Genome-wide Identification of Ethylene Responsive Factor (ERF) Family Genes in Peach and Screening of Genes Related to Germination

doi:10.11983/CBB17117

Abstract

Abstract: In this study, genome-wide identification of ERF family genes in ‘zhongyousihao’ peach was studied by using MEGA 6.0, MEME, GSDS, DNAMAN 6.0. We identified 102 genes, and phylogenetic analyses of the genes indicated that the transcription factors can be classified into 10 different groups (I-X). Gene structure analysis showed that 81 genes had no introns, 20 genes contained an intron, and 1 gene contained 5 introns, which had a large difference from other members. Conservative motif analysis showed that the ERF family contained 20 conserved elements: Motifs 1, 2 and 4 belonged to the APETALA2 (AP2)/ERF domain, and the same conserved motif appeared mainly in the same family; the function of most conserved motifs is unknown. qRT-PCR revealed that the expression of PpeERF068 during dormancy and germination was consistent with the developmental status of leaf buds, which suggested that it might be related to leaf bud germination. The gene expression of peach buds during each period in light culture incubation further showed the relation between PpeERF068 and the germination of leaf buds. So PpeERF068 was named PpeEBB1. We will further study the molecular mechanism of PpeEBB1 to provide theoretical guidance for the cultivation and management of peach.

Key words: peach, ERF family, bud germination, PpeEBB1

Zhao Xuehui, Wang Qingjie, Li Chen, Chen Xiude, Xiao Wei, Gao Dongsheng, Fu Xiling. Genome-wide Identification of Ethylene Responsive Factor (ERF) Family Genes in Peach and Screening of Genes Related to Germination[J]. Chinese Bulletin of Botany, 2018, 53(5): 612-624.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB17117

https://www.chinbullbotany.com/EN/Y2018/V53/I5/612

Figures/Tables 7

References 33

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Locus name	Forward primer (5′-3′)	Reverse primer (5′-3′)
Prupe.3g094700	GCGGAGATAAGAGACCGAAT	AGAAGATGATGAGCAAGGTGAG
Prupe.1g245500	AGTATCACAGACGACGCAGG	ATCGCCCATCACTCAAGA
Prupe.1g212700	TATGCGGCGGAGATAAGA	GGGTGAGATAATGGAGGTGA
Prupe.1g139600	TGGATTCTGGGACAACCA	GGAACTGATGGAGAGCAAGAG
Prupe.4g176200	GCCCAAACTCCAAAGAGA	GTTGTTGTGGCTGTTGATGT
Prupe.4g051400	TCTCGCTCAGGGTGTTAGTA	CAGCCGTTGATGAAACTG
Prupe.8g230600	TTGCCTCACACGCTTGTTA	GAACGGTTTCTTCTCTTTCCTC
Prupe.4g051200	TCTCTCTCTGGACCTCAACAT	CGCCAACATTTCCTACAAC
Prupe.4g222300	AAGCCAAGACCAACTTCCC	TGTCCTGAAACCCGTAACC
Prupe.3g209100	TCCTCATCCTCCGTCGTAGA	ATCACCACAAACCTCACCG
Actin	GTTATTCTTCATCGGCGTCTTCG	CTTCACCATTCCAGTTCCATTGTC

Locus name	Forward primer (5′-3′)	Reverse primer (5′-3′)
Prupe.3g094700	GCGGAGATAAGAGACCGAAT	AGAAGATGATGAGCAAGGTGAG
Prupe.1g245500	AGTATCACAGACGACGCAGG	ATCGCCCATCACTCAAGA
Prupe.1g212700	TATGCGGCGGAGATAAGA	GGGTGAGATAATGGAGGTGA
Prupe.1g139600	TGGATTCTGGGACAACCA	GGAACTGATGGAGAGCAAGAG
Prupe.4g176200	GCCCAAACTCCAAAGAGA	GTTGTTGTGGCTGTTGATGT
Prupe.4g051400	TCTCGCTCAGGGTGTTAGTA	CAGCCGTTGATGAAACTG
Prupe.8g230600	TTGCCTCACACGCTTGTTA	GAACGGTTTCTTCTCTTTCCTC
Prupe.4g051200	TCTCTCTCTGGACCTCAACAT	CGCCAACATTTCCTACAAC
Prupe.4g222300	AAGCCAAGACCAACTTCCC	TGTCCTGAAACCCGTAACC
Prupe.3g209100	TCCTCATCCTCCGTCGTAGA	ATCACCACAAACCTCACCG
Actin	GTTATTCTTCATCGGCGTCTTCG	CTTCACCATTCCAGTTCCATTGTC

Group name	Gene name	Locus name	ORF length (bp)	Size (aa)	Molecular weight (Da)	PI	EST hitting
I	PpeERF#001	Prupe.6g182200	1122	373	41331.3	6.56	13
I	PpeERF#002	Prupe.3g009400	642	213	23101.2	9.79	7
I	PpeERF#003	Prupe.1g513600	1137	378	41236.8	6.37	9
I	PpeERF#004	Prupe.5g117800	933	310	34377.6	8.34	9
I	PpeERF#005	Prupe.3g157100	1386	461	51713.0	5.97	0
I	PpeERF#006	Prupe.1g008400	1230	409	45352.9	7.81	2
I	PpeERF#007	Prupe.8g198700	696	231	26301.6	9.19	0
II	PpeERF#008	Prupe.6g176400	540	179	20308.7	9.51	0
II	PpeERF#009	Prupe.1g432000	528	175	19844.9	9.39	1
II	PpeERF#010	Prupe.1g464400	453	150	17240.2	9.42	2
II	PpeERF#011	Prupe.6g231500	501	166	17849.1	8.72	0
II	PpeERF#012	Prupe.1g546100	501	166	17890.7	5.62	0
II	PpeERF#013	Prupe.1g500900	726	241	26308.4	5.61	0
II	PpeERF#014	Prupe.7g194400	648	215	23980.2	5.16	0
II	PpeERF#015	Prupe.1g001700	552	183	20044.5	7.74	0
III	PpeERF#016	Prupe.5g090700	558	185	19627.0	4.89	0
III	PpeERF#017	Prupe.5g090600	537	178	19407.7	5.67	0
III	PpeERF#018	Prupe.5g090400	543	180	19547.0	5.50	0
III	PpeERF#019	Prupe.5g090300	543	180	19510.8	5.50	0
III	PpeERF#020	Prupe.5g090800	555	184	19705.9	4.64	0
III	PpeERF#021	Prupe.2g289600	696	231	24485.1	4.83	0
III	PpeERF#022	Prupe.7g116300	609	202	21536.7	4.91	0
III	PpeERF#023	Prupe.2g190200	609	202	22713.9	5.87	1
III	PpeERF#024	Prupe.2g123200	831	276	30098.8	4.94	0
III	PpeERF#025	Prupe.5g065300	762	253	28183.5	4.91	0
III	PpeERF#026	Prupe.1g448600	771	256	27960.9	5.11	0
III	PpeERF#027	Prupe.7g222700	789	262	28536.4	4.94	0
III	PpeERF#028	Prupe.3g062800	732	243	26436.2	6.67	1
III	PpeERF#029	Prupe.7g115900	606	201	22481.2	4.95	0
III	PpeERF#030	Prupe.2g289500	690	229	24976.9	5.14	7
III	PpeERF#031	Prupe.5g090500	723	240	27217.8	7.69	0
III	PpeERF#032	Prupe.5g090100	711	236	26352.7	5.17	0
III	PpeERF#033	Prupe.5g090000	693	230	25658.8	5.13	7
III	PpeERF#034	Prupe.5g090200	699	232	26157.5	5.03	1
III	PpeERF#035	Prupe.5g089900	693	230	25521.9	7.78	0
III	PpeERF#036	Prupe.1g545700	522	173	19078.3	5.44	0
III	PpeERF#037	Prupe.1g545400	600	199	22101.0	5.54	0
IV	PpeERF#038	Prupe.2g253000	1041	346	37474.1	6.52	0
IV	PpeERF#039	Prupe.6g284400	1554	517	58370.7	4.74	0
IV	PpeERF#040	Prupe.2g256900	1167	388	42473.1	4.64	3
IV	PpeERF#041	Prupe.3g223300	591	196	21305.5	8.32	0
IV	PpeERF#042	Prupe.7g066700	858	285	32054.9	5.73	0
Group name	Gene name	Locus name	ORF length (bp)	Size (aa)	Molecular weight (Da)	PI	EST hitting
IV	PpeERF#043	Prupe.6g354000	672	223	23337.9	8.50	0
IV	PpeERF#044	Prupe.1g372100	768	255	28137.6	6.55	0
V	PpeERF#045	Prupe.3g096000	639	212	24310.2	5.94	0
V	PpeERF#046	Prupe.1g390800	588	195	22413.4	6.66	6
V	PpeERF#047	Prupe.1g480400	672	223	24759.7	9.10	0
V	PpeERF#048	Prupe.7g243600	732	243	26570.6	7.02	0
V	PpeERF#049	Prupe.3g084600	567	188	20855.3	5.97	0
V	PpeERF#050	Prupe.7g004900	945	314	34636.3	5.44	0
V	PpeERF#051	Prupe.6g004400	867	288	31688.5	6.01	0
V	PpeERF#052	Prupe.3g263000	1275	424	46904.3	4.58	0
V	PpeERF#053	Prupe.5g136200	939	312	33152.5	6.13	0
V	PpeERF#054	Prupe.1g084800	936	311	33626.0	8.92	0
V	PpeERF#055	Prupe.5g213800	675	224	25367.4	8.71	0
VI	PpeERF#056	Prupe.5g114100	1002	333	37019.0	4.98	0
VI	PpeERF#057	Prupe.2g306400	1098	365	41098.9	4.75	2
VI	PpeERF#058	Prupe.2g183200	864	287	32269.0	4.95	0
VI	PpeERF#059	Prupe.3g019900	570	189	20614.4	9.37	0
VI	PpeERF#060	Prupe.7g060700	588	195	21933.2	10.37	2
VI	PpeERF#061	Prupe.6g039700	927	308	34031.9	5.49	2
VI	PpeERF#062	Prupe.5g220700	1311	436	49386.8	6.25	1
VI	PpeERF#063	Prupe.1g310100	1020	339	38021.2	4.92	1
VII	PpeERF#064	Prupe.8g264900	966	321	35682.6	5.68	4
VII	PpeERF#065	Prupe.3g032300	1149	382	42495.9	4.81	84
VII	PpeERF#066	Prupe.1g130300	870	289	31564.0	7.66	31
VIII	PpeERF#067	Prupe.3g094700	870	289	31781.0	9.56	0
VIII	PpeERF#068	Prupe.1g245500	1275	424	46297.0	7.73	0
VIII	PpeERF#069	Prupe.1g212700	831	276	29938.4	4.94	0
VIII	PpeERF#070	Prupe.1g139600	1092	363	39938.7	5.60	0
VIII	PpeERF#071	Prupe.4g176200	687	228	24245.0	9.62	2
VIII	PpeERF#072	Prupe.4g051400	795	264	28447.6	9.47	1
VIII	PpeERF#073	Prupe.8g230600	546	181	19951.0	9.99	0
VIII	PpeERF#074	Prupe.4g051200	519	172	18303.7	9.20	3
VIII	PpeERF#075	Prupe.4g222300	696	231	25022.8	7.62	20
VIII	PpeERF#076	Prupe.3g209100	708	235	25471.3	6.58	3
IX	PpeERF#077	Prupe.2g129700	672	223	24950.8	5.41	0
IX	PpeERF#078	Prupe.2g129500	651	216	23968.9	5.99	0
IX	PpeERF#079	Prupe.2g129600	714	237	25948.7	5.47	0
IX	PpeERF#080	Prupe.2g129300	816	271	29817.0	5.17	0
IX	PpeERF#081	Prupe.2g129400	621	206	22559.1	5.97	0
IX	PpeERF#082	Prupe.5g061800	846	281	30157.0	9.09	10
IX	PpeERF#083	Prupe.6g064700	2115	704	77761.3	9.77	15
IX	PpeERF#084	Prupe.2g272300	783	260	29210.8	6.53	3
IX	PpeERF#085	Prupe.5g062000	1059	352	39322.2	5.90	5
Group name	Gene name	Locus name	ORF length (bp)	Size (aa)	Molecular weight (Da)	PI	EST hitting
IX	PpeERF#086	Prupe.2g272400	945	314	35018.8	6.17	21
IX	PpeERF#087	Prupe.2g272500	726	241	27069.2	5.92	0
IX	PpeERF#088	Prupe.8g224700	540	179	20470.7	6.08	0
IX	PpeERF#089	Prupe.1g037800	492	163	18008.7	6.85	0
IX	PpeERF#090	Prupe.8g224800	465	154	17059.7	7.79	0
IX	PpeERF#091	Prupe.1g037700	417	138	15204.7	6.84	0
IX	PpeERF#092	Prupe.4g055600	795	264	29431.3	5.61	0
IX	PpeERF#093	Prupe.4g055500	564	187	20369.6	9.51	2
IX	PpeERF#094	Prupe.6g348700	744	247	28089.7	4.92	0
IX	PpeERF#095	Prupe.8g224600	759	252	28672.0	4.99	1
IX	PpeERF#096	Prupe.1g037900	699	232	25950.8	5.54	1
X	PpeERF#097	Prupe.8g125100	816	271	30318.2	8.16	0
X	PpeERF#098	Prupe.7g134100	801	266	29255.4	7.67	0
X	PpeERF#099	Prupe.5g141200	696	231	25763.5	9.21	0
X	PpeERF#100	Prupe.6g165700	1215	404	43314.9	7.07	2
X	PpeERF#101	Prupe.5g141300	816	271	30005.0	6.16	0
X	PpeERF#102	Prupe.1g214900	741	246	27203.7	6.23	1

Group name	Gene name	Locus name	ORF length (bp)	Size (aa)	Molecular weight (Da)	PI	EST hitting
I	PpeERF#001	Prupe.6g182200	1122	373	41331.3	6.56	13
I	PpeERF#002	Prupe.3g009400	642	213	23101.2	9.79	7
I	PpeERF#003	Prupe.1g513600	1137	378	41236.8	6.37	9
I	PpeERF#004	Prupe.5g117800	933	310	34377.6	8.34	9
I	PpeERF#005	Prupe.3g157100	1386	461	51713.0	5.97	0
I	PpeERF#006	Prupe.1g008400	1230	409	45352.9	7.81	2
I	PpeERF#007	Prupe.8g198700	696	231	26301.6	9.19	0
II	PpeERF#008	Prupe.6g176400	540	179	20308.7	9.51	0
II	PpeERF#009	Prupe.1g432000	528	175	19844.9	9.39	1
II	PpeERF#010	Prupe.1g464400	453	150	17240.2	9.42	2
II	PpeERF#011	Prupe.6g231500	501	166	17849.1	8.72	0
II	PpeERF#012	Prupe.1g546100	501	166	17890.7	5.62	0
II	PpeERF#013	Prupe.1g500900	726	241	26308.4	5.61	0
II	PpeERF#014	Prupe.7g194400	648	215	23980.2	5.16	0
II	PpeERF#015	Prupe.1g001700	552	183	20044.5	7.74	0
III	PpeERF#016	Prupe.5g090700	558	185	19627.0	4.89	0
III	PpeERF#017	Prupe.5g090600	537	178	19407.7	5.67	0
III	PpeERF#018	Prupe.5g090400	543	180	19547.0	5.50	0
III	PpeERF#019	Prupe.5g090300	543	180	19510.8	5.50	0
III	PpeERF#020	Prupe.5g090800	555	184	19705.9	4.64	0
III	PpeERF#021	Prupe.2g289600	696	231	24485.1	4.83	0
III	PpeERF#022	Prupe.7g116300	609	202	21536.7	4.91	0
III	PpeERF#023	Prupe.2g190200	609	202	22713.9	5.87	1
III	PpeERF#024	Prupe.2g123200	831	276	30098.8	4.94	0
III	PpeERF#025	Prupe.5g065300	762	253	28183.5	4.91	0
III	PpeERF#026	Prupe.1g448600	771	256	27960.9	5.11	0
III	PpeERF#027	Prupe.7g222700	789	262	28536.4	4.94	0
III	PpeERF#028	Prupe.3g062800	732	243	26436.2	6.67	1
III	PpeERF#029	Prupe.7g115900	606	201	22481.2	4.95	0
III	PpeERF#030	Prupe.2g289500	690	229	24976.9	5.14	7
III	PpeERF#031	Prupe.5g090500	723	240	27217.8	7.69	0
III	PpeERF#032	Prupe.5g090100	711	236	26352.7	5.17	0
III	PpeERF#033	Prupe.5g090000	693	230	25658.8	5.13	7
III	PpeERF#034	Prupe.5g090200	699	232	26157.5	5.03	1
III	PpeERF#035	Prupe.5g089900	693	230	25521.9	7.78	0
III	PpeERF#036	Prupe.1g545700	522	173	19078.3	5.44	0
III	PpeERF#037	Prupe.1g545400	600	199	22101.0	5.54	0
IV	PpeERF#038	Prupe.2g253000	1041	346	37474.1	6.52	0
IV	PpeERF#039	Prupe.6g284400	1554	517	58370.7	4.74	0
IV	PpeERF#040	Prupe.2g256900	1167	388	42473.1	4.64	3
IV	PpeERF#041	Prupe.3g223300	591	196	21305.5	8.32	0
IV	PpeERF#042	Prupe.7g066700	858	285	32054.9	5.73	0
Group name	Gene name	Locus name	ORF length (bp)	Size (aa)	Molecular weight (Da)	PI	EST hitting
IV	PpeERF#043	Prupe.6g354000	672	223	23337.9	8.50	0
IV	PpeERF#044	Prupe.1g372100	768	255	28137.6	6.55	0
V	PpeERF#045	Prupe.3g096000	639	212	24310.2	5.94	0
V	PpeERF#046	Prupe.1g390800	588	195	22413.4	6.66	6
V	PpeERF#047	Prupe.1g480400	672	223	24759.7	9.10	0
V	PpeERF#048	Prupe.7g243600	732	243	26570.6	7.02	0
V	PpeERF#049	Prupe.3g084600	567	188	20855.3	5.97	0
V	PpeERF#050	Prupe.7g004900	945	314	34636.3	5.44	0
V	PpeERF#051	Prupe.6g004400	867	288	31688.5	6.01	0
V	PpeERF#052	Prupe.3g263000	1275	424	46904.3	4.58	0
V	PpeERF#053	Prupe.5g136200	939	312	33152.5	6.13	0
V	PpeERF#054	Prupe.1g084800	936	311	33626.0	8.92	0
V	PpeERF#055	Prupe.5g213800	675	224	25367.4	8.71	0
VI	PpeERF#056	Prupe.5g114100	1002	333	37019.0	4.98	0
VI	PpeERF#057	Prupe.2g306400	1098	365	41098.9	4.75	2
VI	PpeERF#058	Prupe.2g183200	864	287	32269.0	4.95	0
VI	PpeERF#059	Prupe.3g019900	570	189	20614.4	9.37	0
VI	PpeERF#060	Prupe.7g060700	588	195	21933.2	10.37	2
VI	PpeERF#061	Prupe.6g039700	927	308	34031.9	5.49	2
VI	PpeERF#062	Prupe.5g220700	1311	436	49386.8	6.25	1
VI	PpeERF#063	Prupe.1g310100	1020	339	38021.2	4.92	1
VII	PpeERF#064	Prupe.8g264900	966	321	35682.6	5.68	4
VII	PpeERF#065	Prupe.3g032300	1149	382	42495.9	4.81	84
VII	PpeERF#066	Prupe.1g130300	870	289	31564.0	7.66	31
VIII	PpeERF#067	Prupe.3g094700	870	289	31781.0	9.56	0
VIII	PpeERF#068	Prupe.1g245500	1275	424	46297.0	7.73	0
VIII	PpeERF#069	Prupe.1g212700	831	276	29938.4	4.94	0
VIII	PpeERF#070	Prupe.1g139600	1092	363	39938.7	5.60	0
VIII	PpeERF#071	Prupe.4g176200	687	228	24245.0	9.62	2
VIII	PpeERF#072	Prupe.4g051400	795	264	28447.6	9.47	1
VIII	PpeERF#073	Prupe.8g230600	546	181	19951.0	9.99	0
VIII	PpeERF#074	Prupe.4g051200	519	172	18303.7	9.20	3
VIII	PpeERF#075	Prupe.4g222300	696	231	25022.8	7.62	20
VIII	PpeERF#076	Prupe.3g209100	708	235	25471.3	6.58	3
IX	PpeERF#077	Prupe.2g129700	672	223	24950.8	5.41	0
IX	PpeERF#078	Prupe.2g129500	651	216	23968.9	5.99	0
IX	PpeERF#079	Prupe.2g129600	714	237	25948.7	5.47	0
IX	PpeERF#080	Prupe.2g129300	816	271	29817.0	5.17	0
IX	PpeERF#081	Prupe.2g129400	621	206	22559.1	5.97	0
IX	PpeERF#082	Prupe.5g061800	846	281	30157.0	9.09	10
IX	PpeERF#083	Prupe.6g064700	2115	704	77761.3	9.77	15
IX	PpeERF#084	Prupe.2g272300	783	260	29210.8	6.53	3
IX	PpeERF#085	Prupe.5g062000	1059	352	39322.2	5.90	5
Group name	Gene name	Locus name	ORF length (bp)	Size (aa)	Molecular weight (Da)	PI	EST hitting
IX	PpeERF#086	Prupe.2g272400	945	314	35018.8	6.17	21
IX	PpeERF#087	Prupe.2g272500	726	241	27069.2	5.92	0
IX	PpeERF#088	Prupe.8g224700	540	179	20470.7	6.08	0
IX	PpeERF#089	Prupe.1g037800	492	163	18008.7	6.85	0
IX	PpeERF#090	Prupe.8g224800	465	154	17059.7	7.79	0
IX	PpeERF#091	Prupe.1g037700	417	138	15204.7	6.84	0
IX	PpeERF#092	Prupe.4g055600	795	264	29431.3	5.61	0
IX	PpeERF#093	Prupe.4g055500	564	187	20369.6	9.51	2
IX	PpeERF#094	Prupe.6g348700	744	247	28089.7	4.92	0
IX	PpeERF#095	Prupe.8g224600	759	252	28672.0	4.99	1
IX	PpeERF#096	Prupe.1g037900	699	232	25950.8	5.54	1
X	PpeERF#097	Prupe.8g125100	816	271	30318.2	8.16	0
X	PpeERF#098	Prupe.7g134100	801	266	29255.4	7.67	0
X	PpeERF#099	Prupe.5g141200	696	231	25763.5	9.21	0
X	PpeERF#100	Prupe.6g165700	1215	404	43314.9	7.07	2
X	PpeERF#101	Prupe.5g141300	816	271	30005.0	6.16	0
X	PpeERF#102	Prupe.1g214900	741	246	27203.7	6.23	1

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