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

Abstract

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

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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Figures/Tables 9

Table 1

Fig. 1

Table 2

Table 3

Table 4

QTLs detected from MCIM for isoflavone content"

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]

Table 4

Fig. 2

Fig. 3

Table 5

Marker/QTL detected for isoflavone component traits"

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

Table 5

Fig. 4

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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

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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