鲜食葡萄果实单萜合成关键基因的eQTL分析

doi:10.3864/j.issn.0578-1752.2022.05.011

中国农业科学 ›› 2022, Vol. 55 ›› Issue (5): 977-990.doi: 10.3864/j.issn.0578-1752.2022.05.011

鲜食葡萄果实单萜合成关键基因的eQTL分析

王慧玲¹(),闫爱玲²,孙磊³,张国军¹,王晓玥¹,任建成¹,徐海英¹()

¹北京市农林科学院林业果树研究所,北京 100093
²北京市落叶果树工程技术研究中心,北京 100097
³农业部华北地区园艺作物生物学与种质创制重点实验室,北京 100097

收稿日期:2021-05-17 接受日期:2021-07-27 出版日期:2022-03-01 发布日期:2022-03-08
通讯作者: 徐海英
作者简介:王慧玲,E-mail： wanghui198216@126.com。
基金资助:
北京市自然科学基金(6182007);国家自然科学基金青年基金(31601712);北京市农林科学院创新能力建设专项(KJCX20200406);财政部和农业农村部：国家现代农业产业技术体系(CARS-29)

eQTL Analysis of Key Monoterpene Biosynthesis Genes in Table Grape

WANG HuiLing¹(),YAN AiLing²,SUN Lei³,ZHANG GuoJun¹,WANG XiaoYue¹,REN JianCheng¹,XU HaiYing¹()

¹Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093
²Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing 100097
³Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing 100097

Received:2021-05-17 Accepted:2021-07-27 Online:2022-03-01 Published:2022-03-08
Contact: HaiYing XU

摘要/Abstract

摘要：

【目的】通过对鲜食葡萄果实单萜合成关键基因进行eQTL定位及候选基因挖掘,深入了解单萜合成调控机制,为优良玫瑰香味葡萄新品种培育及种质改良奠定基础。【方法】以‘摩尔多瓦’×‘瑞都香玉’F₁代群体及亲本为供试材料,分别在转色期和成熟期采集葡萄果实样品;利用实时荧光定量qPCR技术对7个单萜合成途径基因（VvDXS1、VvDXS3、VvDXR、VvHDR、VvLiner、VvTerp和VvGermD）的表达量进行检测获得表达性状表型数据;基于区间作图法,采用MapQTL6.0软件,对单萜基因表达性状进行eQTL定位分析;将eQTL连锁标记定位到基因组区域,通过Ensembl Plants和NCBI数据库进行基因注释;利用葡萄全基因组芯片技术检测不同发育时期亲本果实样品中候选基因的表达谱。【结果】7个单萜合成基因表达量在F₁代群体中呈现连续分布数量遗传特征;各个单萜基因表达之间具有显著的相关性;在转色期,7个表达性状一共定位到13个eQTL,主要位于1号、6号、14号、16号、17号、10号和12号等染色体上,表型解释率介于12.2%—23.5%。其中位于14号染色体的eQTL（qDXS1-v14、qHDR-v14-1和qTerp-v14）覆盖相同的遗传区间57.582—76.979 cM,qLiner-v10、qTerp-v10和qGermD-v10共定位到10号染色体相同的遗传区间;在成熟期,共检测到16个eQTL,主要位于1号、6号、12号、8号、13号和19号等染色体。qDXS1-m6-2、qDXR-m6-2、qLiner-m6和qGermD-m6共定位到6号染色体139.212—143.161 cM遗传区间;针对成熟期与转色期各个基因的表达量比值变化进行定位分析,共检测到18个eQTL,分别位于1号、3号、7号、10号、12号、15号和19号等染色体。定位于12号染色体的qDXS1-r12-1、qDXR-r12-1、qHDR-r12、qLiner-r12和qGermD-r12覆盖相同的遗传区间6.330—6.967 cM。对多个基因表达性状共定位的eQTL区域进行基因注释,共筛选到90个转录因子基因,表达谱及相关性分析最终确定11候选基因。其中4个候选基因（VIT_06s0009g01380、VIT_14s0006g02290、VIT_12s0028g01170和VIT_15s0046g00290）与激素信号通路调控相关,一个候选基因（VIT_12s0028g01110）编码光敏色素作用因子与光响应相关,还有一些编码Myb类、WRKY类转录因子或者未知功能蛋白基因。【结论】在两个不同的生长发育期共检测到37个与单萜合成基因表达性状连锁的eQTL,主要定位于6号、10号、12号和14号染色体。基于基因注释和表达谱分析结果,确定了包含VIT_06s0009g01380和VIT_14s0006g02290在内的11个可能的候选基因,这些候选基因与多个单萜基因表达高度相关。

关键词: 葡萄, 单萜, 关键基因, eQTL

Abstract:

【Objective】The eQTL mapping for monoterpene biosynthesis related gene expression traits were performed and the candidate genes were mined to deeply understand the regulation mechanism of monoterpene synthesis, so as to lay a foundation for the cultivation of new Muscat grape varieties and germplasm improvement.【Method】The F₁ population generated by crossing Moldova and Ruiduxiangyu were used as materials in this study, and the grape berry samples were collected at verasion and ripening stage respectively. The phenotypic data of expression traits were obtained by detecting the expression levels of seven monoterpene synthesis pathway genes (VvDXS1, VvDXS3, VvDXR, VvHDR, VvLiner, VvTerp, and VvGermD) by using real-time quantitative qPCR technique. eQTL mapping of monoterpene gene expression traits were performed with the mapQTL6.0 software based on the interval mapping method. The associated markers of eQTL were mapped to the genomic region, and the genes within eQTLs were annotated and analyzed via the databases of Ensembl Plants and NCBI. The expression profiles of candidate genes in the samples of parents at different developmental stages were detected by grape whole genome microarray.【Result】The expression levels of seven monoterpene biosynthesis related genes in F₁ population showed a continuous quantitative genetic distribution. A significant correlation between the expression of monoterpene genes was observed. At verasion, 13 eQTLs for the seven expression traits were mapped on chromosome 1, 6, 14, 16, 17, 10 and 12, respectively, and the phenotypic explanation value ranged from 12.2% to 23.5%. Among them, eQTLs (qDXS1-v14, qHDR-v14-1 and qTerp-v14) on chromosome 14 covered the same genetic interval of 57.582-76.979 cM, and qLiner-v10, qTerp-v10 and qGermD-v10 were co-located on chromosome 10. At the mature stage, 16 eQTLs were detected, mainly located on chromosome 1, 6, 12, 8, 13 and 19. qDXS1-m6-2, qDXR-m6-2, qLiner-m6 and qGermD-m6 were co-located in the genetic interval 139.212-143.161 cM of chromosome 6. In addition, a total of 18 eQTLs on chromosomes 1, 3, 7, 10, 12, 15 and 19 were detected for the change ratio of each gene expression between maturity and verasion, respectively. qDXS1-r12-1, qDXR-r12-1, qHDR-r12, qLiner-r12 and qGermD-r12 covered the same genetic interval of 6.330-6.967cM on chromosome 12. The eQTL region for multiple expression traits co-located were further annotated, 90 transcription factor genes were screened, and 11 candidate genes were finally identified by expression profile and correlation analysis. Among them, four candidate genes of VIT_06s0009g01380, VIT_14s0006g02290, VIT_12s0028g01170 and VIT_15s0046g00290 were predicted to participate in the regulation of hormone signaling pathway, one candidate gene VIT_12s0028g01110 encodes a phytochrome interacting factor related to light response, and some other genes encode Myb, WRKY transcription factors or unknown functional proteins.【Conclusion】A total of 37 eQTLs linked to monoterpene synthesis gene expression traits were detected at two different development stages, which mainly located on chromosome 6, 12 and 14. Based on the results of gene annotation and expression profile analysis, 11 candidate genes including VIT_14s0006g02290 and VIT_06s0009g01380 were identified, and these candidate genes were highly correlated with the expression of multiple monoterpene genes.

Key words: grape, monoterpenes, key genes, eQTL

王慧玲, 闫爱玲, 孙磊, 张国军, 王晓玥, 任建成, 徐海英. 鲜食葡萄果实单萜合成关键基因的eQTL分析[J]. 中国农业科学, 2022, 55(5): 977-990.

WANG HuiLing, YAN AiLing, SUN Lei, ZHANG GuoJun, WANG XiaoYue, REN JianCheng, XU HaiYing. eQTL Analysis of Key Monoterpene Biosynthesis Genes in Table Grape[J]. Scientia Agricultura Sinica, 2022, 55(5): 977-990.

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图/表 6

图1

表1

表2

中性图谱单萜合成相关基因eQTL信息"

时期 Stage	性状 Trait	eQTL	染色体 Chr	遗传区间 Genetic interval (cM)	连锁标记 Flanking markers	LOD	贡献率 PVE (%)
转色期 Verasion stage	eDXS1	qDXS1-v1	1	82.774-84.732	Marker 2482511-2542941	3.40	17.0
		qDXS1-v6	6	142.161-144.209	Marker1008751-945452	3.34	15.7
		qDXS1-v14	14	57.582-76.979	Marker3121221-2890139	3.25	15.9
	eDXS3	qDXS3-v12	12	19.009-32.463	Marker2115844-2041250	3.31	16.4
		qDXS3-v16	16	101.122-119.350	Marker3956150-4116611	3.89	23.5
		qDXS3-v17	17	150.480-166.103	Marker99497-145961	4.32	23.1
	eDXR	qDXR-v17	17	159.789-171.002	Marker179340-108104	3.48	14.4
	eHDR	qHDR-v14-1	14	55.582-77.612	Marker3121221-3072285	3.47	16.7
	eHDR	qHDR-v14-2	14	118.734-126.198	Marker3063685-2947572	3.27	15.6
	eLiner	qLiner-v10	10	146.183-148.835	Marker352188-357432	3.06	14.8
	eTerp	qTerp-v10	10	141.902-158.171	Marker368243-378995	2.74	13.7
	eTerp	qTerp-v14	14	53.582-77.612	Marker2969612-3072285	2.58	12.2
	eGermD	qGermD-v10	10	145.183-148.835	Marker352188-357432	3.17	16.0
成熟期 Mature stage	eDXS1	qDXS1-m1	1	76.426-80.809	Marker2437047-2596447	3.66	17.7
		qDXS1-m6-1	6	93.373-106.403	Marker924262-876360	3.55	17.2
		qDXS1-m6-2	6	139.212-146.773	Marker930737-877032	3.82	18.3
		qDXS1-m12	12	17.659-19.009	Marker2187251-2115844	3.54	17.1
	eDXS3	qDXS3-m3	3	175.011-175.191	Marker831346-700177	3.07	13.9
	eDXR	qDXR-m1	1	78.832-81.788	Marker2560950-2467293	3.88	18.3
		qDXR-m6-1	6	93.373-114.095	Marker924262-1008711	3.74	18.7
		qDXR-m6-2	6	138.212-147.119	Marker990833-871012	3.68	17.7
		qDXR-m12	12	16.435-19.009	Marker2088221-2115844	3.78	18.2
	eHDR	qHDR-m8	8	152.133-176.371	Marker1386586-1434785	3.4	15.1
	eHDR	qHDR-m13	13	25.115-36.319	Marker1631867-1651434	3.52	18.6
	eLiner	qLiner-m6	6	139.495-141.161	Marker930737-930878	3.53	17.1
	eLiner	qLiner-m12	12	6.330-6.967	Marker2067228-2134286	3.57	17.2
	eTerp	qTerp-m7	7	92.355	Marker2374114	3.52	17.5
	eTerp	qTerp-m19	19	158.927-163.008	Marker3714935-r3520942	3.79	18.2
	eGermD	qGermD-m6	6	139.212-143.161	Marker930737-930878	3.66	17.7
成熟期/转色期 Mature/Verasion	eDXS1	qDXS1-r7	7	92.355-100.371	Marker2345090-Marker2198875	3.72	15.5
		qDXS1-r12-1	12	4.153-11.756	Marker2118601-2076541	3.86	15.7
		qDXS1-r12-2	12	13.602-19.660	Marker2083394-2088370	3.66	14.4
	eDXS3	qDXS3-r1	1	146.688-148.053	Marker2438419-2557770	3.85	15.3
	eDXS3	qDXS3-r3	3	180.498-180.525	Marker751963-733688	3.65	13.6
	eDXR	qDXR-r7	7	92.355	Marker2345090-2374114	3.59	14.1
		qDXR-r12-1	12	6.330-6.967	Marker2067228-2134286	3.54	13.2
		qDXR-r12-2	12	13.602-18.491	Marker2083394-2178064	3.5	12.5
	eHDR	qHDR-r10	10	120.227-130.912	Marker237117-341831	3.8	18.8
		qHDR-r12	12	9.490-10.127	Marker2051100-2158802	3.53	11.0
		qHDR-r15	15	103.260-123.35	Marker1985545-1825916	3.75	14.9
	eLiner	qLiner-r12	12	5.419-10.756	Marker2067228-2076541	3.73	12.9
	eLiner	qLiner-r19	19	159.927-160.217	Marker3714935-3690871	3.58	12.2
	eTerp	qTerp-r7	7	92.355-100.371	Marker2345090-2198875	3.65	16.0
	eTerp	qTerp-r19	19	158.927-163.008	Marker3714935-3520942	3.86	14.8
	eGermD	qGermD-r3	3	178.095-180.525	Marker738834-733688	3.66	15.1
	eGermD	qGermD-r12	12	6.330-6.967	Marker2067228-2134286	3.55	14.6

表2

图2

图3

表3

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性状Traits	eDXS1	eDXS3	eDXR	eHDR	eLiner	eTerp	eGermD
eDXS1		0.65**	0.89**	0.91**	0.86**	0.80**	0.71**
eDXS3	0.34**		0.53**	0.55**	0.54**	0.49**	0.40**
eDXR	0.90**	0.47**		0.85**	0.86**	0.85**	0.79**
eHDR	0.76**	0.41**	0.72**		0.80**	0.77**	0.75**
eLiner	0.85**	0.36**	0.81**	0.54**		0.91**	0.80**
eTerp	0.85**	0.35**	0.79**	0.55**	0.94**		0.85**
eGermD	0.77**	0.34**	0.74**	0.52**	0.80**	0.78**

染色体Chromosome	基因ID Gene ID	基因注释 Gene annotation
6	VIT_06s0009g00880	轴向调控蛋白YABBY2 PREDICTED: Putative axial regulator YABBY 2 [Vitis vinifera]
	VIT_06s0004g05120	未知功能Myb类蛋白LOC100253567 PREDICTED: Uncharacterized protein LOC100253567 [Vitis vinifera] Myb-like
	VIT_06s0009g01380	乙烯不敏感类蛋白3 PREDICTED: Protein ETHYLENE INSENSITIVE 3-like [Vitis vinifera]
14	VIT_14s0006g01280	未知功能蛋白LOC100265568 Uncharacterized protein LOC100265568 [Vitis vinifera]
	VIT_14s0006g01620	转录抑制因子MYB4 PREDICTED: Transcription repressor MYB4 [Vitis vinifera]
	VIT_14s0006g01340	未命名Myb类蛋白 Unnamed protein product [Vitis vinifera] Myb-like
	VIT_14s0006g02290	类乙烯响应转录因子ERF034 PREDICTED: Ethylene-responsive transcription factor ERF034-like [Vitis vinifera]
10	VIT_10s0116g01200	类WRKY 6转录因子 PREDICTED: WRKY transcription factor 6-like [Vitis vinifera]
12	VIT_12s0028g01110	类光敏色素作用因子PIF5 PREDICTED: Transcription factor PIF5-like [Vitis vinifera]
12	VIT_12s0028g01170	类生长素响应因子6 PREDICTED: Auxin response factor 6-like [Vitis vinifera]
15	VIT_15s0046g00290	类生长素响应因子18 PREDICTED: Auxin response factor 18-like [Vitis vinifera]

鲜食葡萄果实单萜合成关键基因的eQTL分析

eQTL Analysis of Key Monoterpene Biosynthesis Genes in Table Grape

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