Genome-wide Identification and Bioinformatics Analysis of GRAS Gene Family in Maize

doi:10.13304/j.nykjdb.2023.0551

Abstract

Abstract:

GRAS gene family is a kind of transcription factor widely distributed in plants， which plays an important role in plant growth and development， biological and abiotic stress， light signal， hormone signal response and other processes. The physicochemical properties， chromosome localization， phylogeny and cis-acting elements of GRAS gene family in maize were analyzed. The results showed that a total of 49 ZmGRAS genes were identified in the whole genome of maize， which were unevenly distributed on chromosomes 1 to 10， and the physicochemical properties of the encoded proteins were very different， which might play a role in different microenvironments. Phylogenetic analysis classified GRAS proteins into 8 subfamilies， which might play important roles in regulating growth and development and stress response. The promoter regions of GRAS genes in maize contained variety of cis-acting elements such as hormone response， light response and stress response， which might be involved in important response such as hormone and stress. Collinear analysis showed that genes with collinear relationships might be the result of replication of chromosome segments， and belonged to the same subfamily with similar structure and function. The identification and analysis of GRAS gene family in maize provided the basis for further research on the function of GRAS genes and their response mechanisms to stress in maize.

Key words: maize, GRAS gene family, complete genome identification, bioinformatics, analysis

摘要：

GRAS基因家族是植物中广泛存在的一类转录因子，在植物生长发育、生物和非生物逆境胁迫、光信号和激素信号应答等多个过程中发挥重要作用。对玉米GRAS基因家族成员的理化性质、染色体定位、系统发育、顺式作用元件等特征进行了分析。结果表明，在玉米全基因组中共鉴定出49个ZmGRAS基因，不均匀地分布于1~10号染色体上，编码蛋白质理化性质差异较大，可能在不同的微环境下发挥作用。系统进化分析将GRAS蛋白分为8个亚家族，可能在调节自身生长发育、逆境应答等过程中具有重要作用。玉米GRAS基因家族的启动子区含有激素应答、光响应、胁迫应答等多种顺式作用元件，推测其可能响应激素、胁迫等多种信号。共线性分析显示，具有共线性关系的基因可能是染色体片段复制的结果，且属于同一亚家族，具有相似的结构和功能。研究结果为进一步研究玉米GRAS基因的功能和逆境胁迫响应机制提供了依据。

关键词: 玉米, GRAS基因家族, 全基因组鉴定, 生物信息学, 分析

CLC Number:

S513

Zhanqing WU, Wei CHEN, Zhan ZHAO, Hailiang XU, Haoyuan LI, Xingxing PENG, Dongxu CHEN, Mingyue ZHANG. Genome-wide Identification and Bioinformatics Analysis of GRAS Gene Family in Maize[J]. Journal of Agricultural Science and Technology, 2024, 26(3): 15-25.

吴占清, 陈威, 赵展, 许海良, 李豪远, 彭星星, 陈东旭, 张明月. 玉米GRAS基因家族的全基因组鉴定及生物信息学分析[J]. 中国农业科技导报, 2024, 26(3): 15-25.

Figures/Tables 6

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基因名称 Gene name	基因ID Gene ID	氨基酸长度Amino acids length/aa	分子量Molecular weight/Da	等电点PI	带负电荷残基总数 Total number of negatively charged residues	带正电荷残基总数 Total number of positively charged residues	不稳定指数 Instability index	脂肪族氨基酸指数 Aliphatic index	平均疏水性 Grand average of hydropathicity
ZmGRAS1	Zm00001eb216610	625	65 742.60	5.18	70	50	46.59	75.66	-0.204
ZmGRAS2	Zm00001eb107910	554	60 835.57	5.84	68	52	53.95	83.83	-0.302
ZmGRAS3	Zm00001eb325750	558	60 991.58	5.71	69	52	55.68	82.17	-0.301
ZmGRAS4	Zm00001eb106490	570	64 511.14	5.99	73	64	46.97	83.72	-0.475
ZmGRAS5	Zm00001eb027720	542	59 914.41	5.76	58	43	48.73	83.86	-0.245
ZmGRAS6	Zm00001eb170110	775	82 511.74	6.19	73	62	63.30	74.27	-0.245
ZmGRAS7	Zm00001eb195650	668	71 162.84	6.15	66	53	57.35	85.21	-0.197
ZmGRAS8	Zm00001eb288400	561	62 826.62	4.92	79	54	46.74	81.23	-0.340
ZmGRAS9	Zm00001eb141310	447	48 471.03	6.36	55	50	54.57	89.44	-0.145
ZmGRAS10	Zm00001eb093670	678	72 083.67	6.18	67	55	56.48	87.23	-0.168
ZmGRAS11	Zm00001eb363140	449	48 889.56	6.26	56	50	56.39	89.49	-0.133
ZmGRAS12	Zm00001eb148290	809	89 139.89	6.06	101	88	44.93	77.00	-0.344
ZmGRAS13	Zm00001eb378590	616	65 472.30	6.30	70	63	45.04	71.62	-0.240
ZmGRAS14	Zm00001eb136350	710	78 391.49	5.30	92	73	53.77	79.77	-0.339
ZmGRAS15	Zm00001eb324600	452	48 411.17	6.05	55	49	58.80	96.26	-0.044
ZmGRAS16	Zm00001eb164530	765	84 654.31	5.30	103	78	49.74	73.02	-0.392
ZmGRAS17	Zm00001eb055700	551	59 842.10	5.20	63	47	56.67	86.03	-0.091
ZmGRAS18	Zm00001eb215870	569	61 233.71	5.08	63	44	57.67	85.59	-0.056
ZmGRAS19	Zm00001eb344400	508	56 088.05	5.91	55	43	35.75	90.08	-0.105
ZmGRAS20	Zm00001eb164480	642	71 250.62	6.67	84	80	52.59	79.63	-0.405
ZmGRAS21	Zm00001eb164490	666	73 486.54	5.51	93	76	51.16	74.25	-0.425
ZmGRAS22	Zm00001eb326020	592	63 904.56	5.67	64	50	58.88	68.06	-0.370
ZmGRAS23	Zm00001eb108250	456	49 134.09	5.32	50	35	40.45	90.99	0.057
ZmGRAS24	Zm00001eb011560	564	59 835.16	5.12	65	44	43.97	75.30	-0.152
ZmGRAS25	Zm00001eb326210	456	49 478.48	5.38	51	36	39.36	89.06	0.011
ZmGRAS26	Zm00001eb108090	586	63 755.58	5.49	66	53	59.45	70.56	-0.343
ZmGRAS27	Zm00001eb081760	607	66 678.45	6.04	77	67	47.34	80.97	-0.287
ZmGRAS28	Zm00001eb020850	630	67 547.26	6.15	65	53	66.00	63.40	-0.416
ZmGRAS29	Zm00001eb073130	623	65 570.98	6.15	60	54	52.23	87.26	-0.116
ZmGRAS30	Zm00001eb187310	607	63 032.09	8.75	54	59	46.96	84.93	-0.109
ZmGRAS31	Zm00001eb428430	623	65 303.67	6.34	58	54	48.36	84.11	-0.137
ZmGRAS32	Zm00001eb164470	645	72 101.21	6.37	78	70	47.76	80.96	-0.356
ZmGRAS33	Zm00001eb165340	639	72 513.56	6.09	85	75	45.77	81.61	-0.384
ZmGRAS34	Zm00001eb236120	416	43 484.86	5.43	48	35	32.57	88.92	-0.042
ZmGRAS35	Zm00001eb291030	497	52 002.72	5.80	51	38	46.41	82.39	-0.007
ZmGRAS36	Zm00001eb291930	426	45 514.68	6.09	48	43	47.88	87.37	-0.100
ZmGRAS37	Zm00001eb115950	599	67 026.72	6.12	76	68	50.16	74.89	-0.375
ZmGRAS38	Zm00001eb074460	721	75 225.55	5.74	62	46	47.98	82.98	-0.050
ZmGRAS39	Zm00001eb429450	718	75 350.35	5.72	64	47	50.61	81.82	-0.081
ZmGRAS40	Zm00001eb186770	708	73 942.10	5.63	65	48	45.89	87.67	0.004
ZmGRAS41	Zm00001eb000470	481	51 254.82	6.10	48	37	41.79	95.88	0.099
ZmGRAS42	Zm00001eb196430	487	51 456.32	6.18	59	53	54.58	89.08	-0.151
ZmGRAS43	Zm00001eb249840	706	73 961.86	5.47	66	44	45.87	85.55	0.001
ZmGRAS44	Zm00001eb202270	473	51 700.38	4.73	62	32	52.48	88.12	0.013
ZmGRAS45	Zm00001eb326550	306	33 520.48	6.05	30	25	33.94	97.32	0.086
ZmGRAS46	Zm00001eb139470	492	52 614.47	5.15	58	39	47.00	87.11	-0.015
ZmGRAS47	Zm00001eb019640	526	54 677.28	6.72	53	51	51.38	76.24	-0.189
ZmGRAS48	Zm00001eb405080	235	25 649.61	6.55	27	25	48.23	99.66	0.063
ZmGRAS49	Zm00001eb002990	313	33 288.60	9.66	25	36	54.58	86.77	0.034

基因名称 Gene name	基因ID Gene ID	氨基酸长度Amino acids length/aa	分子量Molecular weight/Da	等电点PI	带负电荷残基总数 Total number of negatively charged residues	带正电荷残基总数 Total number of positively charged residues	不稳定指数 Instability index	脂肪族氨基酸指数 Aliphatic index	平均疏水性 Grand average of hydropathicity
ZmGRAS1	Zm00001eb216610	625	65 742.60	5.18	70	50	46.59	75.66	-0.204
ZmGRAS2	Zm00001eb107910	554	60 835.57	5.84	68	52	53.95	83.83	-0.302
ZmGRAS3	Zm00001eb325750	558	60 991.58	5.71	69	52	55.68	82.17	-0.301
ZmGRAS4	Zm00001eb106490	570	64 511.14	5.99	73	64	46.97	83.72	-0.475
ZmGRAS5	Zm00001eb027720	542	59 914.41	5.76	58	43	48.73	83.86	-0.245
ZmGRAS6	Zm00001eb170110	775	82 511.74	6.19	73	62	63.30	74.27	-0.245
ZmGRAS7	Zm00001eb195650	668	71 162.84	6.15	66	53	57.35	85.21	-0.197
ZmGRAS8	Zm00001eb288400	561	62 826.62	4.92	79	54	46.74	81.23	-0.340
ZmGRAS9	Zm00001eb141310	447	48 471.03	6.36	55	50	54.57	89.44	-0.145
ZmGRAS10	Zm00001eb093670	678	72 083.67	6.18	67	55	56.48	87.23	-0.168
ZmGRAS11	Zm00001eb363140	449	48 889.56	6.26	56	50	56.39	89.49	-0.133
ZmGRAS12	Zm00001eb148290	809	89 139.89	6.06	101	88	44.93	77.00	-0.344
ZmGRAS13	Zm00001eb378590	616	65 472.30	6.30	70	63	45.04	71.62	-0.240
ZmGRAS14	Zm00001eb136350	710	78 391.49	5.30	92	73	53.77	79.77	-0.339
ZmGRAS15	Zm00001eb324600	452	48 411.17	6.05	55	49	58.80	96.26	-0.044
ZmGRAS16	Zm00001eb164530	765	84 654.31	5.30	103	78	49.74	73.02	-0.392
ZmGRAS17	Zm00001eb055700	551	59 842.10	5.20	63	47	56.67	86.03	-0.091
ZmGRAS18	Zm00001eb215870	569	61 233.71	5.08	63	44	57.67	85.59	-0.056
ZmGRAS19	Zm00001eb344400	508	56 088.05	5.91	55	43	35.75	90.08	-0.105
ZmGRAS20	Zm00001eb164480	642	71 250.62	6.67	84	80	52.59	79.63	-0.405
ZmGRAS21	Zm00001eb164490	666	73 486.54	5.51	93	76	51.16	74.25	-0.425
ZmGRAS22	Zm00001eb326020	592	63 904.56	5.67	64	50	58.88	68.06	-0.370
ZmGRAS23	Zm00001eb108250	456	49 134.09	5.32	50	35	40.45	90.99	0.057
ZmGRAS24	Zm00001eb011560	564	59 835.16	5.12	65	44	43.97	75.30	-0.152
ZmGRAS25	Zm00001eb326210	456	49 478.48	5.38	51	36	39.36	89.06	0.011
ZmGRAS26	Zm00001eb108090	586	63 755.58	5.49	66	53	59.45	70.56	-0.343
ZmGRAS27	Zm00001eb081760	607	66 678.45	6.04	77	67	47.34	80.97	-0.287
ZmGRAS28	Zm00001eb020850	630	67 547.26	6.15	65	53	66.00	63.40	-0.416
ZmGRAS29	Zm00001eb073130	623	65 570.98	6.15	60	54	52.23	87.26	-0.116
ZmGRAS30	Zm00001eb187310	607	63 032.09	8.75	54	59	46.96	84.93	-0.109
ZmGRAS31	Zm00001eb428430	623	65 303.67	6.34	58	54	48.36	84.11	-0.137
ZmGRAS32	Zm00001eb164470	645	72 101.21	6.37	78	70	47.76	80.96	-0.356
ZmGRAS33	Zm00001eb165340	639	72 513.56	6.09	85	75	45.77	81.61	-0.384
ZmGRAS34	Zm00001eb236120	416	43 484.86	5.43	48	35	32.57	88.92	-0.042
ZmGRAS35	Zm00001eb291030	497	52 002.72	5.80	51	38	46.41	82.39	-0.007
ZmGRAS36	Zm00001eb291930	426	45 514.68	6.09	48	43	47.88	87.37	-0.100
ZmGRAS37	Zm00001eb115950	599	67 026.72	6.12	76	68	50.16	74.89	-0.375
ZmGRAS38	Zm00001eb074460	721	75 225.55	5.74	62	46	47.98	82.98	-0.050
ZmGRAS39	Zm00001eb429450	718	75 350.35	5.72	64	47	50.61	81.82	-0.081
ZmGRAS40	Zm00001eb186770	708	73 942.10	5.63	65	48	45.89	87.67	0.004
ZmGRAS41	Zm00001eb000470	481	51 254.82	6.10	48	37	41.79	95.88	0.099
ZmGRAS42	Zm00001eb196430	487	51 456.32	6.18	59	53	54.58	89.08	-0.151
ZmGRAS43	Zm00001eb249840	706	73 961.86	5.47	66	44	45.87	85.55	0.001
ZmGRAS44	Zm00001eb202270	473	51 700.38	4.73	62	32	52.48	88.12	0.013
ZmGRAS45	Zm00001eb326550	306	33 520.48	6.05	30	25	33.94	97.32	0.086
ZmGRAS46	Zm00001eb139470	492	52 614.47	5.15	58	39	47.00	87.11	-0.015
ZmGRAS47	Zm00001eb019640	526	54 677.28	6.72	53	51	51.38	76.24	-0.189
ZmGRAS48	Zm00001eb405080	235	25 649.61	6.55	27	25	48.23	99.66	0.063
ZmGRAS49	Zm00001eb002990	313	33 288.60	9.66	25	36	54.58	86.77	0.034

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