Genome-wide Identification and Comprehensive Analysis of IDD Gene Family in Rice

doi:10.16819/j.1001-7216.2024.240101

Abstract

Abstract:

【Objective】To clarify the characteristics and verify the expression patterns of IDD gene family members in rice, which are plant-specific transcription factors, in order to further investigate the biological functions of OsIDD.【Method】The IDD family members in rice were identified using Pfam, followed by a comprehensive analysis of their nucleic acid and protein sequence features, protein structure, phylogeny, collinearity, and promoter elements. RT-PCR was employed to verify the expression patterns of the OsIDD gene in various tissues, under different hormone treatments, and in response to various abiotic stresses.【Result】The OsIDD family consists of 15 members falling into three subfamilies, which are unevenly distributed across the chromosomes. All members possess nuclear localization signals and highly conserved ID structural domains at the N-terminus. Multiple sequence alignment and motif analysis indicate that these sequences are relatively conserved among different types. Collinearity analysis with the ZmIDD gene family reveals a high degree of homology between the two species. Microarray and RT-PCR analyses showed that OsIDD is predominantly expressed in the panicle and developing endosperm, with its promoter sequences containing hormone and stress-responsive cis-elements.【Conclusion】A comprehensive analysis of the 15 OsIDD members demonstrated structural conservation, strong collinearity with ZmIDD, and high expression levels in panicle and developing endosperm. These findings suggest that OsIDD may be involved in the response to different hormones and various abiotic stresses.

Key words: rice, IDD gene family, comprehensive analysis, expression pattern analysis

摘要：

【目的】明确植物特异转录因子OsIDD基因家族成员特征特性，验证其表达模式，为深入研究水稻IDD基因家族生物学功能奠定基础。【方法】通过Pfam鉴定与明确水稻IDD家族成员，对其核酸与蛋白序列特征、蛋白结构、系统发育与共线性、启动子元件进行综合分析；通过RT-PCR技术验证OsIDD基因在各组织、不同激素处理及不同非生物胁迫下的表达模式。【结果】发现OsIDD家族具有15个成员，为3个亚家族，在染色体上呈不均匀分布，N端均具有核定位信号及高度保守的ID结构域。多重序列比对及motif分析表明其在各个类型中相对保守，与玉米IDD基因家族共线性分析表明两个物种间具有高度同源性。芯片及RT-PCR分析发现OsIDD主要在穗及发育胚乳中表达量较高，其启动子序列均包含激素/胁迫响应顺式元件。【结论】本研究对15个OsIDD成员进行了综合分析，OsIDD结构保守，与ZmIDD共线性强，主要在穗及发育胚乳组织中高表达，可能参与不同激素及多种非生物逆境胁迫响应过程。

关键词: 水稻, IDD基因家族, 综合分析, 表达模式分析

ZHONG Zhihu, QIN Lu, LI Zhili, YANG Zhen, HE Xiaopeng, CAI Yicong. Genome-wide Identification and Comprehensive Analysis of IDD Gene Family in Rice[J]. Chinese Journal OF Rice Science, 2024, 38(6): 638-652.

钟智慧, 秦璐, 黎志力, 杨珍, 贺晓鹏, 蔡怡聪. 水稻IDD基因家族的全基因组鉴定及综合分析[J]. 中国水稻科学, 2024, 38(6): 638-652.

Figures/Tables 14

References 39

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引物名称 Primer name	正向引物序列 Forward sequence (5’-3’)	反向引物序列 Revers sequence(5’-3’)
Actin-RT	CGGGAAATTGTGAGGGACAT	AGGAAGGCTGGAAGAGGACC
OsID1-RT	CTCTTCTCCAGGAAGGACAGCC	GTAGTAGTGATGCTGCTGCTGTTG
OsIDD1-RT	GTTCTGGTCGCGCTGGAAC	GACACAATCATTAGGAGCGGCA
OsIDD2-RT	CGGCAACCCAGATCCTGAG	CTGGTCTCGCTGGAACCC
OsIDD3-RT	GGAAACCCAAATCCAGATGCG	CCGCTGGAACCCCTTGTTG
OsIDD4-RT	CCTTACCAGACCCGGACGC	GTTCTGCTCCCGCTGGAAC
OsIDD5-RT	GGATGAGCAAGAGGTGGTTG	ATCCAGCAGGTTTGAGTCCT
OsIDD6-RT	CCCGGGAATCCAAATCCTGATGC	CTGCTCCCTCTGGAACCCC
OsIDD7-RT	GGAAACCCAGATCCAGATGTTGAG	GGAGGTTCTGGTCTCTCTGGAAG
OsIDD8-RT	CGGCACACCAGATCCGG	CAGGTTCTGGTCTCGCTGG
OsIDD9-RT	GTCTTCTCCAGGCGCGAC	CAGAGCGGAGGTGACCG
OsIDD10-RT	CAACCAACCCAAACCCGGAC	GGTTCTGCTCCCGCTGG
OsIDD11-RT	GCAACCCAGACCCGGAAG	CTGCAGGTTCTGGTCCCTC
OsIDD12-RT	CAGATCACCTGCTACAGCTG	TGACGACGGACGAGACGTA
OsIDD13-RT	GCACGCCAGACCCGGAC	CTGCAGGTTCTGGTCTCGC
OsIDD14-RT	GCGTCTTCTCCCGAGTGG	GGATGACCGGCAGCGTC

引物名称 Primer name	正向引物序列 Forward sequence (5’-3’)	反向引物序列 Revers sequence(5’-3’)
Actin-RT	CGGGAAATTGTGAGGGACAT	AGGAAGGCTGGAAGAGGACC
OsID1-RT	CTCTTCTCCAGGAAGGACAGCC	GTAGTAGTGATGCTGCTGCTGTTG
OsIDD1-RT	GTTCTGGTCGCGCTGGAAC	GACACAATCATTAGGAGCGGCA
OsIDD2-RT	CGGCAACCCAGATCCTGAG	CTGGTCTCGCTGGAACCC
OsIDD3-RT	GGAAACCCAAATCCAGATGCG	CCGCTGGAACCCCTTGTTG
OsIDD4-RT	CCTTACCAGACCCGGACGC	GTTCTGCTCCCGCTGGAAC
OsIDD5-RT	GGATGAGCAAGAGGTGGTTG	ATCCAGCAGGTTTGAGTCCT
OsIDD6-RT	CCCGGGAATCCAAATCCTGATGC	CTGCTCCCTCTGGAACCCC
OsIDD7-RT	GGAAACCCAGATCCAGATGTTGAG	GGAGGTTCTGGTCTCTCTGGAAG
OsIDD8-RT	CGGCACACCAGATCCGG	CAGGTTCTGGTCTCGCTGG
OsIDD9-RT	GTCTTCTCCAGGCGCGAC	CAGAGCGGAGGTGACCG
OsIDD10-RT	CAACCAACCCAAACCCGGAC	GGTTCTGCTCCCGCTGG
OsIDD11-RT	GCAACCCAGACCCGGAAG	CTGCAGGTTCTGGTCCCTC
OsIDD12-RT	CAGATCACCTGCTACAGCTG	TGACGACGGACGAGACGTA
OsIDD13-RT	GCACGCCAGACCCGGAC	CTGCAGGTTCTGGTCTCGC
OsIDD14-RT	GCGTCTTCTCCCGAGTGG	GGATGACCGGCAGCGTC

名称 Name	染色体 Chr.	基因长度 Gene length	氨基酸数目 No. of amino acids	分子量 Molecular weight	理论等电点 Theoretical pI	蛋白质不稳定指数 Instability index	脂溶指数 Aliphatic index	亲水性平均系数 Grand average of hydropathicity	亚细胞定位预测 Predicted subcellular localization
OsID1	10	1230	409	44267.44	8.04870033	51.19	51.19	−0.467	细胞核Nucleus
OsIDD1	3	1659	552	57540.01	8.55090046	75.58	75.58	−0.486	细胞核Nucleus
OsIDD2	1	1464	487	51815.90	8.60980034	48.96	48.96	−0.527	细胞核Nucleus
OsIDD3	9	1608	535	54893.05	9.41469955	46.65	46.65	−0.460	细胞核Nucleus
OsIDD4	2	1848	615	63597.71	8.63129997	46.29	46.29	−0.497	细胞核Nucleus
OsIDD5	7	1902	633	67636.09	6.01849985	55.08	55.08	−0.567	细胞核Nucleus
OsIDD6	8	1659	552	57262.74	9.38479996	49.81	49.81	−0.500	细胞核Nucleus
OsIDD7	2	1479	492	54491.89	7.31449986	59.23	59.23	−0.697	细胞核Nucleus
OsIDD8	1	1488	495	51394.20	8.89400005	49.83	49.83	−0.293	细胞核Nucleus
OsIDD9	1	1431	476	50107.14	7.95529985	52.62	52.62	−0.265	细胞核Nucleus
OsIDD10	4	1842	613	63814.37	9.93620014	52.40	52.4	−0.476	细胞核Nucleus
OsIDD11	1	1614	537	57410.90	7.97130013	62.67	62.67	−0.703	细胞核Nucleus
OsIDD12	8	1602	533	56426.28	9.51509953	62.47	62.47	−0.467	细胞核Nucleus
OsIDD13	9	1515	504	53574.19	8.50090027	62.67	62.67	−0.459	细胞核Nucleus
OsIDD14	3	1317	438	45959.66	10.12440010	70.46	70.46	−0.509	细胞核Nucleus

名称 Name	染色体 Chr.	基因长度 Gene length	氨基酸数目 No. of amino acids	分子量 Molecular weight	理论等电点 Theoretical pI	蛋白质不稳定指数 Instability index	脂溶指数 Aliphatic index	亲水性平均系数 Grand average of hydropathicity	亚细胞定位预测 Predicted subcellular localization
OsID1	10	1230	409	44267.44	8.04870033	51.19	51.19	−0.467	细胞核Nucleus
OsIDD1	3	1659	552	57540.01	8.55090046	75.58	75.58	−0.486	细胞核Nucleus
OsIDD2	1	1464	487	51815.90	8.60980034	48.96	48.96	−0.527	细胞核Nucleus
OsIDD3	9	1608	535	54893.05	9.41469955	46.65	46.65	−0.460	细胞核Nucleus
OsIDD4	2	1848	615	63597.71	8.63129997	46.29	46.29	−0.497	细胞核Nucleus
OsIDD5	7	1902	633	67636.09	6.01849985	55.08	55.08	−0.567	细胞核Nucleus
OsIDD6	8	1659	552	57262.74	9.38479996	49.81	49.81	−0.500	细胞核Nucleus
OsIDD7	2	1479	492	54491.89	7.31449986	59.23	59.23	−0.697	细胞核Nucleus
OsIDD8	1	1488	495	51394.20	8.89400005	49.83	49.83	−0.293	细胞核Nucleus
OsIDD9	1	1431	476	50107.14	7.95529985	52.62	52.62	−0.265	细胞核Nucleus
OsIDD10	4	1842	613	63814.37	9.93620014	52.40	52.4	−0.476	细胞核Nucleus
OsIDD11	1	1614	537	57410.90	7.97130013	62.67	62.67	−0.703	细胞核Nucleus
OsIDD12	8	1602	533	56426.28	9.51509953	62.47	62.47	−0.467	细胞核Nucleus
OsIDD13	9	1515	504	53574.19	8.50090027	62.67	62.67	−0.459	细胞核Nucleus
OsIDD14	3	1317	438	45959.66	10.12440010	70.46	70.46	−0.509	细胞核Nucleus

基因名称 Gene name	α-螺旋 α-helix	延伸链 Extended strand	β-转角 β-turn	无规则卷曲 Random coil
OsID1	92 (22.49%)	89 (21.76%)	33 (8.07%)	195 (47.68%)
OsIDD1	78 (14.13%)	66 (11.96%)	31 (5.62%)	377 (68.30%)
OsIDD2	149 (30.60%)	42 (8.62%)	32 (6.57%)	264 (54.21%)
OsIDD3	97 (18.13%)	71 (13.27%)	30 (5.61%)	337 (62.99%)
OsIDD4	182 (29.59%)	77 (12.52%)	48 (7.80%)	308 (50.08%)
OsIDD5	132 (20.85%)	97 (15.32%)	50 (7.90%)	354 (55.92%)
OsIDD6	150 (27.17%)	87 (15.76%)	48 (8.70%)	267 (48.37%)
OsIDD7	99 (20.12%)	48 (9.76%)	16 (3.25%)	329 (66.87%)
OsIDD8	147 (29.70%)	64 (12.93%)	42 (8.48%)	242 (48.89%)
OsIDD9	112 (23.53%)	68 (14.29%)	45 (9.45%)	251 (52.73%)
OsIDD10	172 (28.06%)	82 (13.38%)	37 (6.04%)	322 (52.53%)
OsIDD11	195 (36.31%)	58 (10.80%)	46 (8.57%)	238 (44.32%)
OsIDD12	200 (37.52%)	69 (12.95%)	33 (6.19%)	231 (43.34%)
OsIDD13	225 (44.64%)	40 (7.94%)	13 (2.58%)	226 (44.84%)
OsIDD14	190 (43.38%)	41 (9.36%)	35 (7.99%)	172 (39.27%)