苹果OFP基因家族的全基因组鉴定与非生物逆境表达分析

doi:10.3864/j.issn.0578-1752.2018.10.014

摘要/Abstract

摘要：

目的从苹果全基因组中鉴定OFP（OVATE family protein）家族蛋白成员,对其进行基因结构特征、组织表达及非生物逆境等系统分析,为研究苹果OFP的潜在功能提供理论基础。方法利用生物信息学手段,在苹果基因组数据库中筛选鉴定OFP基因家族成员;利用MEGA5.0软件进行系统进化树分析;通过MapDraw和GSDS等生物信息学工具分析基因结构及染色体定位;根据已有的苹果芯片数据库结果进行OFP基因表达谱分析;利用实时荧光定量PCR技术检测13个MdOFP的组织表达和诱导表达情况。结果苹果OFP基因家族包含28个成员,根据系统进化关系将其分为4组,分别包含13、6、4和5个成员;苹果中13条染色体上均有OFP基因分布,其中第12条染色体最多,有6个MdOFP成员,该基因家族的分布具有广泛性;芯片表达谱分析结果表明该类基因家族在花、果实和叶中的表达量较高,qRT-PCR验证结果较一致;经NaCl和PEG处理后,苹果根部与地上部呈现出不同程度的响应差异,NaCl处理明显诱导两组织中MdOFP04和MdOFP20的表达,MdOFP01、MdOFP12和MdOFP18的表达在根部与地上部组织则相反;温度胁迫明显影响MdOFPs的表达量,其中MdOFP04和MdOFP17经高温和低温胁迫处理后均明显上调。结论苹果OFP基因家族共有28个成员,分布于13条染色体上,该家族成员呈现出不同的组织表达模式和胁迫响应模式。

关键词: 苹果, OFP基因家族, 系统进化, 胁迫, 基因表达

Abstract:

【Objective】 Identification of the OFP (OVATE family protein) genes from apple genome and analysis of gene characteristic, tissue expression pattern and response to abiotic stresses of OFP family genes in apple will be useful to the functional analysis of plant OFP genes. 【Method】 Based on apple genome database, the OFP gene family members were identified and the genes were analyzed using bioinformatics methods. A phylogenetic tree was created using the MEGA5.0 program. Gene structure and chromosomes location were carried out by MapDraw and GSDS separately. Expression pattern analysis of OFP genes in different tissues was done based on the existing microarray database and qRT-PCR. The expression of 13 MdOFPs genes was also analyzed under various stress conditions using qRT-PCR. 【Result】 A total of 28 OFP genes was systematically identified from apple genome and classified into 4 groups including 13, 6, 4 and 5 members according to the gene structure and conserved domain phylogeny relationship. All OFP genes are distributed on 13 apple chromosomes with the largest number six MdOFP on Chr12, suggesting that they have an extensive distribution on the apple chromosomes. Most of the OFP genes have distinctive expression patterns in tissues and response to NaCl and PEG treatment stresses in root and shoot, respectively. MdOFP04 and MdOFP20 were up-regulated obviously in root and shoot, while MdOFP01, MdOFP12 and MdOFP18 have opposite expression pattern in root and shoot under NaCl stress. Temperature stresses significantly regulate the expression of MdOFP and the expression of MdOFP04 and MdOFP17 were significantly increased after high temperature and low temperature stresses. 【Conclusion】 Twenty-eight OFP genes in apple were identified by genome-wide screening. They are classified into four groups and distributed on 13 chromosomes with different tissue patterns and different stress response patterns. These results will be helpful to the functional analysis of OFP genes in apple.

Key words: apple, OFP gene family, phylogeny analysis, stress, gene expression

许瑞瑞, 李睿, 王小非, 郝玉金. 苹果OFP基因家族的全基因组鉴定与非生物逆境表达分析[J]. 中国农业科学, 2018, 51(10): 1948-1959.

RuiRui XU, Rui LI, XiaoFei WANG, YuJin HAO. Identification and Expression Analysis Under Abiotic Stresses of OFP Gene Family in Apple[J]. Scientia Agricultura Sinica, 2018, 51(10): 1948-1959.

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图/表 9

表1

表2

苹果OFP基因家族信息"

基因名称Gene name	基因ID号 Gene Identifier	染色体定位 Chromosome location	编码序列长度 CDS length (bp)	外显子数目 Exon no.	大小 Size (aa)	分子量Molecular weight (Da)	等电点Isoelectric Point	拟南芥同源基因 Best homologs in Arabidopsis
MdOFP01	MDP0000243940	chr2:4251394..4252275	882	1	293	33533.3	9.13	AT5G66270.1
MdOFP02	MDP0000155311	chr2:13187873..13188835	963	1	320	25246.9	9.10	AT1G19860.1
MdOFP03	MDP0000684645	chr3:4952419..4953570	1152	1	383	41697.8	8.99	AT1G19860.1
MdOFP04	MDP0000141642	chr3:16219260..16220244	675	2	224	25723.6	9.51	AT1G19860.1
MdOFP05	MDP0000733399	chr3:31034178..31034924	747	1	248	79142.9	5.58	AT2G02160.1
MdOFP06	MDP0000134728	chr4:17309604..17310695	1092	1	363	72112.4	6.00	AT5G12440.3
MdOFP07	MDP0000147045	chr4:17310063..17310721	627	2	208	26669.0	8.73	AT3G12130.1
MdOFP08	MDP0000158931	chr5:941980..942486	507	1	168	51797.0	8.27	AT5G18550.1
MdOFP09	MDP0000241313	chr5:5755844..5757320	1296	2	431	30624.6	9.44	AT3G12130.1
MdOFP10	MDP0000402356	chr7:5438947..5439702	756	1	251	40999.8	8.81	AT3G08505
MdOFP11	MDP0000296199	chr8:3579420..3580445	1026	1	341	47229.3	7.10	AT2G41900.1
MdOFP12	MDP0000155705	chr10:26964000..26965493	1296	2	431	79656.8	6.14	AT3G51950
MdOFP13	MDP0000909475	chr10:32149450..32149956	507	1	168	16845.6	8.27	AT5G26749.1
MdOFP14	MDP0000156202	chr11:4775252..4776394	1143	1	380	91640.3	7.22	AT1G10320.1
MdOFP15	MDP0000311969	chr11:22625025..22626007	549	2	182	75934.3	6.24	AT1G30460.1
MdOFP16	MDP0000127146	chr11:32348926..32350337	912	2	303	73772.2	6.10	AT1G30460.1
MdOFP17	MDP0000669940	chr12:3242911..3248219	957	3	318	20954.5	6.24	AT3G48440.1
MdOFP18	MDP0000137053	chr12:3317131..3317688	558	1	185	65503.5	9.21	AT1G19860.1
MdOFP19	MDP0000456557	chr12:14175298..14181532	1317	3	438	98062.9	5.78	AT3G51120.1
MdOFP20	MDP0000692068	chr12:21920389..21922396	1098	2	365	20469.1	9.34	AT1G66810.1
MdOFP21	MDP0000238712	chr12:21920806..21921922	1065	2	354	93378.1	8.34	AT3G27700
MdOFP22	MDP0000332435	chr12:25821429..25822584	1161	1	386	77290.9	6.31	AT2G33835.1
MdOFP23	MDP0000410437	chr13:18948503..18949252	750	1	249	76306.6	6.34	AT2G41900.1
MdOFP24	MDP0000943578	chr13:25670394..25671158	765	1	254	57322.6	5.28	AT1G01350.1
MdOFP25	MDP0000243386	chr14:4693458..4695714	1020	2	339	22465.2	6.99	AT3G19360.1
MdOFP26	MDP0000140421	chr15:11737514..11738332	822	1	273	44526	9.32	AT3G47120.1
MdOFP27	MDP0000259366	chr17:16535235..16536098	864	1	287	76587.0	5.93	AT2G02160.1
MdOFP28	MDP0000921224	chr0:61416319..61416894	576	1	191	172448.5	8.12	AT1G21580.1

表2

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基因名称 Gene name	上游引物（5′-3′） Forward primer (5′-3′)	下游引物（5′-3′） Reverse primer (5′-3′)
MdOFP01	TCCCGTTTAGTTCTTCATCTTTC	CAGTGTGTCAATCTCGTCATC
MdOFP03	CGTGGTAGAAAGAGTGTGTC	GATAGCAAGCAAGCAGGTC
MdOFP04	CAACAACAACTCGTCCTTACAG	TTCCTTCACCACCGCAATG
MdOFP06	CGGAGGATGGGTTGGATTC	TTCTTGTTCTTCTTCAGTTCGC
MdOFP07	CGGAGGATGGGTTGGATTC	TTCTTGTTCTTCTTCAGTTCGC
MdOFP08	CAATGGAGGAAATGGTGGAATG	AGCAGAAAGAGCAAGAAGGAG
MdOFP11	GGAGGAGAAGACGCAATAGAG	CCCATCACCACCATCATCAG
MdOFP12	TTCAAGCCGTTCAGCCTCAG	GTTCATCACAAGACCGCCATC
MdOFP13	AGAGAGAAACACCACCGAAG	TTGCCCTGAGCGAGAAAG
MdOFP16	CTCCTTCTTGCTCTTTCTGC	CATCCTCCTCCTGACCTTG
MdOFP17	AGGGTGAATGGTAAGAGCAATC	GACGACAGCGACGAAGAAG
MdOFP18	TGCTGTGGTGAAGAAGTCG	CCCTGTGATGGTGTGTCG
MdOFP20	TCCTCCTCGCAGTCACAC	TTCCTTCACCACCGCAATG
Md18S	ACACGGGGAGGTAGTGACAA	CCTCCAATGGATCCTCGTTA