QTL Mapping and Candidate Gene Identification of Effective Spike Number in Ricinus communis L.

doi:10.7668/hbnxb.20194396

Abstract

Abstract:

Effective spike number is an important component of castor yield.In order to reveal the genetic basis and mining candidate genes of effective spike number,the QTLs conferring effective spike number per plant(ESNPP)and number of effective primary branch spike(EPBSN)were mapped by genotyping with SSR primers and by the 2 detection methods(CIM and ICIM-ADD)in the populations F₂ and BC₁ (F₁×P₂)derived from 2 parents with significant phenotypic differences,and QTL remapping was conducted in S₁ population by the same method.A total of 9/5(CIM/ICIM-ADD,the same below) QTLs were identified in the F₂ population,including 3/2 and 6/3 underlying ESNPP and EPBSN,with a phenotypic variation explained(PVE)of 6.70%/11.87% and 25.15%/13.87%,respectively.The mapping results in BC₁ population were generally consistent with those in F₂ population.Among them, qESNPP3.1 and qEPBSN3.1 were stable QTLs with contribution rates close to 10%,and the latter was detected again in S₁ population with a PVE of 13.27%;the stable QTLs were overlappingly located in the marker interval RCM915—RCM950,and together constituted a main-effect QTL cluster underlying the effective spike number.Two candidate genes,Rc-US03g04880 and Rc-US03g05950,were annotated from the marker interval,which were differentially expressed in multiple branching tissues of both parents.The above results provided essential molecular markers for marker-assisted selection of the effective spike number and necessary candidate genes for its genetic and physiologic mechanism study in castor.

Key words: Castor, Effective spike number, QTL mapping, Candidate gene, Main-effect QTL

HUANG Guanrong, YIN Xuegui, LU Jiannong, ZHANG Liuqin, LIU Chaoyu, ZHANG Xiaoxiao, LIN Haihong, ZUO Jinying. QTL Mapping and Candidate Gene Identification of Effective Spike Number in Ricinus communis L.[J]. Acta Agriculturae Boreali-Sinica, 2023, 38(6): 36-44. doi: 10.7668/hbnxb.20194396.

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References 47

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性状 Trait	世代 Generation	群体规模 Population size	极差 Range	均值±标准差 Mean±s	变异系数/% CV	偏度 Skewness	峰度 Kurtosis
单株有效穗数	P₁	25	3~4	3.64±0.50A	13.87	-0.66	-1.96
Effective spike	P₂	25	5~6	5.36±0.50B	9.28	0.67	-1.84
number per plant	F₁	25	7~11	9.08±1.24	13.65	0.16	-0.61
	F₂	282	1~20	6.38±2.87	45.06	0.76	1.15
	BC₁	250	1~18	8.95±3.36	37.52	-0.02	-0.30
一级分枝有效穗数	P₁	25	2~3	2.64±0.50A	19.14	-0.66	-1.96
Number of effective	P₂	25	3~4	3.36±0.50B	14.81	0.67	-1.84
primary branch spike	F₁	25	3~5	3.67±0.78	21.23	0.72	-0.79
	F₂	282	1~10	4.11±1.62	39.47	0.81	0.53
	BC₁	250	1~10	4.94±1.61	32.47	0.19	0.15

性状 Trait	世代 Generation	群体规模 Population size	极差 Range	均值±标准差 Mean±s	变异系数/% CV	偏度 Skewness	峰度 Kurtosis
单株有效穗数	P₁	25	3~4	3.64±0.50A	13.87	-0.66	-1.96
Effective spike	P₂	25	5~6	5.36±0.50B	9.28	0.67	-1.84
number per plant	F₁	25	7~11	9.08±1.24	13.65	0.16	-0.61
	F₂	282	1~20	6.38±2.87	45.06	0.76	1.15
	BC₁	250	1~18	8.95±3.36	37.52	-0.02	-0.30
一级分枝有效穗数	P₁	25	2~3	2.64±0.50A	19.14	-0.66	-1.96
Number of effective	P₂	25	3~4	3.36±0.50B	14.81	0.67	-1.84
primary branch spike	F₁	25	3~5	3.67±0.78	21.23	0.72	-0.79
	F₂	282	1~10	4.11±1.62	39.47	0.81	0.53
	BC₁	250	1~10	4.94±1.61	32.47	0.19	0.15

群体 Pop	方法 Method	性状 Trait	QTL	染色体 Chr	连锁群 LG	位置 Pos	LOD	加性 Add	显性 Dom	贡献率/% PVE	置信区间 CI		标记区间 MI
F₂	CIM	ESNPP	FqESNPP6.1	6	7	4.01	2.70	-0.48	-1.21	0.09	0~	12.7	RCM1556~	RCM1521
			FqESNPP1.1	1	8	8.01	2.01	-0.16	-1.12	0.44	0~	14.0	RCM150~	RCM1824
			qESNPP3.1	3	10	20.81	5.29	-1.15	-0.32	6.17	15.7~	30.0	RCM915~	RCM950
		EPBSN	FqEPBSN9.1	9	1	7.01	2.98	-0.73	-0.53	2.55	0.9~	16.8	RCM1335~	RCM1336
			FqEPBSN10.1	10	4	25.61	2.16	-0.76	0.09	5.87	14.2~	27.7	RCM938~	RCM279
			FqEPBSN6.3	6	5	11.01	3.52	0.75	-0.01	5.49	2.9~	16.7	RCM562~	RCM98
			FqEPBSN6.2	6	5	27.51	2.47	-0.61	-0.20	1.73	27.2~	41.1	RCM98~	RCM581
			FqEPBSN6.1	6	7	7.01	2.21	-0.35	-0.56	0.13	0~	21.2	RCM1556~	RCM1523
			qEPBSN3.1	3	10	23.11	4.55	-0.64	0.16	9.38	17.8~	30.7	RCM915~	RCM950
	ICIM-	ESNPP	FqESNPP6.1	6	7	4.00	2.90	-0.55	-1.20	4.93	0~	12.5	RCM1556~	RCM1521
	ADD		qESNPP3.1	3	10	23.00	4.61	-1.14	-0.33	6.94	16.5~	31.5	RCM917~	RCM950
		EPBSN	FqEPBSN9.2	9	1	18.00	2.16	-0.33	-0.39	3.16	16.5~	18.0	RCM1336~	RCM1338
			FqEPBSN6.1	6	7	7.00	2.46	-0.40	-0.58	5.29	0~	17.5	RCM1556~	RCM1521
			qEPBSN3.1	3	10	23.00	3.25	-0.56	0.11	5.42	17.5~	33.5	RCM917~	RCM950
BC₁	CIM	ESNPP	BqESNPP7.1	7	1	1.00	5.01	2.12	-	3.52	0.4~	13.3	RCM1778~	RCM1772
			qESNPP3.1	3	4	4.00	18.81	3.61	-	6.27	12.3~	26.3	RCM950~	RCM931
		EPBSN	BqEPBSN7.1	7	1	1.00	5.01	2.31	-	4.42	2.6~	6.0	RCM1778~	RCM1625
			qEPBSN3.1	3	4	4.00	18.81	3.18	-	5.62	13.5~	26.8	RCM950~	RCM931
	ICIM-	ESNPP	qESNPP3.1	3	4	19.00	4.45	-1.96	-	7.92	12.5~	21.5	RCM920~	RCM917
	ADD	EPBSN	qEPBSN3.1	3	4	21.00	3.95	-0.87	-	7.21	17.5~	27.5	RCM920~	RCM917
S₁	CIM	EPBSN	qEPBSN3.1	3	1	15.01	2.18	-0.47	0.23	13.27	1.5~	23.5	RCM915~	RCM950

群体 Pop	方法 Method	性状 Trait	QTL	染色体 Chr	连锁群 LG	位置 Pos	LOD	加性 Add	显性 Dom	贡献率/% PVE	置信区间 CI		标记区间 MI
F₂	CIM	ESNPP	FqESNPP6.1	6	7	4.01	2.70	-0.48	-1.21	0.09	0~	12.7	RCM1556~	RCM1521
			FqESNPP1.1	1	8	8.01	2.01	-0.16	-1.12	0.44	0~	14.0	RCM150~	RCM1824
			qESNPP3.1	3	10	20.81	5.29	-1.15	-0.32	6.17	15.7~	30.0	RCM915~	RCM950
		EPBSN	FqEPBSN9.1	9	1	7.01	2.98	-0.73	-0.53	2.55	0.9~	16.8	RCM1335~	RCM1336
			FqEPBSN10.1	10	4	25.61	2.16	-0.76	0.09	5.87	14.2~	27.7	RCM938~	RCM279
			FqEPBSN6.3	6	5	11.01	3.52	0.75	-0.01	5.49	2.9~	16.7	RCM562~	RCM98
			FqEPBSN6.2	6	5	27.51	2.47	-0.61	-0.20	1.73	27.2~	41.1	RCM98~	RCM581
			FqEPBSN6.1	6	7	7.01	2.21	-0.35	-0.56	0.13	0~	21.2	RCM1556~	RCM1523
			qEPBSN3.1	3	10	23.11	4.55	-0.64	0.16	9.38	17.8~	30.7	RCM915~	RCM950
	ICIM-	ESNPP	FqESNPP6.1	6	7	4.00	2.90	-0.55	-1.20	4.93	0~	12.5	RCM1556~	RCM1521
	ADD		qESNPP3.1	3	10	23.00	4.61	-1.14	-0.33	6.94	16.5~	31.5	RCM917~	RCM950
		EPBSN	FqEPBSN9.2	9	1	18.00	2.16	-0.33	-0.39	3.16	16.5~	18.0	RCM1336~	RCM1338
			FqEPBSN6.1	6	7	7.00	2.46	-0.40	-0.58	5.29	0~	17.5	RCM1556~	RCM1521
			qEPBSN3.1	3	10	23.00	3.25	-0.56	0.11	5.42	17.5~	33.5	RCM917~	RCM950
BC₁	CIM	ESNPP	BqESNPP7.1	7	1	1.00	5.01	2.12	-	3.52	0.4~	13.3	RCM1778~	RCM1772
			qESNPP3.1	3	4	4.00	18.81	3.61	-	6.27	12.3~	26.3	RCM950~	RCM931
		EPBSN	BqEPBSN7.1	7	1	1.00	5.01	2.31	-	4.42	2.6~	6.0	RCM1778~	RCM1625
			qEPBSN3.1	3	4	4.00	18.81	3.18	-	5.62	13.5~	26.8	RCM950~	RCM931
	ICIM-	ESNPP	qESNPP3.1	3	4	19.00	4.45	-1.96	-	7.92	12.5~	21.5	RCM920~	RCM917
	ADD	EPBSN	qEPBSN3.1	3	4	21.00	3.95	-0.87	-	7.21	17.5~	27.5	RCM920~	RCM917
S₁	CIM	EPBSN	qEPBSN3.1	3	1	15.01	2.18	-0.47	0.23	13.27	1.5~	23.5	RCM915~	RCM950

QTL_1	染色体_1 Chr_1		位置_1 Pos_1		标记区间_1 MI_1		QTL_2		染色体_2 Chr_2		位置_2 Pos_2		标记区间_2 MI_2
FqEPBSN7.1	7		15		RCM1769~RCM1843		FqEPBSN7.2		7		170		RCM550~RCM1848
LOD	贡献率/% PVE	加性_1 Add_1		加性_2 Add_2		显性_1 Dom_1		显性_2 Dom_2		AA		AD		DA	DD
5.36	2.45	0.76		-0.26		0.90		1.24		-0.15		-2.51		1.14	-2.58

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