谷子III型PRX基因家族全基因组鉴定及干旱胁迫下表达分析

doi:10.3724/SP.J.1006.2022.14185

作物学报 ›› 2022, Vol. 48 ›› Issue (10): 2517-2532.doi: 10.3724/SP.J.1006.2022.14185

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

谷子III型PRX基因家族全基因组鉴定及干旱胁迫下表达分析

马鑫磊¹^,²(), 许瑞琪², 索晓曼², 李婧实¹^,², 顾鹏鹏¹^,², 姚锐¹^,², 林小虎¹^,²^,^*(), 高慧¹^,²^,^*()

¹河北省作物逆境生物学重点实验室, 河北秦皇岛 066004
²河北科技师范学院农学与生物科技学院, 河北秦皇岛 066004

收稿日期:2021-10-12 接受日期:2022-01-05 出版日期:2022-10-12 网络出版日期:2022-02-15
通讯作者: 林小虎,高慧
作者简介:第一作者联系方式: E-mail: maxinlei5966@126.com
基金资助:
国家“十三五”重点研发计划项目(2019YFD1001701-2);河北省现代农业产业技术体系创新团队(杂粮杂豆)项目(HBCT2018070404);河北省自然科学基金项目(C2019407089);河北省高等学校科学技术研究项目(QN2020154);河北省在读研究生创新能力培养资助项目(CXZZSS2021152)

Genome-wide identification of the Class III PRX gene family in foxtail millet (Setaria italica L.) and expression analysis under drought stress

MA Xin-Lei¹^,²(), XU Rui-Qi², SUO Xiao-Man², LI Jing-Shi¹^,², GU Peng-Peng¹^,², YAO Rui¹^,², LIN Xiao-Hu¹^,²^,^*(), GAO Hui¹^,²^,^*()

¹Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao 066004, Hebei, China
²College of Life Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066004, Hebei, China

Received:2021-10-12 Accepted:2022-01-05 Published:2022-10-12 Published online:2022-02-15
Contact: LIN Xiao-Hu,GAO Hui
Supported by:
National Key Research and Development Program of the 13th Five-Year Plan of China(2019YFD1001701-2);Modern Agricultural Industrial Technology System Innovation Team (Grain and Soybean) Project of Hebei Province(HBCT2018070404);National Natural Science Foundation of Hebei Province(C2019407089);Science and Technology Research Project of Higher Education in Hebei Province(QN2020154);Innovation Ability Training Project of Postgraduate Students in Hebei Province(CXZZSS2021152)

摘要/Abstract

摘要：

III型过氧化物酶(Class III peroxidase, PRX)是植物中特有的过氧化物酶家族, 在植物生长发育以及非生物胁迫中发挥重要作用。谷子作为C₄植物是禾本科抗逆研究的模式植物, 然而目前对于谷子中III型过氧化物酶家族基因功能鲜有报道。为探究谷子III型过氧化物酶基因家族(SitPRXs)在干旱胁迫和ABA诱导下的表达模式, 进行了全基因组表达分析。本研究利用生物信息学方法在谷子全基因组中鉴定出132个III型PRX基因家族成员, 并根据其在染色体上位置顺序依次命名为SitPRX1~SitPRX132。通过对谷子、拟南芥和水稻的系统进化分析将其分为5个亚家族, 基因结构和保守基序分析表明同一亚家族具有较高的保守性。基因复制分析显示, 17个SitPRX基因(13%)存在片段复制, 78个SitPRX基因(59%)存在串联复制, 串联复制事件在SitPRX基因扩增中起重要作用。谷子与拟南芥、水稻和玉米的物种间同源性分析显示谷子中大多数SitPRXs是在双子叶植物和单子叶植物分化后形成的。转录组分析显示, SitPRX基因家族成员在谷子幼苗、根、茎、叶以及圆锥花序中表达存在差异。启动子顺式作用元件分析显示, 79个SitPRXs含有与干旱胁迫响应相关的顺式作用元件, 进一步qRT-PCR分析显示, SitPRX12、SitPRX41、SitPRX81、SitPRX110和SitPRX126受PEG和ABA诱导表达, 表明这些基因可能通过ABA依赖的信号通路来调控和响应干旱胁迫, 可作为进一步研究III型PRX基因家族抗旱功能的候选基因。研究结果为全面解析SitPRX基因结构与生物学功能、抗旱分子机制以及分子育种提供了新信息, 以期为今后培育高效抗逆作物新品种提供思路。

关键词: III型过氧化物酶, 基因家族分析, 干旱胁迫响应, 谷子

Abstract:

Class III peroxidases (PRX) are a family of plant-specific peroxidases that play an important role in plant growth and development as well as in abiotic stresses. Foxtail millet (Setaria italica L.), as a C₄ plant, is a model plant for stress resistance. However, the function of class III peroxidases family genes is rarely reported in foxtail millet. A genome-wide expression analysis was conducted to investigate the expression pattern of class III peroxidase gene family (SitPRXs) under drought stress and ABA induction. In this study, 132 members of the Class III PRX gene family were identified in the whole genome in foxtail millet by bioinformatics and named SitPRX1-SitPRX132 according to their chromosomal position. 132 members were classified into Mα, Mβ, Mγ, MIKC^C, and MIKC^* subfamilies by phylogenetic analysis of foxtail millet, Arabidopsis, and rice. Gene structure and conserved motif analysis indicated a high level of conservation in the same subfamily. Gene duplication analysis revealed fragmental duplication in 17 SitPRX genes (13%) and tandem duplication in 78 SitPRX genes (59%), thus tandem duplication events playing an important role in SitPRX gene amplification. Interspecies homology analysis with Arabidopsis, rice and maize revealed that most SitPRXs were formed after dicotyledonous and monocotyledonous plants diverged. Transcriptome analysis implied that members of the SitPRX gene family were differentially expressed in seedlings, roots, stems, and leaves, as well as in panicles in foxtail millet. Analysis of promoter cis-acting elements showed that 79 SitPRXs contained cis-acting elements associated with drought stress response, and further qRT-PCR analysis showed that SitPRX12, SitPRX41, SitPRX81, SitPRX110, and SitPRX126 were induced to be expressed by PEG and ABA, suggesting that these genes may be regulated through an ABA-dependent signalling pathway in response to drought stress and could be used as these genes may be candidates for further studies on the drought resistance function of the class III PRX gene family. These results of this study provide new information for the comprehensive analysis of the structure and biological functions of SitPRX genes, the molecular mechanism of drought resistance, and molecular breeding in foxtail millet, with a view of providing ideas for the breeding of new varieties of highly efficient stress-resistant crops in the future.

Key words: class III peroxidase, gene family analysis, drought stress response, Setaria italica

马鑫磊, 许瑞琪, 索晓曼, 李婧实, 顾鹏鹏, 姚锐, 林小虎, 高慧. 谷子III型PRX基因家族全基因组鉴定及干旱胁迫下表达分析[J]. 作物学报, 2022, 48(10): 2517-2532.

MA Xin-Lei, XU Rui-Qi, SUO Xiao-Man, LI Jing-Shi, GU Peng-Peng, YAO Rui, LIN Xiao-Hu, GAO Hui. Genome-wide identification of the Class III PRX gene family in foxtail millet (Setaria italica L.) and expression analysis under drought stress[J]. Acta Agronomica Sinica, 2022, 48(10): 2517-2532.

图/表 11

附表1

附表2

SitPRX基因家族蛋白质理化性质"

基因名称 Gene name	序列名称 Sequence ID	染色体 Chr.	氨基酸 Size (aa)	分子量 Molecular weight (kD)	等电点 pI	不稳定系数 Instability index	脂肪系数 Aliphatic index
SitPRX1	Seita.1G022200	1	323	34.01297	4.65	46.44	86.19
SitPRX2	Seita.1G022300	1	320	33.99131	6.06	35.99	86.94
SitPRX3	Seita.1G022500	1	321	34.06693	6.93	35.87	94.92
SitPRX4	Seita.1G022900	1	323	32.94039	8.77	35.46	85.76
SitPRX5	Seita.1G023000	1	320	32.79593	5.16	34.89	87.69
SitPRX6	Seita.1G023100	1	325	33.59487	8.61	50.68	84.25
SitPRX7	Seita.1G079000	1	347	36.77990	8.08	43.59	83.00
SitPRX8	Seita.1G170200	1	342	36.70845	6.44	24.42	85.67
SitPRX9	Seita.1G192100	1	478	51.19841	5.18	50.25	67.80
SitPRX10	Seita.1G281400	1	331	35.85566	5.74	40.75	79.64
SitPRX11	Seita.1G380000	1	327	33.90540	7.10	43.36	83.49
SitPRX12	Seita.2G236400	2	343	37.36357	5.82	35.23	81.40
SitPRX13	Seita.2G266900	2	337	35.49031	6.00	33.43	80.53
SitPRX14	Seita.2G320200	2	357	38.91543	9.00	30.86	79.58
SitPRX15	Seita.2G371600	2	324	33.41573	9.27	41.70	84.51
SitPRX16	Seita.2G406700	2	413	44.45746	6.41	46.79	70.70
SitPRX17	Seita.2G407000	2	364	38.15130	5.98	44.02	79.95
SitPRX18	Seita.2G407100	2	372	39.60795	6.89	30.53	86.34
SitPRX19	Seita.2G407200	2	553	57.24306	7.56	78.21	59.89
SitPRX20	Seita.2G407400	2	350	37.48503	9.07	39.39	82.80
SitPRX21	Seita.2G411900	2	328	35.06796	6.33	38.71	82.77
SitPRX22	Seita.2G430900	2	317	33.14664	9.11	38.83	90.98
SitPRX23	Seita.2G431000	2	351	36.48558	6.57	35.11	94.93
SitPRX24	Seita.2G431100	2	312	33.15028	5.48	48.85	84.87
SitPRX25	Seita.2G431200	2	312	32.73764	5.67	44.13	84.55
SitPRX26	Seita.2G431300	2	318	33.09396	6.19	40.08	79.91
SitPRX27	Seita.2G431500	2	311	32.45267	6.97	39.19	87.97
SitPRX28	Seita.3G004800	3	323	33.71242	6.23	33.82	97.99
SitPRX29	Seita.3G004900	3	332	35.23111	6.89	42.79	90.33
SitPRX30	Seita.3G005100	3	348	36.75468	5.05	38.65	93.42
SitPRX31	Seita.3G005200	3	350	37.21731	5.65	42.99	91.23
SitPRX32	Seita.3G022600	3	333	35.59788	9.16	40.76	91.23
SitPRX33	Seita.3G052400	3	344	37.47289	8.51	32.37	91.10
基因名称 Gene name	序列名称 Sequence ID	染色体 Chr.	氨基酸 Size (aa)	分子量 Molecular weight (kD)	等电点 pI	不稳定系数 Instability index	脂肪系数 Aliphatic index
SitPRX34	Seita.3G052500	3	328	34.69369	8.34	32.54	83.63
SitPRX35	Seita.3G052600	3	321	33.78561	6.30	32.81	80.9
SitPRX36	Seita.3G052700	3	328	34.82772	8.33	32.72	83.35
SitPRX37	Seita.3G052800	3	325	33.93987	7.51	36.99	85.97
SitPRX38	Seita.3G052900	3	333	36.42036	6.26	38.96	79.97
SitPRX39	Seita.3G053000	3	334	35.86602	9.36	37.01	85.36
SitPRX40	Seita.3G053100	3	336	36.71877	7.13	42.16	78.96
SitPRX41	Seita.3G190300	3	345	37.79519	5.54	43.42	85.10
SitPRX42	Seita.3G190400	3	326	35.42539	6.25	34.41	79.05
SitPRX43	Seita.3G234900	3	318	34.02132	5.41	42.17	87.52
SitPRX44	Seita.3G235000	3	317	34.15256	5.68	46.78	87.76
SitPRX45	Seita.3G235100	3	324	34.70026	6.65	45.38	86.51
SitPRX46	Seita.3G270300	3	337	36.09192	7.52	34.24	83.59
SitPRX47	Seita.3G347500	3	344	35.56654	8.59	39.48	88.72
SitPRX48	Seita.4G105100	4	342	36.82120	8.78	38.15	81.40
SitPRX49	Seita.4G122600	4	378	41.42903	5.03	27.18	78.23
SitPRX50	Seita.4G134900	4	364	39.37921	7.09	34.97	94.64
SitPRX51	Seita.4G135000	4	328	35.59600	8.29	28.43	91.34
SitPRX52	Seita.4G135100	4	327	35.10916	6.45	28.98	88.44
SitPRX53	Seita.4G165000	4	331	35.97672	5.20	47.40	82.90
SitPRX54	Seita.4G165100	4	330	35.90367	5.20	48.44	83.42
SitPRX55	Seita.4G165200	4	333	36.09562	5.34	47.66	76.58
SitPRX56	Seita.4G176600	4	359	38.13847	9.37	37.13	87.10
SitPRX57	Seita.4G176800	4	312	33.60469	10.58	48.94	78.37
SitPRX58	Seita.4G247300	4	339	36.26934	8.95	36.81	78.94
SitPRX59	Seita.4G247400	4	319	34.40781	6.72	39.28	79.56
SitPRX60	Seita.4G247500	4	318	34.20550	5.93	39.72	76.76
SitPRX61	Seita.4G247600	4	319	34.11854	5.24	33.72	80.00
SitPRX62	Seita.5G029700	5	347	38.28653	5.96	33.92	92.51
SitPRX63	Seita.5G029800	5	348	38.20653	6.31	34.03	93.65
SitPRX64	Seita.5G030000	5	330	34.54058	4.73	33.19	82.00
SitPRX65	Seita.5G030100	5	317	33.48703	6.30	42.21	82.65
SitPRX66	Seita.5G030300	5	335	36.55180	9.82	36.56	89.13
SitPRX67	Seita.5G046600	5	347	36.50828	9.00	38.16	84.18
SitPRX68	Seita.5G053000	5	367	39.71532	8.83	47.85	86.65
SitPRX69	Seita.5G053100	5	338	36.02722	9.03	36.04	92.43
SitPRX70	Seita.5G053200	5	338	36.38048	7.61	34.48	90.65
SitPRX71	Seita.5G053300	5	347	38.32482	7.62	39.97	88.85
SitPRX72	Seita.5G122000	5	327	35.14673	5.97	42.75	84.77
SitPRX73	Seita.5G145500	5	321	33.72513	8.87	35.40	84.98
SitPRX74	Seita.5G155100	5	359	37.33727	6.11	35.90	84.37
SitPRX75	Seita.5G155200	5	370	38.68255	5.64	41.43	87.65
SitPRX76	Seita.5G155300	5	362	38.49054	6.44	37.28	83.62
SitPRX77	Seita.5G164800	5	344	36.95184	6.69	45.91	84.24
SitPRX78	Seita.5G170000	5	322	33.87709	9.27	36.20	90.09
SitPRX79	Seita.5G191900	5	337	36.27433	8.39	45.24	88.37
SitPRX80	Seita.5G293800	5	367	39.46438	5.10	43.22	78.45
SitPRX81	Seita.5G344000	5	343	37.01494	4.79	38.86	86.21
SitPRX82	Seita.5G462500	5	357	38.14559	6.11	34.90	94.87
SitPRX83	Seita.5G463200	5	356	37.71887	8.59	45.69	84.44
基因名称 Gene name	序列名称 Sequence ID	染色体 Chr.	氨基酸 Size (aa)	分子量 Molecular weight (kD)	等电点 pI	不稳定系数 Instability index	脂肪系数 Aliphatic index
SitPRX84	Seita.5G463300	6	362	39.21183	9.01	35.06	87.10
SitPRX85	Seita.6G090100	6	319	34.70663	5.30	35.00	85.92
SitPRX86	Seita.6G224300	6	334	36.59959	6.39	47.66	78.56
SitPRX87	Seita.6G239800	6	288	31.41981	7.02	35.54	84.44
SitPRX88	Seita.7G006800	7	330	35.41114	5.21	31.65	90.64
SitPRX89	Seita.7G023900	7	292	31.98142	6.67	42.64	76.95
SitPRX90	Seita.7G102200	7	342	36.98169	8.79	40.93	72.13
SitPRX91	Seita.7G128200	7	336	35.92006	9.45	44.80	85.03
SitPRX92	Seita.7G154400	7	495	50.08982	8.99	68.05	75.66
SitPRX93	Seita.7G247400	7	359	38.99986	8.75	44.15	85.32
SitPRX94	Seita.7G265300	7	320	33.99704	4.82	33.00	80.28
SitPRX95	Seita.7G271000	7	364	38.88408	6.98	41.86	80.19
SitPRX96	Seita.7G271100	7	362	38.69103	8.01	37.25	84.97
SitPRX97	Seita.7G271400	7	337	35.63451	6.92	37.98	85.19
SitPRX98	Seita.7G277800	7	331	34.16931	4.39	34.08	93.02
SitPRX99	Seita.7G283600	7	311	33.94250	7.13	45.64	78.55
SitPRX100	Seita.7G327600	7	321	33.66502	8.06	35.56	80.56
SitPRX101	Seita.7G327800	7	317	33.97633	8.32	34.29	78.52
SitPRX102	Seita.8G015100	8	331	34.92851	8.31	35.24	81.99
SitPRX103	Seita.8G015200	8	355	37.31111	8.71	40.05	80.82
SitPRX104	Seita.8G100100	8	339	35.55516	6.10	32.34	85.75
SitPRX105	Seita.8G106600	8	321	34.59168	8.90	45.52	82.99
SitPRX106	Seita.9G081300	9	324	34.07148	4.44	33.58	93.77
SitPRX107	Seita.9G081400	9	326	34.65617	5.28	36.89	84.48
SitPRX108	Seita.9G186200	9	345	37.93747	9.15	34.05	87.33
SitPRX109	Seita.9G186300	9	333	35.75638	9.36	59.24	96.37
SitPRX110	Seita.9G282900	9	327	35.40278	4.73	28.03	88.53
SitPRX111	Seita.9G298200	9	340	36.51632	4.92	38.22	86.15
SitPRX112	Seita.9G298300	9	343	36.40207	5.40	28.97	84.26
SitPRX113	Seita.9G298400	9	338	36.05723	4.52	34.97	82.28
SitPRX114	Seita.9G298500	9	342	36.79289	4.50	43.85	76.78
SitPRX115	Seita.9G316400	9	330	35.44946	8.90	37.57	89.33
SitPRX116	Seita.9G316500	9	325	34.91006	5.95	32.18	94.00
SitPRX117	Seita.9G316600	9	260	28.07594	8.94	43.80	81.04
SitPRX118	Seita.9G316700	9	329	35.34733	9.09	36.90	89.27
SitPRX119	Seita.9G342200	9	323	33.49696	7.55	34.67	83.10
SitPRX120	Seita.9G355500	9	330	34.04416	5.30	37.53	87.73
SitPRX121	Seita.9G392700	9	330	34.59363	7.06	38.68	84.88
SitPRX122	Seita.9G392800	9	343	36.74207	5.66	45.64	85.63
SitPRX123	Seita.9G393100	9	330	35.86731	9.12	42.48	82.52
SitPRX124	Seita.9G393200	9	322	34.4055	7.47	35.87	82.11
SitPRX125	Seita.9G411500	9	330	34.90751	8.08	40.40	86.48
SitPRX126	Seita.9G444200	9	250	27.32902	5.69	40.56	75.80
SitPRX127	Seita.9G477900	9	332	34.68019	5.54	31.09	91.17
SitPRX128	Seita.9G478000	9	392	42.26585	9.00	44.72	75.97
SitPRX129	Seita.9G478300	9	339	36.23680	4.83	44.50	82.18
SitPRX130	Seita.9G537300	9	498	52.30507	5.63	40.28	86.65
SitPRX131	Seita.9G562400	9	334	35.11090	5.62	42.16	81.92
SitPRX132	Seita.9G562600	9	331	34.28555	5.22	29.95	81.48

附表2

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图5

图6

图7

图8

图9

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基因名称 Gene name	正向引物 Forward primer (5°-3°)	反向引物 Reverse primer (5°-3°)
SitPRX9	AGCCAACGCTGGTCTGATT	TTCTGTGACATCCACCCGTC
SitPRX12	GGCCAGCCCTCGTTTTCTAT	TTTGCTCTGCTCCGCTGTTT
SitPRX33	ACTGCTTCGTCAGGGGTTG	GTCGTCGATCACCTCGAACG
SitPRX41	GTCCGTCGCACTTGAT	AAGGCTGAGACGATGATC
SitPRX49	ACTACTCCAAGACATGCCCG	ACTGATCCATCACATCCCTGC
SitPRX72	TGATGCCGTTGATCTGACCG	TGTGGGCACCGACTAATGTT
SitPRX81	GTGTCGTCCAGTTCTACC	CTCGGCAAGCGTTGAA
SitPRX87	ACGTGATTCGTCAGTGTGCC	GGATGAGCCTTTCCCAGAGT
SitPRX110	GTCGTGGTCTTATCGGGAGC	TCCAGCGTCGGATCTACTGA
SitPRX126	GAGCCCGTGAAGGAGGAGTT	CCTCAGATGGTCAGAACCCTTA
SitEF1a-2	TGACTGTGCTGTCCTCATCA	GTTGCAGCAGCAAATCATCT

谷子III型PRX基因家族全基因组鉴定及干旱胁迫下表达分析

Genome-wide identification of the Class III PRX gene family in foxtail millet (Setaria italica L.) and expression analysis under drought stress

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