基于SNP遗传图谱对甘蓝型油菜部分脂肪酸 组成性状的QTL定位

doi:10.3864/j.issn.0578-1752.2019.21.002

摘要/Abstract

摘要：

目的菜籽油在烹饪、食品加工及工业生产中广泛应用,因此,根据生产需要改善菜籽油脂肪酸组分是油菜育种的重要目标。通过对2种环境下甘蓝型油菜主要脂肪酸组成进行QTL定位分析,寻找甘蓝型油菜脂肪酸组分的QTL及影响本群体脂肪酸组分的候选基因。方法以人工合成甘蓝型油菜10D130和甘蓝型油菜常规品种中双11构建高世代重组自交系（RIL）为研究材料,分别于2016-2017年和2017-2018年2个年度在重庆市北碚区2个不同的环境中设置田间试验,收获自交种子,采用气相色谱法3次重复对种子的脂肪酸组分进行分析。利用油菜6K SNP芯片对该RIL群体进行基因分型,DNA样品预处理及芯片处理严格按照Illumina Inc 公司Infinium HD Assay Ultra操作说明进行。取最小阈值LOD 2.0利用JoinMap4.0软件构建高密度遗传连锁图谱。通过QTL IciMapping V4.1完备区间作图法对油菜主要脂肪酸组成进行QTL定位。结果 2种环境中,两亲本各性状间差异及RIL群体各性状在株系间差异均达到显著或极显著水平,且6种脂肪酸含量在2个环境中均表现为连续分布,适合进行QTL检测。构建用于QTL定位的遗传图谱包含1 897个多态性SNP标记,覆盖甘蓝型油菜基因组3 214.19 cM,平均图距1.69 cM。利用此图谱,在2个环境共检测到位于8条染色体上的23个控制脂肪酸组分QTL位点,与硬脂酸、油酸、亚油酸、亚麻酸、廿碳烯酸和芥酸含量相关的QTL位点分别为6、3、4、5、2和3个,其中在A05、A08和C03染色体上发现多种脂肪酸含量的QTL“富集区”。在A05染色体上检测到亚油酸和亚麻酸含量重叠的主效QTL,亚油酸与亚麻酸表现加性效应相同;在A08和C03上都检测到油酸、廿碳烯酸和芥酸含量重叠的主效QTL,油酸与廿碳烯酸及芥酸表现加性效应相反。与拟南芥脂肪酸代谢基因进行同源性比对分析,在17个QTL置信区间内筛选到22个候选基因,主要通过编码脂肪酸去饱和酶、全羧化酶合酶、碳链延长酶和参与酰基辅酶A生物合成等途径调控脂质的生物合成和代谢。结论利用甘蓝型油菜6K SNP芯片准确定位了2种环境条件脂肪酸组成的QTL位点,筛选到位于A05、A08和C03染色体上多种脂肪酸QTL的“富集区”,并与拟南芥脂肪酸代谢基因比对出该群体油菜脂肪酸代谢基因,可作为改善油菜籽脂肪酸组成的重要区段及候选基因。

关键词: 甘蓝型油菜, 脂肪酸, 遗传图谱, QTL, 候选基因

Abstract:

【Objective】 Rapeseed oil is widely used in cooking, food processing and industrial production. Therefore, improving the fatty acid composition of rapeseed oil according to the specific production objective is an important goal of rapeseed breeding. In this study, QTL mapping of main fatty acid composition in Brassica napus under two environments was conducted, which was designed to search for the QTL and related candidate genes of fatty acid components in Brassica napus.【Method】 The high generation recombinant inbred lines (RILs) were used as experiment materials, which were derived from synthetic 10D130 and conventional variety Zhongshuang11, and field experiments were conducted in 2016-2017 and 2017-2018 with two different environments in Beibei District of Chongqing City, respectively. After self-pollinated seeds were harvested each year, fatty acid components of seeds were measured by GC with three technical repeats. Then, the RIL population genotype was analyzed with the rapeseed 6K SNP chip array. The DNA preparation and the chip preparation were processed strictly according to Infinium HD Assay Ultra manual of Illumina Inc. The SNP linkage map was constructed by using JoinMap 4.0 program with minimum LOD 2.0. QTL mapping of main fatty acid composition was conducted by composite interval mapping using software Windows QTL IciMapping V4.1.【Result】 In the two environments, the differences of parents’ traits and RILs population’s traits reached significant or extremely significant levels, and the contents of six fatty acids showed continuous distribution, which were suitable for the detection of QTLs. The reference SNP genetic map contains 1 897 polymorphic SNP markers, covering 3 214.19 cM of Brassica napus genome with an average map distance of 1.69 cM. Twenty-three QTLs loci of fatty acid components on 8 chromosomes were detected in two environments. The QTLs loci related to stearic acid, oleic acid, linoleic acid, linolenic acid, eicosapentaenoic acid and erucic acid contents were 6, 3, 4, 5, 2 and 3, respectively. And the “enrichment regions” of multiple fatty acid contents were found on chromosomes A05, A08 and C03. Meantime, the main QTL with overlapping linoleic acid and linolenic acid content was detected on A05 chromosome, showing the same additive effect. And the main effect QTLs, oleic acid with overlapping contents of eicosenic acid and erucic acid were detected on A08 and C03, which was opposite to the additive effect of eicosenic acid and erucic acid. Twenty-two candidate genes of fatty acid metabolic were found underlying confidence intervals of seventeen QTLs by comparing with homologous genes in Arabidopsis thaliana. These genes regulate lipid biosynthesis and metabolism through encoding fatty acid desaturase, total carboxylase synthase, carbon chain lengthening enzyme and participating in acyl coenzyme A biosynthesis. 【Conclusion】 The fatty acid composition QTL under two environments were mapped accurately with the 6K SNP chip of rapeseed, and the “enrichment regions” of multiple fatty acid QTLs on chromosomes A05, A08 and C03 were screened. Compared with Arabidopsis thaliana fatty acid metabolic genes, candidate genes for fatty acid metabolism in this population were detected, which could be used for improving fatty acid composition in rapeseed.

Key words: Brassica napus, fatty acid, genetic map, QTL, candidate gene

叶桑,崔翠,郜欢欢,雷维,王刘艳,王瑞莉,陈柳依,曲存民,唐章林,李加纳,周清元. 基于SNP遗传图谱对甘蓝型油菜部分脂肪酸组成性状的QTL定位[J]. 中国农业科学, 2019, 52(21): 3733-3747.

YE Sang,CUI Cui,GAO HuanHuan,LEI Wei,WANG LiuYan,WANG RuiLi,CHEN LiuYi,QU CunMin,TANG ZhangLin,LI JiaNa,ZHOU QingYuan. QTL Identification for Fatty Acid Content in Brassica napus Using the High Density SNP Genetic Map[J]. Scientia Agricultura Sinica, 2019, 52(21): 3733-3747.

图/表 6

图1

表2

表3

油菜主要脂肪酸含量在2个环境中的QTL位点"

性状 Trait	环境 Envi.	QTL	染色体 Chr.	标记区间 Position	置信区间¹⁾ Confidence interval	LOD	加性效应 Additive effect	贡献率 R²(%)
C18:0	17Cq	qA08ST-1	A08	S-95505568-S-95506507	43.27-48.50	6.13	-0.22	14.00
		qC03ST	C03	S-177827612-S-95636886	216.25-219.73	5.11	-0.20	11.59
	18Cq	qA01ST	A01	S-95637833-S-95664701	116.00-118.62	4.94	0.13	5.08
		qA05ST	A05	S-177830309-S-86232724	107.59-110.16	6.07	0.15	6.27
		qA08ST-2	A08	S-95506569-S-95506120	29.90-31.07	20.45	-0.29	25.49
		qA09ST	A09	S-182142581-S-182167880	224.50-229.51	8.76	-0.18	9.45
		qC03ST	C03	S-95665809-S-95636886	215.70-219.73	8.31	-0.17	9.12
C18:1	17Cq	qA05OL	A05	S-182087654-S-86232724	106.33-110.16	4.59	3.81	3.80
		qA08OL	A08	S-95507415-S-95663297	26.79-30.00	31.31	-11.42	34.39
		qC03OL	C03	S-105305847-S-182158964	218.48-222.84	29.65	-10.95	31.80
	18Cq	qA05OL	A05	S-182087654-S-86232724	106.33-110.16	8.40	3.91	5.70
		qA08OL	A08	S-95507415-S-95663297	26.79-30.00	31.83	-8.66	28.28
		qC03OL	C03	S-105338742-S-182138971	219.51-224.50	42.44	-10.75	43.68
C18:2	17Cq	qA05LI	A05	S-182087654-S-86232724	106.33-110.16	18.43	-2.37	22.67
		qA08LI	A08	S-177633794-S-95506569	25.61-29.50	8.45	-1.48	8.91
		qC03LI-1	C03	S-105306222-S-95637726	235.80-239.65	14.65	-2.06	17.00
		qC03LI-2	C03	S-105309588-S-105307276	250.03-253.95	6.28	1.28	6.69
	18Cq	qA05LI	A05	S-182087654-S-86232724	106.33-110.16	19.71	-1.84	25.25
		qA08LI	A08	S-95507415-S-95663297	26.79-30.00	9.44	-1.18	10.49
		qC03LI-1	C03	S-95637910-S-105307365	237.50-239.83	11.09	-1.30	12.56
C18:3	17Cq	qA02LN	A02	S-95666343-S-95638378	55.50-64.85	4.96	-0.44	8.49
		qC07LN	C07	S-105339086-S-179307020	6.50-11.97	5.84	0.51	11.66
	18Cq	qA05LN	A05	S-182087654-S-86232724	106.33-110.16	33.12	-1.12	23.66
		qA09LN	A09	S-182142581-S-182167880	224.50-229.51	8.28	0.47	4.24
		qA10LN	A10	S-177910390-S-95636447	59.94-63.16	4.90	0.35	2.37
C20:1	17Cq	qC03EI	C03	S-105338742-S-182138971	219.51-224.50	7.45	2.27	17.23
	18Cq	qA08EI	A08	S-95507415-S-95663297	26.79-30.00	6.07	2.14	11.18
		qC03EI	C03	S-105338742-S-182138971	219.51-224.50	11.44	3.05	22.69
C22:1	17Cq	qA08ER-1	A08	S-95506362-S-95664454	10.05-12.58	11.30	5.00	9.39
		qA08ER-2	A08	S-95507415-S-95663297	26.79-30.00	27.90	9.13	32.21
		qC03ER	C03	S-105305847-S-182158964	218.48-222.84	32.17	9.62	36.01
	18Cq	qA08ER-2	A08	S-95507415-S-95663297	26.79-30.00	96.68	17.53	67.26
		qC03ER	C03	S-105305847-S-182158964	218.48-222.84	50.41	8.64	16.45

表3

图2

表4

在甘蓝型油菜脂肪酸含量QTL置信区间比对拟南芥相关基因获得的候选基因"

染色体 Chr.	预测基因 Gene prediction	物理位置 Physical position (Mb)	拟南芥相关基因 Related genes in A. thaliana
染色体 Chr.	预测基因 Gene prediction	物理位置 Physical position (Mb)	基因名称 Gene name	基因登录号 Gene accession	E值 E-value	描述 Description
A01	BnaA01g27100D	18.94	HAL3A	AT3G18030	E^-60	辅酶A生物合成过程 Coenzyme A biosynthetic process
	BnaA01g27120D	18.94	HAL3B	AT1G48605	5E^-23	辅酶A生物合成过程 Coenzyme A biosynthetic process
A02	BnaA02g13270D	7.29	LACS9	AT1G77590	2E^-52	长链酰基辅酶A合成酶9 Long chain acyl-CoA synthetase 9
	BnaA02g13310D	7.31	KCR1	AT1G67730	2E^-74	β-酮酰辅酶A还原酶1 Beta-ketoacyl-CoA reductase 1
	BnaA02g13630D	7.49	HCS1	AT2G25710	2E^-58	全羧化酶合成酶1 Holocarboxylase synthase 1
A05	BnaA05g26430D	19.37	ALIS1	AT3G12740	2E^-93	参与磷脂转运 Involved in phospholipid transport
	BnaA05g26900D	19.54	FAD2	AT3G12120	0	不饱和脂肪酸生物合成过程 Unsaturated fatty acid biosynthetic process
	BnaA05g25110D	18.65	ATOBL1	AT3G14360	E^-156	脂质代谢过程 Lipid metabolic process
	BnaA05g25210D	18.70	GLIP3	AT1G53990	4E^-17	脂质分解过程 Lipid catabolic process
	BnaA05g25220D	18.70	GLIP4	AT3G14225	E^-117	脂质分解过程 Lipid catabolic process
	BnaA05g26460D	19.38	DALL4	AT1G06800	2E^-27	脂质代谢过程 Lipid metabolic process
A08	BnaA08g09510D	9.09	OGOX2	AT4G20840	0	FAD-结合小檗碱家族蛋白 FAD-binding Berberine family protein
	BnaA08g11130D	10.19	FAE1	AT4G34520	0	3-酮酰辅酶A合成酶18 3-ketoacyl-CoA synthase 18
	BnaA08g11140D	10.19	KCS17	AT4G34510	0	3-酮酰辅酶A合成酶17 3-ketoacyl-CoA synthase 17
	BnaA08g11440D	10.39	FAR3	AT4G33790	8E^-46	脂肪酸还原酶3 FATTY ACID REDUCTASE 3
	BnaA08g11650D	10.51	MCCB	AT4G34030	E^-119	3-甲基巴豆酰辅酶A羧化酶 3-methylcrotonyl-CoA carboxylase
	BnaA08g12370D	11.04	WIN2	AT4G31750	3E^-71	编码HopW1-1-相互作用蛋白2 Encodes HopW1-1-Interacting protein 2
A09	BnaA09g39290D	27.87	SLD1	AT3G61580	0	脂肪酸去饱和酶 Fatty acid desaturase
A10	BnaA10g10590D	9.01	未知Unknown	AT5G56350	0	丙酮酸激酶家族蛋白 Pyruvate kinase family protein
	BnaA10g10730D	9.08	END2	AT5G56480	4E^-62	脂质转移蛋白 Lipid-transfer protein
C03	BnaC03g63920D	53.41	OGOX2	AT4G20840	0	FAD-结合小檗碱家族蛋白 FAD-binding Berberine family protein
	BnaC03g63930D	53.42	BBE22	AT4G20860	5E^-23	FAD-结合小檗碱家族蛋白 FAD-binding Berberine family protein
	BnaC03g64130D	53.56	SPHK2	AT4G21534	4E^-55	二酰基甘油激酶家族蛋白 Diacylglycerol kinase family protein
	BnaC03g65980D	55.68	FAE1	AT4G34520	0	3-酮酰辅酶A合成酶18 3-ketoacyl-CoA synthase 18
	BnaC03g66040D	55.81	KCS17	AT4G34510	0	3-酮酰辅酶A合成酶17 3-ketoacyl-CoA synthase 17
	BnaC03g66380D	56.21	FAR3	AT4G33790	3E^-49	脂肪酸还原酶3 FATTY ACID REDUCTASE 3
	BnaC03g67410D	57.10	WIN2	AT4G31750	2E^-73	编码HopW1-1-相互作用蛋白2 Encodes HopW1-1-Interacting protein 2

表4

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环境 Environment	性状 Trait	亲本 Parents
环境 Environment	性状 Trait	10D130	ZS11	最大值 Max	最小值 Min	均值 Average	标准差 SE	变异系数 CV (%)
17Cq	C18:0	1.21^a	2.84^b	6.17	1.00	1.77**	0.61	34.47
	C18:1	18.83^A	64.27^B	83.15	13.17	38.25**	19.11	49.95
	C18:2	10.86^A	23.27^B	31.18	6.15	14.49**	4.50	31.04
	C18:3	7.68^a	9.55^b	12.79	4.04	8.65*	1.59	18.35
	C20:1	8.08^A	0.07^B	19.33	0.00	10.26**	5.86	57.12
	C22:1	53.34^A	0.00^B	57.96	0.00	26.56**	17.70	66.62
18Cq	C18:0	1.52^a	2.68^b	4.73	0.47	1.98**	0.56	28.13
	C18:1	17.91^A	63.03^B	78.79	12.69	39.14**	18.03	46.07
	C18:2	12.08^A	22.94^B	26.41	9.27	15.47**	3.94	25.46
	C18:3	8.92^a	10.44^b	12.20	6.14	8.89*	1.36	15.27
	C20:1	8.86^A	0.91^B	19.99	0.70	11.20**	6.43	57.44
	C22:1	50.71^A	0.00^B	51.62	0.00	23.02**	15.79	68.59

测定指标 Index	C18:0	C18:1	C18:2	C18:3	C20:1	C22:1
C18:0		0.58**	0.18*	-0.32**	-0.28**	-0.59**
C18:1	0.65**		0.36**	-0.13	-0.68**	-0.95**
C18:2	0.03	0.43**		0.45**	-0.50**	-0.52**
C18:3	-0.29**	0.11	0.49**		-0.12	-0.01
C20:1	-0.31**	-0.77**	-0.57**	-0.28**		0.56**
C22:1	-0.64**	-0.96**	-0.54**	-0.20**	0.64**