甘薯Dof基因家族挖掘及表达分析

doi:10.3724/SP.J.1006.2022.14004

作物学报 ›› 2022, Vol. 48 ›› Issue (3): 608-623.doi: 10.3724/SP.J.1006.2022.14004

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

甘薯Dof基因家族挖掘及表达分析

靳容¹(), 蒋薇¹, 刘明¹, 赵鹏¹, 张强强¹, 李铁鑫², 王丹凤¹, 范文静², 张爱君¹, 唐忠厚¹^,^*()

¹江苏徐淮地区徐州农业科学研究所/江苏徐州甘薯研究中心/农业农村部甘薯生物学与遗传育种重点实验室, 江苏徐州 221131
²安徽农业大学, 安徽合肥 230036

收稿日期:2021-01-11 接受日期:2021-04-26 出版日期:2022-03-12 网络出版日期:2021-05-20
通讯作者: 唐忠厚
作者简介:E-mail: jinrong_2012@126.com
基金资助:
国家农业现代产业技术体系建设专项(CARS-11-B-13);农业农村部薯类作物生物学与遗传育种综合性重点实验开放课题(NYBSL201802)

Genome-wide characterization and expression analysis of Dof family genes in sweetpotato

JIN Rong¹(), JIANG Wei¹, LIU Ming¹, ZHAO Peng¹, ZHANG Qiang-Qiang¹, LI Tie-Xin², WANG Dan-Feng¹, FAN Wen-Jing², ZHANG Ai-Jun¹, TANG Zhong-Hou¹^,^*()

¹Xuzhou Institute of Agricultural Sciences of Xuhuai District of Jiangsu Province/Xuzhou Sweetpotato Research Center of Jiangsu Province/Key Laboratory of Sweetpotato Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Xuzhou 221131, Jiangsu, China
²Anhui Agricultural University, Hefei 230036, Anhui, China

Received:2021-01-11 Accepted:2021-04-26 Published:2022-03-12 Published online:2021-05-20
Contact: TANG Zhong-Hou
Supported by:
China Agriculture Research System(CARS-11-B-13);Open Project of Ministry of Agriculture and Rural Affairs: Key Laboratory of Biology, Genetics and Breeding of Potato Crops(NYBSL201802)

摘要/Abstract

摘要：

单锌指蛋白超家族Dof (DNA binding with one finger)转录因子广泛参与植物的各种生命活动。以甘薯泰中6号基因组为参照挖掘得到46个甘薯Dof基因, 每个家族成员均具有C₂C₂-Dof锌指结构, 按照其在染色体上的位置, 命名为IbDof1~IbDof46。该基因家族可分为4个亚家族(A~D), 且不同亚族的基因结构和基序的分布差异显著。基序1和基序2存在于所有亚家族中; 基序5和基序9只存在于亚家族A中; 基序6、基序7、基序8和基序10只存在亚家族D中。IbDof的进化极为保守, 共有12对染色体复制事件和5对串联重复序列事件(IbDof2/IbDof3、IbDof12/IbDof13、IbDof9/IbDof10、IbDof28/IbDof29和IbDof32/IbDof33), 分歧时间平均是3552万年前和186万年前, Ka/Ks比值范围从0.07 (IbDof12/IbDof13)到0.68 (IbDof6/IbDof25), 且与甘薯野生近缘种Ipomoea trifida同一染色体上的Dof同源基因对有38对。组织特异性分析表明, IbDof各亚族在各个组织器官中表达强度不同, 且亚族内部呈现不同的表达趋势。IbDof启动子序列中包含逆境和激素响应等相关元件, 实时荧光定量PCR进一步分析表明, IDof基因受低温、干旱、高盐和H₂O₂等非生物胁迫诱导表达。比如大部分IbDof受低温调控表达; IbDof10和IbDof14受干旱胁迫诱导表达; IbDof2、IbDof14、IbDof37、IbDof41和IbDof43受高盐诱导表达; 而IbDof8、IbDof10、IbDof25和IbDof41则受H₂O₂诱导表达, 这说明IbDof家族成员协同控制了甘薯的生长发育及参与非生物胁迫过程。

关键词: 甘薯, Dof基因家族, 系统进化, 表达分析

Abstract:

DNA-binding One Zinc Finger (Dof) transcription factors are widely involved in various life activities of plants. Forty-six IbDof genes from sweetpotato cv. Taizhong 6 with a highly conserved Dof domain structured as a C2C2-type zinc finger were identified and named from IbDof1 to IbDof46 according to their position on the chromosomes. IbDof family could be divided into four subgroups (A-D), which shared the similar motifs and gene structures. Motif 1 and Motf 2 occurred in all of the identified IbDofs, Motif 5 and Motif 9 only occurred in subgroup A, and Motif 6-Motif 8 and Motif 10 only occurred in subgroup D. Twelve segment duplicated gene pairs and five tandem duplicated gene pairs of IbDofs (IbDof2/IbDof3, IbDof12/IbDof13, IbDof9/IbDof10, IbDof28/IbDof29, and IbDof32/IbDof33) contributed to the expansion of IbDof family in sweetpotato. The average divergence times of segmental duplication gene pairs and tandem duplicated gene pairs seemed to have emerged 35.22 MYA and 1.86 MYA, and the Ka/Ks ratios of the paralogous IbDofs were range from 0.07 (IbDof12/IbDof13) to 0.68 (IbDof6/IbDof25). Tirty-eight orthologous IbDof gene pairs between sweetpotato and their wild relative species Ipomoea trifida were involved in duplicated genomic blocks based on synteny analysis. Transcriptome analysis indicated different subgroups expressed specifically in various tissues, and IbDofs in the same subgroup also revealed different expression tends. Various hormones and stresses response element were identified in the promoters of IbDof genes, and qRT-PCR demonstrated specific IbDof genes responded to various environmental stresses, including cold, drought, salt, and H₂O₂. Most IbDof genes were regulated by cold treatment; IbDof10 and IbDof14 were up-regulated by drought treatment; IbDof-2, -14, -37, -41, -43 were up regulated by high salt stress; and IbDof-8, -10, -25, -41 were up regulated by H₂O₂ treatment. In summary, our result indicated that IbDof family genes coordinately regulated the growth and development of sweetpotato and been involved in the various abiotic stresses process.

Key words: sweetpotato, Dof gene family, evolution analysis, gene expression profiling

靳容, 蒋薇, 刘明, 赵鹏, 张强强, 李铁鑫, 王丹凤, 范文静, 张爱君, 唐忠厚. 甘薯Dof基因家族挖掘及表达分析[J]. 作物学报, 2022, 48(3): 608-623.

JIN Rong, JIANG Wei, LIU Ming, ZHAO Peng, ZHANG Qiang-Qiang, LI Tie-Xin, WANG Dan-Feng, FAN Wen-Jing, ZHANG Ai-Jun, TANG Zhong-Hou. Genome-wide characterization and expression analysis of Dof family genes in sweetpotato[J]. Acta Agronomica Sinica, 2022, 48(3): 608-623.

图/表 13

表1

表2

IbDof基因家族相关信息"

基因名称 Gene name	基因编号 Gene ID	染色体定位 Chromosome	CDS长度 Coding domain sequence (bp)	氨基酸长度 Amino acid length	等电点 Isoelectric point (pI)	分子量 Molecular weight (kD)	亚细胞定位 Subcellular location	分组 Group
IbDof1	g1970.t1	1	891	297	6.35	31.96	细胞核 Nucleus	D3
IbDof2	g5563.t1	1	807	269	4.94	29.78	细胞核 Nucleus	D3
IbDof3	g5605.t1	1	807	269	4.94	29.76	细胞核 Nucleus	D3
IbDof4	g6131.t1	1	600	200	9.16	20.99	细胞核 Nucleus	C2.2
IbDof5	g9564.t1	2	1164	388	9.33	42.57	细胞核 Nucleus	B1
IbDof6	g10705.t1	2	561	187	9.60	21.15	细胞核 Nucleus	B2
IbDof7	g11533.t1	3	1542	514	5.28	55.81	细胞核 Nucleus	B1
IbDof8	g11556.t1	3	1494	498	5.09	53.53	细胞核 Nucleus	B1
IbDof9	g15022.t1	3	759	253	8.15	27.43	细胞核 Nucleus	D1
IbDof10	g15141.t1	3	732	244	8.90	26.49	细胞核 Nucleus	D1
IbDof11	g17470.t1	4	330	110	9.66	12.60	细胞核 Nucleus	B2
IbDof12	g21747.t1	4	960	320	9.20	33.86	细胞核 Nucleus	A
IbDof13	g21785.t1	4	957	319	9.20	33.80	细胞核 Nucleus	A
IbDof14	g21856.t1	4	846	282	6.78	30.99	细胞核 Nucleus	D2
IbDof15	g26198.t1	5	1587	529	6.19	58.14	细胞核 Nucleus	B1
IbDof16	g26413.t1	5	786	262	9.18	27.65	细胞核 Nucleus	C1
IbDof17	g26723.t1	5	825	275	7.17	29.90	细胞核 Nucleus	D1
IbDof18	g27204.t1	5	807	269	5.03	29.57	细胞核 Nucleus	D3
IbDof19	g28361.t1	6	498	166	9.73	19.31	细胞核 Nucleus	B2
IbDof20	g28392.t1	6	606	202	9.32	22.91	细胞核 Nucleus	B2
IbDof21	g28584.t1	6	606	202	8.45	22.54	细胞核 Nucleus	B2
IbDof22	g28692.t1	6	687	229	8.79	25.43	细胞核 Nucleus	B2
IbDof23	g31777.t1	6	630	210	8.16	22.06	细胞核 Nucleus	C2.2
IbDof24	g32164.t1	6	1164	388	9.05	42.28	细胞核 Nucleus	C2.2
IbDof26	g34747.t1	7	786	262	8.64	28.71	细胞核 Nucleus	D2
IbDof27	g34761.t1	7	786	262	8.49	28.58	细胞核 Nucleus	D2
IbDof28	g38905.t1	8	657	219	8.84	23.95	细胞核 Nucleus	D1
IbDof29	g38982.t1	8	1038	346	8.83	38.71	细胞核 Nucleus	D1
IbDof30	g42311.t1	9	939	313	9.33	34.08	细胞核 Nucleus	C3
IbDof31	g42323.t1	9	1014	338	9.14	36.42	细胞核 Nucleus	C3
IbDof32	g46228.t1	9	972	324	9.60	33.39	细胞核 Nucleus	A
IbDof33	g46266.t1	9	1032	344	9.30	35.94	细胞核 Nucleus	A
IbDof34	g48623.t1	10	861	287	6.19	31.08	细胞核 Nucleus	D3
IbDof35	g50844.t1	10	1050	350	8.90	37.73	细胞核 Nucleus	C3
IbDof36	g50864.t1	10	837	279	6.15	30.23	细胞核 Nucleus	B1
IbDof37	g53865.t1	11	1398	466	5.76	50.71	细胞核 Nucleus	B1
基因名称 Gene name	基因编号 Gene ID	染色体定位 Chromosome	CDS长度 Coding domain sequence (bp)	氨基酸长度 Amino acid length	等电点 Isoelectric point (pI)	分子量 Molecular weight (kD)	亚细胞定位 Subcellular location	分组 Group
IbDof38	g55460.t1	11	1050	350	6.97	38.44	细胞核 Nucleus	D2
IbDof39	g57153.t1	12	1002	334	9.63	35.93	细胞核 Nucleus	A
IbDof40	g58686.t1	12	1008	336	8.24	36.37	细胞核 Nucleus	D1
IbDof41	g59490.t1	12	1011	337	8.21	36.31	细胞核 Nucleus	D1
IbDof42	g59977.t1	12	939	313	9.48	33.42	细胞核 Nucleus	A
IbDof43	g65472.t1	14	1317	439	7.22	47.43	细胞核 Nucleus	B1
IbDof44	g65553.t1	14	1053	351	8.99	39.00	细胞核 Nucleus	B2
IbDof45	g68289.t1	14	804	268	8.24	29.58	细胞核 Nucleus	D2
IbDof46	g68388.t1	14	882	294	9.17	30.81	细胞核 Nucleus	A

表2

图1

图2

图3

表3

甘薯Dof基因复制事件类型、同义替换率、非同义替换率及其比值"

基因I Gene I	基因II Gene II	复制类型 Type of duplication	同义替换率 Ka	非同义替换率 Ks	Ka/Ks	分歧时间(百万年前) Divergence time (MYA)
IbDof2	IbDof3	串联重复序列 Tandem duplicated gene pairs	0.001611	0.016886	0.095413	0.562876
IbDof4	IbDof25	染色体片段复制 Segmental duplication gene pairs	0.158131	0.233118	0.678330	7.77059
IbDof7	IbDof15	染色体片段复制 Segmental duplication gene pairs	0.275346	0.952055	0.289212	31.73516
IbDof9	IbDof10	串联重复序列 Tandem duplicated gene pairs	0.016325	0.053043	0.307773	1.768089
IbDof10	IbDof17	染色体片段复制 Segmental duplication gene pairs	0.291817	1.563082	0.186693	52.10274
IbDof12	IbDof13	串联重复序列 Tandem duplicated gene pairs	0.006995	0.097434	0.071789	3.247803
IbDof14	IbDof27	染色体片段复制 Segmental duplication gene pairs	0.228799	1.117142	0.204807	37.23806
IbDof28	IbDof29	串联重复序列 Tandem duplicated gene pairs	0.008162	0.020799	0.392429	0.693285
IbDof32	IbDof33	串联重复序列 Tandem duplicated gene pairs	0.030506	0.102014	0.299038	3.400458
IbDof35	IbDof30	染色体片段复制 Segmental duplication gene pairs	0.495625	1.024638	0.483707	34.15461
IbDof39	IbDof12	染色体片段复制 Segmental duplication gene pairs	0.624101	1.595607	0.391137	53.1869
基因I Gene I	基因II Gene II	复制类型 Type of duplication	同义替换率 Ka	非同义替换率 Ks	Ka/Ks	分歧时间(百万年前) Divergence time (MYA)
IbDof40	IbDof41	染色体片段复制 Segmental duplication gene pairs	0.006582	0.044195	0.148927	1.47318
IbDof40	IbDof29	染色体片段复制 Segmental duplication gene pairs	0.338989	0.932423	0.363557	31.08075
IbDof45	IbDof14	染色体片段复制 Segmental duplication gene pairs	0.290234	0.953107	0.304514	31.77022
IbDof45	IbDof27	染色体片段复制 Segmental duplication gene pairs	0.287356	1.117214	0.257208	37.24048
IbDof46	IbDof13	染色体片段复制 Segmental duplication gene pairs	0.217848	1.104950	0.197156	36.83168
IbDof46	IbDof12	染色体片段复制 Segmental duplication gene pairs	0.192186	1.127080	0.170517	37.56932

表3

图4

图5

图6

图7

图8

图9

图10

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基因名称 Gene name	正向引物序列 Forward sequence (5'-3')	反向引物序列 Reverse sequence (5'-3')
Dof2	GCTGTTGTTGTTGGATTATC	CGTTGTTAGGTAGAGTTGTC
Dof5	CTCATTGCCGTCATATTACC	TCCTGCCATAGAACTTGTAG
Dof8	GCTGGAGATAATGGAGATGA	AACTGCGGTCAATGGATAA
Dof10	GGTTGTGGAGAATGTTGTG	GAGGAAGAAGATGATAAGGAAG
Dof14	GAAGGTGATGATGACAACAG	CCATGCCAAGAAGAACCA
Dof15	GCTTCATCTCCTCCTCCT	GTTCCTTCATCCTCTTCACT
Dof17	CAACTATGGCGACTGATAATC	GATGTTCCTCCTCCTCCT
Dof21	TTACTGTCGAACATGCAGACGC	GTGGTTGGAGTTGAGGTAGTGA
基因名称 Gene name	正向引物序列 Forward sequence (5'-3')	反向引物序列 Reverse sequence (5'-3')
Dof24	CGACGAGATATTGGAACCTT	GGCTGGCTCTGTTGAATC
Dof25	CTACAACAACTACAACCTCTC	AGCAATGACGTGAAGGAG
Dof33	TCCGTTCCTCGATCCAAT	TGATGGTGTGATTGTTGTTG
Dof37	CGACCAAGACTGAAGATGA	GGTGATGTGGCAATGAGA
Dof40	CTCCATCATCATCATCATCATC	GGCAGCAGTAGTCATTCC
Dof41	CATCATCATCATCATCTCCATC	GGCAGCAGTAGTCATTCC
Dof43	TTCTGTTACGACACCTTCC	TACTGCTTCTACCGACTCT

甘薯Dof基因家族挖掘及表达分析

Genome-wide characterization and expression analysis of Dof family genes in sweetpotato

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