基于RIL和CSSL群体定位大豆脂肪酸组分QTL

doi:10.3864/j.issn.0578-1752.2021.15.003

摘要/Abstract

摘要：

【目的】大豆（Glycine max）原产于中国,高品质的大豆在食品、饲料、纺织品等多种加工业中广泛应用,因此,选育高品质大豆已成为育种者和生产者的聚焦问题。通过对大豆脂肪酸各组分进行QTL定位及候选基因的筛选,为大豆品质改良奠定分子基础。【方法】以美国大豆品种Charleston和东农594为亲本构建重组自交系（RILs）、以栽培大豆绥农14与野生大豆ZYD00006为亲本构建染色体片段代换系（CSSLs）为试验材料。利用气相色谱法测定2个群体的脂肪酸含量,根据东北农业大学农学院大豆遗传改良实验室已构建的遗传图谱,通过Windows QTL Cartographer 2.5和ICIMapping软件对2017—2018年RIL群体与CSSL群体中的大豆脂肪酸组分进行QTL定位研究,并对所获得的QTL置信区间进行候选基因的挖掘。【结果】 2017—2018年,RIL群体和CSSL群体分别定位到34和20个与脂肪酸组分相关的QTL,分布在除B2、C1、G、H、J、M和O以外的13个连锁群上。比较2个群体的QTL定位结果,发现在2个群体中重复检测到10对QTL,其中,分布在A1、C2、D1a、F、K和N连锁群上的QTL与多种脂肪酸含量相关,在A1连锁群上检测到亚油酸和油分含量重叠的QTL;在C2连锁群上检测到硬脂酸和油分含量重叠的QTL;在D1a连锁群上检测到硬脂酸和油分含量重叠的QTL;在F连锁群上检测到棕榈酸、硬脂酸和油分含量重叠的QTL;在K连锁群上检测到亚油酸和亚麻酸含量重叠的QTL;在N连锁群上检测到棕榈酸和油分含量重叠的QTL、油酸和亚油酸含量重叠的QTL。对QTL定位获得的所有置信区间进行候选基因的挖掘,从基因注释数据集中共筛选出485个候选基因,其中,271个候选基因具有GO注释,进一步进行GO富集数据分析,共有15个候选基因与脂肪酸相关。主要通过编码植物酰基-酰基载体蛋白（ACP）硫酯酶、脂肪酸去饱和酶、磷脂酶D1、脂肪酸-羟化酶、丙酮酸激酶和参与酰基辅酶A生物合成、调节脂肪酸链的延伸,从而影响脂肪酸的合成。【结论】共检测到54个与大豆脂肪酸各组分相关的QTL,在2个群体中重复检测到10对QTL,对QTL定位获得的置信区间进行候选基因的筛选,共有15个候选基因与脂肪酸相关。这些稳定的脂肪酸相关的QTL和脂肪酸相关的候选基因可用于大豆脂肪酸改良的分子标记辅助选择。

关键词: 大豆, 导入系, 气相色谱法, QTL定位, 基因挖掘, 富集分析

Abstract:

【Objective】 Soybeans (Glycine max) originated from China. High-quality soybeans are widely used in various processing industries such as food, feeding, textiles, etc. Therefore, high-quality soybean breeding is a key point for soybean breeders and producers. This study conducted QTL mapping of each component of soybean fatty acid and screening of candidate genes, which would lay the molecular foundation for soybean quality improvement. 【Method】 A recombinant inbred lines (RILs) population crossed by Charleston (American soybean varieties ) and Dongnong 594, and a chromosome segment substitution lines (CSSLs) population crossed by Suinong 14 (cultivated soybean) and ZYD00006 (wild soybean) were used for QTL mapping. We used gas chromatography to determine the fatty acid content of these two populations. As the genetic maps have been published by the soybean genetic improvement laboratory of the Agricultural College of Northeast Agricultural University before, QTL mapping of soybean fatty acid components in RIL and CSL populations were performed by the Windows QTL Cartographer 2.5 and ICIMapping software. And the candidate genes were screened from the QTL interval. 【Result】 Based on 2017 to 2018 years data, 34 and 20 QTLs related to fatty acid components were mapped in the RIL population and the CSSL population, respectively. These QTLs distribute in 13 linkage groups except B2, C1, G, H, J, M, and O. QTL mapping of the two populations was compared that ten pairs of QTLs were detected in the two populations. We found that QTLs distributed in the A1, C2, D1a, F, K, and N linkage groups were related to the content of multiple fatty acids components. An overlapping QTL related to linoleic acid and oil content was detected on the A1 linkage group, QTL related to stearic acid and oil content on the C2, QTL related to stearic acid and oil content on the D1a, QTLs related to palmitic acid, stearic acid and oil content on the F, QTLs related to linoleic acid and linolenic acid content on the K, QTLs related to palmitic acid and oil content, and QTL related to oleic acid and linoleic acid content on the N. Candidate genes were screened out from QTL intervals. In total, 485 candidate genes were screened from the gene annotation data set and 271 of them annotated within GO annotations. GO enrichment analysis showed that 15 candidate genes involved in fatty acids pathway. These genes affect synthesis of fatty acids mainly through encoding plant acyl carrier protein (ACP) thioesterase, fatty acid desaturase, phospholipase D1, fatty acid-hydroxylase and pyruvate kinase, participating in the biosynthesis of acyl-CoA, and regulating the extension of fatty acid chain. 【Conclusion】 54 QTLs related to soybean fatty acid were detected, and 10 pairs QTLs were stable detected from the two mapping populations. We used the confidence intervals from QTL mapping to screen candidate genes, and 15 candidate genes related to fatty acids pathway were screened out. These stable QTLs and candidate genes can be used for molecular marker-assisted selection of soybean fatty acid improvement.

Key words: soybean, introduction line, gas chromatography, QTL mapping, gene mining, enrichment analysis

渠可心,韩露,谢建国,潘文婧,张泽鑫,辛大伟,刘春燕,陈庆山,齐照明. 基于RIL和CSSL群体定位大豆脂肪酸组分QTL[J]. 中国农业科学, 2021, 54(15): 3168-3182.

QU KeXin,HAN Lu,XIE JianGuo,PAN WenJing,ZHANG ZeXin,XIN DaWei,LIU ChunYan,CHEN QingShan,QI ZhaoMing. Mapping QTL for Soybean Fatty Acid Composition Based on RIL and CSSL Population[J]. Scientia Agricultura Sinica, 2021, 54(15): 3168-3182.

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https://www.chinaagrisci.com/CN/Y2021/V54/I15/3168

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RIL群体脂肪酸含量QTL定位"

性状 Trait	年份 Year	QTL名称 QTL name	染色体 Chromosome	起始位置 Start position (Mb)	终止位置 End position (Mb)	距离 Size (Mb)	LOD	贡献率 R² (%)	加性效应 Additive effect
棕榈酸 PA	2017	qPA-N-1	3	14.80	18.50	3.70	4.00	9.56	0.15
	2017	qPA-C2-1	6	20.47	21.61	1.14	4.44	10.51	-0.05
	2017	qPA-C2-2	6	27.37	27.84	0.46	3.74	8.95	-0.04
	2017	qPA-E-1	15	33.29	33.49	0.21	2.64	6.66	-0.06
	2017	qPA-E-2	15	32.53	32.61	0.07	5.60	13.50	-0.09
	2017	qPA-E-3	15	28.34	28.72	0.37	3.84	9.05	0.07
	2017	qPA-E-4	15	22.73	22.77	0.04	2.70	6.47	0.05
	2018	qPA-D1b-1	2	42.46	42.49	0.03	3.73	8.99	-0.05
	2018	qPA-A1-1	5	34.54	34.55	0.01	2.89	6.96	-0.04
	2018	qPA-F-1	13	15.74	15.83	0.09	5.32	13.16	0.09
硬脂酸 SA	2017	qSA-N-1	3	40.50	44.10	3.60	2.98	7.62	-0.03
	2018	qSA-D1b-1	2	42.61	42.62	0.01	2.84	6.90	-0.03
	2018	qSA-F-1	13	15.74	15.83	0.09	4.51	11.11	0.06
	2018	qSA-D2-1	17	38.23	38.91	0.68	3.20	7.73	0.03
油酸 OA	2017	qOA-D1a-1	1	13.87	14.26	0.39	3.24	7.71	0.10
	2017	qOA-N-1	3	23.25	23.29	0.04	3.86	9.09	-0.11
	2017	qOA-N-2	3	24.72	24.96	0.24	3.89	9.17	-0.11
	2017	qOA-A1-1	5	38.94	39.09	0.15	2.65	5.64	0.10
	2017	qOA-D2-1	17	36.95	37.10	0.16	2.94	7.40	0.10
	2018	qOA-A1-2	5	38.94	39.09	0.15	3.65	7.64	0.13
	2018	qOA-D2-2	17	36.95	37.10	0.16	3.94	9.43	0.12
亚油酸 LA	2017	qLA-N-1	3	23.05	23.11	0.06	2.76	6.99	-0.24
	2017	qLA-N-2	3	28.10	28.27	0.17	3.25	8.29	0.26
	2017	qLA-K-1	9	33.51	33.52	0.01	3.26	8.34	-0.19
	2017	qLA-L-1	19	42.92	43.49	0.57	2.86	7.26	0.19
	2018	qLA- A1-1	5	0.03	0.80	0.77	3.10	8.03	0.17
	2018	qLA-I-1	20	24.43	24.44	0.02	2.54	6.40	-0.16
亚麻酸 LNA	2017	qLNA-N-1	3	37.15	37.22	0.07	4.19	10.13	0.05
	2017	qLNA-K-1	9	33.51	33.52	0.01	5.46	13.49	-0.05
	2017	qLNA-B1-1	11	38.31	38.71	0.39	3.25	7.74	-0.04
	2018	qLNA -B1-2	11	38.31	38.71	0.39	4.25	9.89	-0.07
	2018	qLNA-I-1	20	45.55	45.74	0.19	3.20	8.16	0.03
油分 OIL	2017	qOIL- D1b-1	2	6.25	6.51	0.25	2.67	6.95	-0.60
油分 OIL	2018	qOIL-F-1	13	15.74	15.83	0.09	3.79	10.04	0.58

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性状 Trait	群体 Population	亲本Parent		群体Population
性状 Trait	群体 Population	父本 Male	母本 Female	最小值 Minimum	最大值 Maximum	平均值 Mean	标准差 SD	变异系数 CV	偏度 Skewness	峰度 Kurtosis
棕榈酸 PA (%)	17-RIL	12.80	13.15	11.48	13.98	13.05	0.42	3.21	-0.76	1.82
	17-CSSL	12.75	13.17	12.62	13.33	13.03	0.15	1.13	-0.18	-0.61
	18-RIL	12.74	13.09	12.11	13.27	12.90	0.18	1.42	-0.63	-1.04
	18-CSSL	12.81	13.12	12.70	13.60	13.05	0.15	1.16	-0.09	-0.05
硬脂酸 SA (%)	17-RIL	4.09	4.28	3.59	5.19	4.40	0.31	6.99	-0.43	0.15
	17-CSSL	3.94	4.17	3.64	4.95	4.19	0.17	4.17	0.21	1.19
	18-RIL	4.03	4.23	3.92	4.99	4.53	0.27	5.88	-0.28	-0.86
	18-CSSL	4.04	4.15	3.80	4.68	4.23	0.17	3.91	0.28	-0.01
油酸 OA (%)	17-RIL	19.19	20.35	17.00	23.53	19.33	1.12	5.78	0.84	1.59
	17-CSSL	19.10	20.71	17.00	22.20	19.61	1.17	5.94	0.16	-0.63
	18-RIL	19.13	20.06	18.09	22.25	19.53	0.83	4.25	0.64	0.59
	18-CSSL	19.29	20.72	17.03	22.25	19.45	0.98	5.03	0.43	-0.13
亚油酸 LA (%)	17-RIL	54.81	53.35	51.15	57.37	54.28	1.16	2.13	0.12	0.46
	17-CSSL	55.17	53.19	51.59	57.37	54.20	1.25	2.31	-0.07	-0.62
	18-RIL	54.97	53.76	51.47	56.12	54.10	0.95	1.76	-0.14	-0.06
	18-CSSL	54.85	53.14	51.65	57.09	54.27	1.06	1.95	-0.29	-0.29
亚麻酸 LNA (%)	17-RIL	9.11	8.87	7.75	10.87	8.94	0.40	4.51	0.47	3.93
	17-CSSL	9.04	8.76	8.52	9.63	8.98	0.20	2.25	0.22	-0.42
	18-RIL	9.13	8.86	8.29	9.34	8.93	0.19	2.11	-0.81	0.37
	18-CSSL	9.01	8.87	8.30	9.63	8.99	0.19	2.12	-0.26	0.96
油分 OIL (%)	17-RIL	20.25	21.62	19.82	24.26	21.94	0.99	4.53	-0.08	-0.44
	17-CSSL	20.79	21.34	19.74	23.35	21.70	0.96	4.40	-0.24	-0.97
	18-RIL	20.11	21.46	19.66	23.38	21.58	1.04	4.83	-0.11	-1.04
	18-CSSL	20.53	21.19	19.87	23.33	21.74	1.00	4.59	-0.36	-0.93

性状 Traits	棕榈酸PA	硬脂酸SA	油酸OA	亚油酸LA	亚麻酸LNA
棕榈酸PA	1	0.388**	-0.387**	0.582**	0.261**
硬脂酸SA	0.301**	1	-0.561**	0.714**	0.605**
油酸OA	-0.015	-0.171*	1	-0.939**	-0.790**
亚油酸LA	0.336**	0.398**	-0.853**	1	0.717**
亚麻酸LNA	0.301**	0.275**	-0.352**	0.230**	1

性状 Traits	棕榈酸PA	硬脂酸SA	油酸OA	亚油酸LA	亚麻酸LNA
棕榈酸PA	1	0.649**	-0.846**	0.873**	0.855**
硬脂酸SA	0.815**	1	-0.651**	0.726**	0.684**
油酸OA	-0.862**	-0.778**	1	-0.987**	-0.883**
亚油酸LA	0.895**	0.830**	-0.991**	1	0.868**
亚麻酸LNA	0.843**	0.771**	-0.881**	0.864**	1

性状 Trait	年份 Year	QTL名称 QTL name	染色体 Chromosome	起始位置 Start position (Mb)	终止位置 End position (Mb)	距离 Size （Mb)	LOD值 LOD	贡献率 PVE (%)	加性效应 Additive effect
棕榈酸 PA	2017	qPA-N-2	3	18.57	19.23	0.66	2.86	4.62	0.16
棕榈酸 PA	2018	qPA-N-3	3	18.57	19.23	0.66	6.87	7.75	0.16
硬脂酸 SA	2017	qSA-C2-1	6	49.19	49.24	0.05	1.78	3.21	0.41
硬脂酸 SA	2018	qSA-D1a-1	1	5.71	5.79	0.08	2.95	5.00	0.27
油酸 OA	2017	qOA-F-1	13	13.72	13.81	0.09	9.60	8.80	0.30
	2017	qOA-E-1	15	40.66	40.67	0.01	3.98	5.22	0.29
	2018	qOA-D2-3	17	14.17	14.25	0.09	2.75	4.49	0.22
亚油酸 LA	2017	qLA-A1-2	5	0.51	0.53	0.02	11.65	22.09	0.33
亚油酸 LA	2018	qLA-A1-3	5	0.51	0.53	0.02	2.59	4.28	1.02
亚麻酸 LNA	2017	qLNA-A1-1	5	34.40	34.44	0.04	3.80	3.93	0.05
	2017	qLNA-A2-1	8	2.45	2.49	0.03	4.43	4.73	0.03
	2018	qLNA-K-2	9	2.35	2.40	0.05	2.31	2.92	0.23
	2018	qLNA-F-1	13	0.80	0.82	0.02	2.96	2.97	0.07
	2018	qLNA-F-2	13	11.48	11.55	0.07	5.51	5.86	-0.04
	2018	qLNA-E-1	15	49.40	49.44	0.03	2.97	3.01	0.04
油分 OIL	2017	qOIL- D1a-1	1	5.71	5.79	0.08	3.59	7.96	0.43
	2017	qOIL-N-1	3	18.57	19.23	0.66	3.37	7.44	0.31
	2017	qOIL-C2-1	6	49.19	49.24	0.05	3.67	8.14	0.52
	2018	qOIL-A1-1	5	0.51	0.53	0.02	1.84	3.02	1.43
	2018	qOIL-F-2	13	31.17	31.19	0.02	2.74	3.71	0.36

基因 Gene	KO注释 KO annotation	GO注释 GO annotation	同源基因 Homologous gene	基因功能 Gene description
Glyma.02G073800		GO:0016747	Glyma.06G211200	乙醇-乙酰基转移酶Alcohol-acetyltransferase
Glyma.02G073800		GO:0016747	Glyma.13G044100	乙醇-乙酰基转移酶Alcohol-acetyltransferase
Glyma.02G074000		GO:0008080		酰基辅酶a/酰基转移酶Acyl-CoA/N-acyltransferases (NAT)
Glyma.03G070200	K00167	GO:0008152		α-酮酸脱羧酶E1β亚基Alpha-keto acid decarboxylase E1 beta subunit
Glyma.05G007700		GO:0016788	Glyma.13G044500	脂肪酶/酰基水解酶Lipase/Acyl hydrolase
			Glyma.19G171000
			Glyma.20G221200
Glyma.05G008100	K00326	GO:0016491		FAD/NAD（P）结合氧化还原酶 FAD/NAD(P)-binding oxidoreductase
Glyma.05G208900	K15398	GO:0055114		脂肪酸ω-羟化酶（CYP86A4S）Fatty acid omega-hydroxylase (CYP86A4S)
Glyma.05G000700	K00873	GO:0030955		丙酮酸激酶家族蛋白Pyruvate kinase family protein
Glyma.06G211300	K10781	GO:0006633		脂肪酰基-ACP硫酯酶B Fatty acyl-ACP thioesterases B
Glyma.17G219100				磷脂酶D1 Phospholipase D1
Glyma.17G228400	K13076	GO:0006629		脂肪酸去饱和酶Fatty acid desaturase