大豆重组自交系群体异黄酮含量QTL连锁定位与关联定位的比较研究

doi:10.3864/j.issn.0578-1752.2020.09.006

中国农业科学 ›› 2020, Vol. 53 ›› Issue (9): 1756-1772.doi: 10.3864/j.issn.0578-1752.2020.09.006

• 专题：限制性两阶段多位点全基因组关联分析法的应用 • 上一篇下一篇

大豆重组自交系群体异黄酮含量QTL连锁定位与关联定位的比较研究

刘再东,孟珊,贺建波(),邢光南,王吴彬,赵团结,盖钧镒()

南京农业大学大豆研究所/国家大豆改良中心/农业部大豆生物学与遗传育种重点实验室/作物遗传与种质创新国家重点实验室/江苏省现代作物生产协同创新中心,南京 210095

收稿日期:2019-09-09 接受日期:2020-01-02 出版日期:2020-05-01 发布日期:2020-05-13
通讯作者: 贺建波,盖钧镒
作者简介:刘再东,E-mail：2714699171@qq.com。|孟珊,E-mail：mshan84@163.com。
基金资助:
国家自然科学基金(31701447);国家作物育种重点研发计划(2017YFD0101500);国家作物育种重点研发计划(2017YFD0102002);长江学者和创新团队发展计划(PCSIRT_17R55);教育部111项目(B08025);中央高校基本科研业务费项目(KYT201801);农业部国家大豆产业技术体系CARS-04;江苏省优势学科建设工程专项;江苏省JCIC-MCP项目

A Comparative Study on Linkage and Association QTL Mapping for Seed Isoflavone Contents in a Recombinant Inbred Line Population of Soybean

ZaiDong LIU,Shan MENG,JianBo HE(),GuangNan XING,WuBin WANG,TuanJie ZHAO,JunYi GAI()

Soybean Research Institute, Nanjing Agricultural University/National Center for Soybean Improvement/Key Laboratory of Biology and Genetic Improvement of Soybean (General), Ministry of Agriculture/State Key Laboratory for Crop Genetics and Germplasm Enhancement/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095

Received:2019-09-09 Accepted:2020-01-02 Online:2020-05-01 Published:2020-05-13
Contact: JianBo HE,JunYi GAI

摘要/Abstract

摘要：

【目的】异黄酮是大豆等豆类植物中富含的一类次生代谢产物,对食品和保健产业有重要作用。大豆籽粒可分离出12种异黄酮组分,可归为三大类：大豆苷类异黄酮、染料木苷类异黄酮和黄豆苷类异黄酮。通过鉴定大豆籽粒异黄酮总含量及3个组分含量性状的加性及上位性QTL,进而全面解析其复杂的遗传构成。【方法】利用先进2号和赶泰2-2双亲衍生的大豆重组自交系群体NJRSXG,在5个环境下测定4个异黄酮含量性状：异黄酮总含量（total isoflavone content,SIFC）、大豆苷类异黄酮总含量（total daidzin group content,TDC）、染料木苷类异黄酮总含量（total genistin group content,TGC）和黄豆苷类异黄酮总含量（total glycitin group content,TGLC）。选用混合模型复合区间作图法（mixed-model-based composite interval mapping,MCIM）和限制性两阶段多位点全基因组关联分析方法（restricted two-stage multi-locus genome-wide association analysis,RTM-GWAS）进行异黄酮含量QTL检测。【结果】2个亲本在4个异黄酮含量性状上均存在较大差异,重组自交系群体异黄酮含量在高值、低值2个方向上均出现超亲分离,低值方向分离趋势强于高值方向。利用连锁定位MCIM方法共检测到4个异黄酮含量性状的19个加性QTL和16对上位性QTL,分布于15条染色体上。第14染色体重要标记区间GNE186b—Sat020内检测到3个新加性QTL：qSifc-14-1、qTdc-14-2和qTgc-14-1,且表型变异解释率最高。利用关联定位RTM-GWAS方法分别检测到4个异黄酮含量性状的51、66、42和36个关联标记位点,表型变异解释率为39.7%—52.5%,检测到的位点中覆盖了MCIM方法检测的19个加性QTL中的11个以及11个上位性QTL。候选基因分析分别在加性QTL区域和上位性QTL区域检测到93和100个候选基因,富集分析显示在第14染色体重要标记区间GNE186b—Satt020内,Glyma14g33227、Glyma14g33244和Glyma14g33715的功能与异黄酮代谢有关。【结论】连锁定位和关联定位2种方法结合能相对全面地检测异黄酮含量QTL。与连锁定位方法MCIM相比,关联定位方法RTM-GWAS检测的QTL更多,总遗传贡献率更高,但尚不能检测上位性QTL,2种方法定位结果可相互验证补充,大豆籽粒异黄酮含量由大量QTL/基因控制。

关键词: 大豆, 重组自交系群体, 异黄酮, 连锁作图, 关联定位, QTL

Abstract:

【Objective】Isoflavones are a group of phenolic secondary metabolites which are relatively abundant in soybean and some other legumes, and are important for food and healthcare industry. A total of 12 kinds of components are isolated from soybean seed, and can be grouped into three categories: daidzin group, genistin group and glycitin group. To understand the complex genetic constitutions of isoflavone content in soybean, the additive and epistatic quantitative trait loci (QTLs) conferring the total isoflavone content and its component contents were detected in the present study. 【Method】The NJRSXG recombinant inbred line (RIL) population derived from Xianjin 2 and Gantai-2-2 were used in this study. Four isoflavone content traits, i.e. the total seed isoflavone content (SIFC), the total daidzin group content (TDC), the total genistin group content (TGC) and the total glycitin group content (TGLC) were tested in five environments. The mixed model composite interval mapping (MCIM) and restricted two-stage multi-locus genome-wide association analysis (RTM-GWAS) were used for QTL detection. 【Result】There was a large difference in isoflavone content between the two parental lines of NJRSXG population, and transgressive segregations were observed in NJRSXG population while the transgressive trend in low isoflavone content direction were stronger than that in high isoflavone content direction. A total of 19 additive QTLs and 16 pairs of epistatic QTLs for the four isoflavone traits on 15 chromosomes were detected by MCIM. Three novel additive QTLs, i.e. qSifc-14-1, qTdc-14-2 and qTgc-14-1, were detected in the same important marker interval GNE186b-Sat020 on chromosome 14, and explained the highest phenotypic variation. A total of 51, 66, 42 and 36 significantly associated markers were detected by RTM-GWAS for SIFC, TDC, TGC and TGLC, respectively. The phenotypic variation explained by these markers was ranged from 39.7% to 52.5%, covering 11 additive QTLs and 11 epistatic QTLs detected by MCIM. Furthermore, a total of 93 and 100 candidate genes were annotated in the additive and epistatic QTL regions, respectively. Gene enrichment analysis indicated that three genes located in the important marker interval GNE186b-Satt020 on chromosome 14, i.e. Glyma14g33227, Glyma14g33244 and Glyma14g33715, were related to isoflavone metabolism. 【Conclusion】A relatively thorough detection of isoflavone content QTLs was achieved by using linkage and association mapping. Compared with the linkage mapping method MCIM, the association mapping method RTM-GWAS can detect more QTLs with larger total contribution to phenotypic variation, but cannot detect epistatic QTLs as in MCIM. The QTLs detected from the two methods can be used for complementary verification from each other. A large number of QTLs/genes are involved in the seed isoflavone contents of soybean.

Key words: soybean [Glycine max (L.) Merr.], isoflavone, genetic dissection, linkage mapping, association mapping, QTL

刘再东,孟珊,贺建波,邢光南,王吴彬,赵团结,盖钧镒. 大豆重组自交系群体异黄酮含量QTL连锁定位与关联定位的比较研究[J]. 中国农业科学, 2020, 53(9): 1756-1772.

ZaiDong LIU,Shan MENG,JianBo HE,GuangNan XING,WuBin WANG,TuanJie ZHAO,JunYi GAI. A Comparative Study on Linkage and Association QTL Mapping for Seed Isoflavone Contents in a Recombinant Inbred Line Population of Soybean[J]. Scientia Agricultura Sinica, 2020, 53(9): 1756-1772.

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图/表 9

表1

图1

表2

表3

表4

MCIM方法检测的异黄酮含量QTL"

性状 Trait	QTL	连锁群 Group	位置 Position(cM)	标记区间 Marker interval	区间长度 Interval length (cM)	h²_Add (%)	互作QTL Epistatic QTL	h²_Epi (%)	参考文献 Reference
SIFC	qSifc-03-1	3	32.4	Satt521—GNE324	11.1	4.2			[11,14]
	qSifc-10-1	10	33.6	GNE061—GNB130	4.0		qSifc-17-1	1.0
	qSifc-14-1	14	13.9	GNE186b—Satt020	2.9	10.6			[15]
	qSifc-17-1	17	20.4	Sat_022—Satt186	10.2		qSifc-10-1	1.0	[11]
	qSifc-18-1	18	1.4	Sat_210—Sat_168	1.1	4.4			[41]
	qSifc-19-1	19	38.1	Satt481—GNE091	0.1	6.6			[13]
TDC	qTdc-01-1	1-1	9.1	Sat_353—Satt532b	3.4		qTdc-10-1	1.3
	qTdc-02-1	2	57.1	BF070293—Satt634	0.9		qTdc-02-2	2.7
	qTdc-02-2	2	23.8	Satt282—Satt124c	18.2		qTdc-02-1	2.7
	qTdc-03-1	3	67.3	Satt584—GNE333	2.2		qTdc-10-2	3.4
	qTdc-03-2	3	20.1	Satt339—Satt660	1.3	3.1
	qTdc-08-1	8-2	2.2	Satt089—Satt455b	0.6	3.8
	qTdc-08-2	8-2	82.3	Satt409—GNE376	10.3	2.3			[18]
	qTdc-10-1	10	22.1	Satt153—Satt188	6.3		qTdc-01-1	1.3
	qTdc-10-2	10	1.8	GNB134—Sat_282	1.2		qTdc-03-1	3.4
	qTdc-10-3	10	29.9	GNE262—GNE057	0.9		qTdc-17-1	1.2
	qTdc-12-1	12	17.2	GNE229—Satt192	9.3		qTdc-16-1	0.5	[18,21-22]
	qTdc-14-1	14	0.0	Satt304—Sat_191a	3.4		qTdc-15-1	3.3
	qTdc-14-2	14	13.9	GNE186b—Satt020	2.9	8.7
	qTdc-15-1	15-2	0.0	Satt651—Satt691	20.2		qTdc-14-1	3.3	[15]
	qTdc-16-1	16	52.1	Sat_151—Satt529	0.2		qTdc-12-1	0.5	[22]
	qTdc-17-1	17	99.8	Satt002—GNE158	12.5		qTdc-10-3	1.2
	qTdc-18-1	18	1.0	Satt038—Sat_210	1.4	5.8
TGC	qTgc-02-1	2	2.0	GNE278—Satt141	9.4		qTgc-19-3	3.3
	qTgc-03-1	3	31.4	Satt521—GNE324	11.1	4.1
	qTgc-03-2	3	5.4	Sat_306—Sat_239	3.9		qTgc-08-1	0.2
	qTgc-08-1	8-1	3.4	Satt177a—Sat_406	12.5		qTgc-03-2	0.2	[14-15]
	qTgc-10-1	10	2.8	GNB134—Sat_282	1.2		qTgc-19-2	1.1
	qTgc-10-2	10	33.6	GNE061—GNB130	4.0		qTgc-17-1	0.8
	qTgc-13-1	13	21.4	GNB007—Satt362	4.3	2.5
	qTgc-14-1	14	13.9	GNE186b—Satt020	2.9	10.3
	qTgc-17-1	17	23.4	Sat_022—Satt186	10.2		qTgc-10-2	0.8	[12-13]
	qTgc-18-1	18	19.4	GNE001b—Satt324	21.4	3.9
	qTgc-19-1	19	58.5	Satt232—Satt681	8.4	0.2
	qTgc-19-2	19	48.1	GNE091—GNE397b	14.7		qTgc-10-1	1.1
	qTgc-19-3	19	38.1	Satt481—GNE091	0.1	6.3	qTgc-02-1	3.3	[13,21-22]
TGLC	qTglc-01-1	1-1	9.1	Sat_353—Satt532b	3.4		qTglc-14-1	3.6	[41]
	qTglc-02-1	2	14.0	Satt483—Satt579	0.2		qTglc-14-2	2.4
	qTglc-05-1	5	47.2	Satt619a—GNE055	1.7		qTglc-12-1	3.6
	qTglc-05-2	5	12.6	GNE041—Satt174	3.8		qTglc-12-2	1.2	[21]
	qTglc-06-1	6	78.8	Satt079—GNB215a	13.0	5.3			[15,21]
	qTglc-08-1	8-2	4.8	GNE072b—Satt525	3.9	4.5			[13,41]
	qTglc-10-1	10	50.9	Satt259—Satt455a	10.9	2.9	qTglc-17-1	4.6
	qTglc-12-1	12	15.2	GNE229—Satt192	9.3		qTglc-05-1	3.6	[14]
	qTglc-12-2	12	40.8	GNE351—Satt279	15.1		qTglc-05-2	1.2	[14]
	qTglc-14-1	14	3.4	Sat_191a—Sat_355	0.6		qTglc-01-1	3.6
	qTglc-14-2	14	11.3	Satt556—GNE421	2.0		qTglc-02-1	2.4
	qTglc-17-1	17	80.8	Sat_220—Satt397	7.1	3.2	qTglc-10-1	4.6	[15-16,22]

表4

图2

图3

表5

异黄酮含量关联标记/QTL"

性状 Trait	标记/QTL Marker/QTL	连锁群 Group	位置 Position (cM)	Model^a -lgP	QTL		QTL×Env.^b
性状 Trait	标记/QTL Marker/QTL	连锁群 Group	位置 Position (cM)	Model^a -lgP	-lgP	R² (%)	-lgP	R² (%)
SIFC	GNE332	2	78.5	5.5	21.8	1.3	-	-
	Sat_239	3	6.3	13.3	31.4	2.0	-	-
	Satt339	3	20.1	2.8	32.0	2.0	1.9	0.2
	Satt521	3	29.4	5.2	21.8	1.3	3.5	0.3
	Satt718	4	13.2	3.4	19.1	1.1	-	-
	Satt225	5	19.1	6.4	26.3	1.6	-	-
	GNE397a	6	5.2	8.5	27.3	1.7	2.9	0.2
	Sat_418b	6	47.1	4.1	17.3	1.0	-	-
	GNE072b	8-2	4.8	9.8	29.0	1.8	2.4	0.2
	Satt460	10	13.8	5.0	31.0	1.9	3.1	0.3
	Satt549b*	10	29.7	7.0	15.3	0.9	5.4	0.4
	GNE262*	10	29.9	3.4	3.7	0.2	-	-
	GNE057*	10	30.9	6.4	3.0	0.2	-	-
	GNE187*	10	32.6	4.8	18.4	1.1	-	-
	Satt420a*	10	33.1	3.7	8.6	0.5	-	-
	Satt192	12	20.5	3.5	22.2	1.3	-	-
	Satt030	13	91.6	23.3	89.2	6.3	-	-
	Satt556	14	10.3	3.6	29.1	1.8	-	-
	Sat_168	18	2.5	4.5	15.5	0.9	-	-
	Sat_141	18	5.7	6.0	6.2	0.3	-	-
	GNE397b	19	52.8	5.8	17.7	1.1	-	-
LC QTL					15	27.4
SC QTL					30	12.3
总Total	51 (3/4;1/2)				45	39.7	21	4.7
TDC	GNE498	1-1	19.6	8.8	35.4	1.8	-	-
	Satt506	2	10.4	11.1	67.0	3.7	-	-
	Sat_424b	3	18.6	3.9	14.4	0.7	5.2	0.3
	Satt660	3	21.4	6.0	15.5	0.7	-	-
	GNE397a	6	5.2	11.4	34.3	1.8	4.6	0.3
	Satt684	7	67.1	9.2	28.8	1.5	2.9	0.2
	Sat_199a	8-2	0.0	3.2	4.1	0.2	-	-
	Satt333	8-2	40.2	3.3	23.0	1.1	-	-
	Satt188*	10	28.4	3.9	3.0	0.1	-	-
	Satt549b*	10	29.7	5.9	13.6	0.7	2.4	0.2
	GNE001a	11	20.6	11.6	34.2	1.8	2.7	0.2
	Satt192*	12	20.5	8.7	18.1	0.9	3.4	0.2
	Satt146	13	88.7	8.8	34.6	1.8	-	-
	Satt653	13	90.2	4.2	22.3	1.1	-	-
	Sat_191a*	14	3.4	4.1	3.0	0.1	-	-
	GNE186b	14	13.9	44.6	134.5	8.6	5.1	0.3
	GNB191*	16	56.7	7.9	34.7	1.8	-	-
	Satt669	17	85.3	9.9	33.8	1.7	-	-
	Sat_210	18	1.4	3.1	9.4	0.4	-	-
	Sat_141	18	5.7	2.7	4.0	0.2	-	-
	Sat_421	20	21.9	5.0	23.0	1.1	-	-
LC QTL					12	27.7
SC QTL					48	19.3
性状 Trait	标记/QTL Marker/QTL	连锁群 Group	位置 Position (cM)	Model^a -lgP	QTL		QTL×Env.^b
性状 Trait	标记/QTL Marker/QTL	连锁群 Group	位置 Position (cM)	Model^a -lgP	-lgP	R² (%)	-lgP	R² (%)
总Total	66 (4/5;4/12)				60	47.0	30	5.5
TGC	GNE332	2	78.5	4.6	20.1	1.4	-	-
	Satt339	3	20.1	3.6	17.5	1.2	-	-
	Satt521	3	29.4	3.9	34.5	2.4	-	-
	GMAC7L	6	16.6	9.1	20.1	1.4	-	-
	Sat_148	7	37.6	6.8	31.1	2.2	3.1	0.3
	GNE072b	8-2	4.8	8.5	15.6	1.0	5.1	0.4
	Sat_193*	10	6.4	3.2	7.6	0.5	-	-
	Satt460	10	13.8	5.5	27.7	1.9	3.0	0.3
	Satt549b*	10	29.7	4.6	12.2	0.8	2.0	0.2
	Satt442	12	28.0	4.3	26.4	1.8	2.0	0.2
	GNB125	13	11.1	5.4	15.6	1.0	-	-
	Satt030	13	91.6	13.1	68.6	5.2	-	-
	Satt020	14	16.7	2.9	39.2	2.8	2.0	0.2
	Sat_210	18	1.4	4.7	17.0	1.1	-	-
LC QTL					12	23.5
SC QTL					28	11.4
总Total	42 (2/6; 2/8)				40	34.9	18	4.8
TGLC	Satt147	1-2	18.5	7.7	11.1	1.1	2.8	0.4
	Sat_306	3	2.4	8.0	15.9	1.6	-	-
	Satt354	5	26.1	9.4	16.1	1.6	3.1	0.4
	GNE055*	5	47.8	4.6	9.6	1.0	-	-
	GNB215a	6	79.8	21.0	46.4	5.0	2.3	0.3
	GNB022b	7	0.0	10.4	22.3	2.3	-	-
	Sat_140	8-2	1.6	14.7	33.4	3.5	-	-
	Satt576	10	16.7	13.3	30.4	3.1	-	-
	Satt259*	10	50.9	13.5	29.3	3.0	-	-
	Satt332	11	5.1	5.0	11.6	1.1	-	-
	GNB177	13	8.3	8.2	16.9	1.7	-	-
	Satt304*	14	0.0	7.8	15.7	1.5	-	-
	Satt651	15-2	0.0	6.7	13.9	1.4	-	-
	Satt669*	17	85.3	10.2	21.0	2.1	-	-
	Sat_143	18	73.6	7.8	14.6	1.4	-	-
	GNE493	18	108.5	4.9	10.9	1.0	-	-
LC QTL					15	31.3
SC QTL					21	12.0
总Total	36 (2/4;4/10)				36	43.3	7	2.3

表5

图4

参考文献 46

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性状Trait	SIFC	TDC	TGC
TDC	0.95**
TGC	0.97**	0.87**
TGLC	0.39**	0.26**	0.32**

性状 Trait	基因型变异 h² Genotype variation (%)			基因型×环境变异 h² Genotype×Env. variation (%)
性状 Trait	总计Total	Add.QTL	Epi.QTL	总计Total	Add.QTL×Env.	Epi.QTL×Env.
SIFC	94.1	25.8 (4)	1.0 (1)	3.9	0.5	0.1
TDC	95.4	23.7 (5)	12.0 (6)	3.1	0.6	0.7
TGC	92.7	27.3 (6)	5.4 (4)	5.0	1.4	0.8
TGLC	94.0	15.9 (4)	15.0 (5)	3.3	0.8	0.9

大豆重组自交系群体异黄酮含量QTL连锁定位与关联定位的比较研究

A Comparative Study on Linkage and Association QTL Mapping for Seed Isoflavone Contents in a Recombinant Inbred Line Population of Soybean

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性状 Trait	组中值及频数 Midpoint and frequency										N	P₁	P₂	平均值 Mean	变幅 Range	GCV (%)	h² (%)
SIFC	22	27	32	37	42	47	52	57	62	67
	2	8	32	23	36	24	10	7	3	1	146	63.0	34.0	40.6	21.9—67.7	20.9	94.1
TDC	7.0	9.5	12.0	14.5	17.0	19.5	22.0	24.5	27.0	29.5
	5	13	33	40	27	11	11	3	2	1	146	28.4	12.8	15.1	7.3—29.5	26.9	95.4
TGC	12.0	14.5	17.0	19.5	22.0	24.5	27.0	29.5	32.0	34.5
	1	7	14	27	34	21	21	12	6	3	146	28.9	19.1	23.1	12.6—35.6	19.5	92.7
TGLC	1.2	1.6	2.0	2.4	2.8	3.2	3.6	4.0	4.4	4.8
	9	22	30	24	23	13	10	10	2	3	146	5 .8	2.2	2.5	1.1—5.0	32.3	94.0

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