements， chromosomal localisation， evolutionary tree construction and covariance were analyzed using the bioinformatics methods. The results showed that 12 GRF genes were identified. The length of rice GRF proteins was 211~456 aa， the molecular weight was 22.3~49.3 kD， the isoelectric point was 4.78~9.85， and the subcellular localisation was mainly located in the nucleus. The rice GRF genes contained 2~5 exons， and the promoter elements were mainly related to hormone regulation， stress response and light response. 12 GRF genes were unevenly distributed on chromosomes 2， 3， 4， 6， 7， 11 and 12. GRF genes in rice were closely related to maize， and had low homology with tomato and Arabidopsis. There were no tandem duplication events in the rice GRF genes， and large segmental duplications were the main expansion modes. Above results provided a theoretical basis for the in-depth study of rice GRF gene function.

Key words: rice, growth regulating factor, GRF gene family, bioinformatics

中图分类号:

S511

刘之恩, 何勇, 王志成, 詹逍康, 王廷宝, 刘耀威, 田志宏. 水稻生长调节因子GRF基因家族的鉴定及生物信息学分析[J]. 中国农业科技导报, 2025, 27(8): 18-27.

Zhien LIU, Yong HE, Zhicheng WANG, Xiaokang ZHAN, Tingbao WANG, Yaowei LIU, Zhihong TIAN. Identification and Bioinformatics Analysis of Growth Regulating Factor GRF Gene Family in Rice[J]. Journal of Agricultural Science and Technology, 2025, 27(8): 18-27.

图/表 10

表1 水稻GRF基因编码蛋白的理化性质

Table 1 Physicochemical properties of proteins encoded by the GRF genes in rice

基因ID Gene ID	氨基酸长度 Amino acids length/aa	分子量 Molecular weight/Da	等电点 pI	不稳定指数 Instability index	脂肪酸指数 Aliphatic index	平均亲水系数 GRAVY
Os02g0776900	397	43 565.42	7.10	58.65	45.21	-0.817
Os06g0204800	301	32 227.89	7.76	49.63	58.01	-0.569
Os04g0600900	384	41 286.02	6.41	51.04	61.64	-0.428
Os02g0701300	394	41 835.59	8.57	60.17	64.57	-0.448
Os06g0116200	348	37 814.97	8.56	57.48	55.34	-0.665
Os03g0729500	456	49 361.83	6.97	57.27	66.82	-0.534
Os12g0484900	413	44 171.36	9.25	50.44	70.17	-0.499
Os11g0551900	409	43 896.85	8.94	59.17	60.32	-0.630
Os03g0674700	426	47 852.03	9.30	58.65	57.11	-0.816
Os02g0678800	211	22 310.32	9.35	47.08	68.96	-0.362
Os07g0467500	269	28 000.97	4.78	63.81	59.55	-0.645
Os04g0574500	236	24 970.55	9.85	49.81	75.30	-0.200

图1 水稻GRF蛋白的多序列比对

Fig. 1 Multi-sequence comparison of GRF proteins in rice

图2 水稻GRF蛋白的二级结构预测注：蓝色—α螺旋；红色—延伸链；绿色—β转角；紫色—无规则卷曲。

Fig. 2 Secondary structure prediction of GRF proteins in riceNote： Blue—Alpha helix； Red—Extended strand； Green—Beta turn； Purple—Random coil.

表2 水稻GRF蛋白二级结构和亚细胞定位

Table 2 Secondary structure analysis and subcellular localization of GRF proteins in rice

基因ID Gene ID	α螺旋 Alpha helix/%	延伸链 Extended strand/%	β转角 Beta turn/%	无规则卷曲 Random coil/%	亚细胞定位 Subcellular localization
Os02g0776900	23.93	12.34	6.30	57.43	细胞核Nucleus
Os06g0204800	28.90	4.98	2.99	63.12	细胞核Nucleus
Os04g0600900	20.31	5.73	3.39	70.57	细胞核Nucleus
Os02g0701300	22.59	7.87	3.30	66.24	细胞核Nucleus
Os06g0116200	14.66	9.48	4.60	71.26	细胞核Nucleus
Os03g0729500	19.96	10.53	1.97	67.54	细胞核Nucleus
Os12g0484900	18.73	11.92	2.19	67.15	细胞核Nucleus
Os11g0551900	19.07	13.45	6.60	60.88	细胞核Nucleus
Os03g0674700	27.70	9.15	4.69	58.45	细胞核Nucleus
Os02g0678800	30.33	8.53	3.79	57.35	细胞核Nucleus
Os07g0467500	33.46	11.90	2.97	51.67	细胞核/叶绿体 Nucleus/chloroplast
Os04g0574500	19.49	14.83	7.20	58.47	叶绿体/线粒体 Chloroplast/mitochondrion

图3 水稻GRF蛋白的三级结构预测注：图中蛋白质三级结构按照氨基端-羧基端进行着色。

Fig. 3 Tertiary structure prediction of GRF proteins in riceNote： The protein tertiary structure in the figure is colored in the order of amino terminus to carboxyl terminus.

图4 水稻GRF基因编码蛋白的保守基序分析和基因结构分析

Fig. 4 Analysis of conserved motif and gene structure of GRF genes and coden proteins in rice

图5 水稻GRF基因启动子区的顺式作用元件

Fig. 5 Cis-acting elements in promoters region of GRF genes in rice

图6 不同物种GRF蛋白的系统进化树注：Os—粳稻；GRMZM—玉米；AT—拟南芥；Solyc—番茄；BG—籼稻。

Fig. 6 Phylogenetic tree of GRF proteins from different speciesNote： Os—Oryza sativa subsp. japonica； GRMZM—Zea mays； At—Arabidopsis thaliana； Solyc—Solanum lycopersicum； BG—Oryza sativa subsp. indica.

图7 水稻GRF基因在染色体上的分布

Fig. 7 Chromosomal distribution of GRF genes in rice

图8 水稻GRF基因的共线性分析注：右侧蓝色到红色刻度表示0.1 Mb范围内基因的数量。

Fig. 8 Collinearity analysis of GRF genes in riceNote： The blue to red scale on the right indicates the number of genes within 0.1 Mb.

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