vvi-miR172s及其靶基因响应赤霉素调控葡萄果实发育的作用分析

doi:10.3864/j.issn.0578-1752.2021.06.011

摘要/Abstract

摘要：

【目的】miR172是植物生长发育的重要调节因子,阐释vvi-miR172s及其靶基因应答赤霉素在葡萄果实不同组织发育过程中的作用,从miRNA角度认识GA调控葡萄果实发育的作用机制。【方法】以‘白罗莎里奥’葡萄为材料,以miR-RACE和PCR技术克隆vvi-miR172a/b/c/d的成熟体和前体序列,由psRNA Target软件预测vvi-miR172s的靶基因;利用RLM-RACE技术验证vvi-miR172s剪切靶基因的裂解作用及其作用位点;采用生物信息学软件对靶基因、靶蛋白进行系统进化、序列结构分析及亚细胞定位预测;通过在线软件PLANTCARE进行启动子作用元件分析;通过qRT-PCR和芯片数据分析vvi-miR172s和靶基因在不同器官、不同发育阶段的基因表达图谱,以及应答GA₃在果实不同组织中的时空表达模式。【结果】克隆鉴定了vvi-miR172a/b/c/d的成熟体和前体序列,预测到VvAP2、VvRAP2-1、VvRAP2-2和VvRAP2-3四个靶基因,验证到裂解产物及其裂解位点,证明它们为vvi-miR172s的真实靶基因。序列结构分析显示,VvAP2、VvRAP2-1、VvRAP2-2、VvRAP2-3均含有10个外显子和9个内含子,其motif元件的种类和数量相似,均含有两个排列顺序相近的AP2蛋白结构域,表明其结构和功能具有一定的保守性;且VvAP2、VvRAP2-1和VvRAP2-2与杨树的亲缘关系较近,VvRAP2-3与大豆具有较高的同源性;靶基因蛋白二级结构均为α-螺旋,可进一步折叠为稳定的三级结构;4个靶蛋白亚细胞定位主要位于细胞核内。启动子作用元件分析发现vvi-miR172c和VvRAP2-1中含有赤霉素响应元件,表明它们可能响应赤霉素调控葡萄生长发育;芯片数据分析显示vvi-miR172c和靶基因的表达模式具有组织或器官特异性,且它们之间呈现一定的负相关,表明它们之间存在负调控作用;RT-qPCR结果显示,随着葡萄果实的发育,果皮中vvi-miR172a/b/d呈下降的表达趋势,而靶基因VvRAP2-1的表达模式相反,表明vvi-miR172a/b/d对VvRAP2-1负调控;果肉中vvi-miR172d的表达水平降低,而靶基因VvAP2的表达水平增加,表明vvi-miR172d与VvAP2呈负相关性。另外,GA₃处理改变了vvi-miR172s的靶模式,增强了果肉和果皮组织中vvi-miR172d与VvRAP2-1的负相关性,同时诱导了vvi-miR172c对VvAP2/VvRAP2-2/VvVvRAP2-3的负调控作用。【结论】VvAP2、VvRAP2-1、VvRAP2-2、VvRAP2-3均为葡萄miR172a/b/c/d的真实靶基因,vvi-miR172家族可能通过vvi-miR172a/b/d和vvi-miR172d分别介导靶基因VvRAP2-1和VvAP2调控果皮和果肉组织的发育过程,而vvi-miR172c和vvi-miR172d及其靶基因可能是GA调控葡萄果皮与果肉组织发育的主要作用因子。

关键词: 葡萄, 果实发育, 赤霉素, miR172, 靶基因

Abstract:

【Objective】 miR172 is an important regulator of plant growth and development. The purpose of this research was to clarify the roles and modes response to gibberellin (GA) of the miR172 family and its target genes in development of different tissues of grape berry. 【Method】The mature and precursor sequences of vvi-miR172a/b/c/d were cloned and identified by miR-RACE and PCR techniques from grapevine cv. Rosario Bianco. The target genes of vvi-miR172s were predicted by psRNA Target software, and the phylogenetic, structure analysis and subcellular localization were performed by bioinformatics tools. RLM-RACE verified the cleavage roles of four target genes by vvi-miR172s. The cis-elements analysis of their promoters was predicted by PLANTCARE software. The qRT-PCR method was used to detect the temporal and spatial expression patterns of vvi-miR172s and target genes in different tissues of grape berry induced by exogenous GA₃ application. 【Result】The mature and precursor sequences of vvi-miR172a/b/c/d were cloned, and four target genes (VvAP2, VvRAP2-1, VvRAP2-2 and VvRAP2-3) were identified from grape genome. The cleavage sites of vvi-miR172s on target genes were detected by RLM-RACE, which proved that VvAP2, VvRAP2-1, VvRAP2-2 and VvRAP2-3 were the true target genes. Gene structure analysis result showed that all target genes contained 10 exons, 9 introns and 2 AP2 domains. The type and number of motif elements were similar, indicating that gene structures were highly conserved. Phylogenetic analysis showed that VvAP2, VvRAP2-1, and VvRAP2-2 were closer to poplar, and VvRAP2-3 had high homology with soybean. The secondary structure prediction of target proteins indicated that they existed in the form of alpha-helix and further folded into the stable tertiary structure. Subcellular localization results showed that all target proteins were mainly located in the nucleus. Both vvi-miR172c and VvRAP2-1 had the hormone related cis-elements response to GA₃, suggesting that they might be involved in the regulation of grape berry development by responding to corresponding hormones. Microarray data analysis revealed that the expression patterns of vvi-miR172c and target genes were tissue or orGA₃n specific. RT-qPCR analysis showed that vvi-miR172a/b/d showed a decrease expression trend in pericarp, while VvRAR2-1 exhibited a reverse expression trend to the former, indicating that vvi-miR172a/b/d neGA₃tively regulated VvRAR2-1. However, in flesh, VvAP2 was contradictory to vvi-miR172d, with the increased expression during grape development, suggesting that there was a significant neGA₃tive correlation between vvi-miR172d and VvAP2. Interestingly, GA₃ treatment promoted the neGA₃tive regulation of vvi-miR172d on VvRAP2-1 and induced the neGA₃tive regulation of vvi-miR172c on VvAP2/VvRAP2-1/VvRAP2-3. 【Conclusion】VvAP2, VvRAP2-1, VvRAP2-2, and VvRAP2-3 were the real target genes of vvi-miR172s. Among the vvi-miR172 family, vvi-miR172 a/b/d might mediate VvRAP2-1 regulation of pericarp development, whereas vvi-miR172d might mediate VvAP2 involved in the development of grape flesh. vvi-miR172c/d and their target genes might participate in the regulation of grape pericarp and flesh development in response to exogenous GA.

Key words: grape, fruit development, gibberellin, miR172, target gene

宣旭娴,盛子璐,解振强,黄雨晴,巩培杰,张川,郑婷,王晨,房经贵. vvi-miR172s及其靶基因响应赤霉素调控葡萄果实发育的作用分析[J]. 中国农业科学, 2021, 54(6): 1199-1217.

XuXian XUAN,ZiLu SHENG,ZhenQiang XIE,YuQing HUANG,PeiJie GONG,Chuan ZHANG,Ting ZHENG,Chen WANG,JingGui FANG. Function Analysis of vvi-miR172s and Their Target Genes Response to Gibberellin Regulation of Grape Berry Development[J]. Scientia Agricultura Sinica, 2021, 54(6): 1199-1217.

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链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2021.06.011

https://www.chinaagrisci.com/CN/Y2021/V54/I6/1199

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引物名称 Primer name	引物序列 Primer sequence	引物用途 Primer use
vvi-miR172a-F	AAGCTTTCGTAGTTGTCTACAAAATGATCTCT	vvi-miR172a前体序列的扩增 Amplification of vvi-miR172a precursor
vvi-miR172a-R	GGATCCCATCGCTTTACATTTTAGCCACT	vvi-miR172a前体序列的扩增 Amplification of vvi-miR172a precursor
vvi-miR172b-F	AAGCTTCGGCATCTTTCTCCTCATACC	vvi-miR172b前体序列的扩增 Amplification of vvi-miR172b precursor
vvi-miR172b-R	GGATCCGGGTTGAAGACGTACATAAATCTCA	vvi-miR172b前体序列的扩增 Amplification of vvi-miR172b precursor
vvi-miR172c-F	AAGCTTTTTGAAGCGTTCTGCTGTC	vvi-miR172c前体序列的扩增 Amplification of vvi-miR172c precursor
vvi-miR172c-R	GGATCCCAGATGAAACACTTCCAAGAGA	vvi-miR172c前体序列的扩增 Amplification of vvi-miR172c precursor
vvi-miR172d-F	AAGCTTGAAGCGAGATCCGTATCCTC	vvi-miR172d前体序列的扩增 Amplification of vvi-miR172d precursor
vvi-miR172d-F	GGATCCATCTCAAATTACTGCATGATTTCAA	vvi-miR172d前体序列的扩增 Amplification of vvi-miR172d precursor
Actin-F	TACAATTCCATCATGAAGTGTGATG	Actin内参引物 Actin internal reference primer
Actin-R	TTAGAAGCACTTCCTGTGAACAATG	Actin内参引物 Actin internal reference primer
VvAP2 qRT-F	CTCGCGCATATGATAGGGCT	VvAP2定量RT-PCR引物 Real-time PCR of VvAP2
VvAP2 qRT-R	ACTTTGTCGGCGAAGGACAT	VvAP2定量RT-PCR引物 Real-time PCR of VvAP2
VvRAP2-1 qRT-F	CAACACTGGGGGTTCATCCA	VvRAP2-1定量RT-PCR引物 Real-time PCR of VvRAP2-1
VvRAP2-1 qRT-R	TTTTGCCATGCCCAGTTTGG	VvRAP2-1定量RT-PCR引物 Real-time PCR of VvRAP2-1
VvRAP2-2 qRT-F	CTGACTACCGTGCAAGGGTT	VvRAP2-2定量RT-PCR引物 Real-time PCR of VvRAP-22
VvRAP2-2 qRT-R	TTTGATCACCCTGGCCTAGC	VvRAP2-2定量RT-PCR引物 Real-time PCR of VvRAP-22
VvRAP2-3 qRT-F	GGGCTAGCAATGACATCGGA	VvRAP2-3定量RT-PCR引物 Real-time PCR of VvRAP2-3
VvRAP2-3 qRT-R	CATTTGCCACCCCCAGTTTG	VvRAP2-3定量RT-PCR引物 Real-time PCR of VvRAP2-3

miRNAs	MiRNA成熟体长度 Length of miRNA	靶基因编号 Target_Acc.	靶基因长度 Length of target	靶区 Target regions	靶区起始、终止位点 Target start and stop sites	错配率 Expectation	允许不匹配的最大能量 UPE	切割方式 Interaction mode
vvi-miR172a/b	21	VIT_07s0031g00220(VvAP2)	2565	CDS:1870-1890	C、C	2.5	15.05	裂解Cleavage
	21	VIT_08s0040g03180(VvRAP2-1)	1730	CDS:1331-1351	C、T	2.5	11.489	裂解Cleavage
	21	VIT_13s0019g03550(VvRAP2-2)	2217	CDS:1566-1586	C、C	2.5	17.172	裂解Cleavage
	21	VIT_06s0004g03590(VvRAP2-3)	2347	CDS:1806-1826	C、T	2.5	14.04	裂解Cleavage
vvi-miR172c	21	VIT_07s0031g00220(VvAP2)	2565	CDS:1870-1890	C、C	0.5	15.05	裂解Cleavage
	21	VIT_08s0040g03180(VvRAP2-1)	1730	CDS:1331-1351	C、T	1.0	11.489	裂解Cleavage
	21	VIT_13s0019g03550(VvRAP2-2)	2217	CDS:1566-1586	C、C	0.5	17.172	裂解Cleavage
	21	VIT_06s0004g03590(VvRAP2-3)	2347	CDS:1806-1826	C、T	1.0	14.04	裂解Cleavage
vvi-miR172d	23	VIT_07s0031g00220(VvAP2)	2565	CDS:1870-1892	C、A	2.0	15.552	裂解Cleavage
	23	VIT_08s0040g03180(VvRAP2-1)	1730	CDS:1331-1353	C、G	1.5	9.197	裂解Cleavage
	23	VIT_13s0019g03550(VvRAP2-2)	2217	CSS:1566-1588	G、A	2.5	22.9	裂解Cleavage
	23	VIT_06s0004g03590(VvRAP2-3)	2347	CDS:1806-1828	C、A	0.5	14.075	裂解Cleavage