QTL Mapping and Candidate Gene Analysis for Harvest Index and Related Traits in Castor

doi:10.7668/hbnxb.20194641

Abstract

Abstract:

In order to reveal the genetic law of Ricinus communis harvest index and explore its candidate genes,and provide a reference for the genetic improvement of castor harvest index.F₂ and BC₁(F₁ × P₂)populations were constructed by 9048×16-201 hybrid combination.The phenotypic traits and QTL mapping of harvest index and related traits were studied by inclusive composite interval mapping(ICIM-ADD)method and the main QTL cluster was verified in S₁ population with the same method.It was found that the harvest index was significantly positively correlated with yield per plant,capsule number per plant,grain number per plant,seed setting rate of main panicle,positively correlated with seed setting rate per plant,seed setting rate of primary branch panicle,seed setting rate of secondary branch panicle,100-grain weight per plant and effective panicle number per plant,and negatively correlated with biomass and root weight.The yield per plant was positively correlated with other traits.A total of 31/21 QTLs underlying harvest index and related traits were detected in F₂/BC₁ populations,with a contribution ratio of 1.64%—19.96%/0.90%—11.51%,including 4 stable QTLs with favorable alleles from 16-201 and 5 major QTLs.Significantly,3 stable QTLs(FqSRPS3-3,FqSRPBS3-3 and BqSRSBS3-1)and 2 major QTLs(FqSRPS3-3/BqSRPS3-1 and BqSRPBS3-1)were clustered on the QTL-cluster1(RCM915—RCM950,997.10 kb)on chromosome 3,and 8 allelic QTLs from QTL-cluster1 were found in S₁ population repeatedly.Therefore,3 candidate genes(Rc-US03g04790,Rc-US03g05640 and Rc-US03g05810)were selected in QTL-cluster1,which were differentially expressed in multiple tissues of both parents.The relative expression levels of each candidate gene in high-expression parents were 2.34—880.06 times,1.85—51.56 times and 2.01—236.03 times higher than those in low-expression parents.

Key words: Castor, Harvest index, QTL mapping, Major QTL, Candidate genes

ZHANG Xiaoxiao, YIN Xuegui, LU Jiannong, HUANG Guanrong, ZHANG Liuqin, LIU Chaoyu, LIN Haihong, ZUO Jinying. QTL Mapping and Candidate Gene Analysis for Harvest Index and Related Traits in Castor[J]. Acta Agriculturae Boreali-Sinica, 2024, 39(3): 77-87. doi: 10.7668/hbnxb.20194641.

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References 45

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性状 Trait	亲本 Parent		F₁	F₂群体 F₂ population						BC₁群体 BC₁ population
性状 Trait	16-201	9048	F₁	范围 Range	平均值 Mean	变异系数/% CV	偏度 Skewness	峰度 Kurtosis		范围 Range	平均值 Mean	变异系数% CV	偏度 Skewness	峰度 Kurtosis
收获指数/% HI	21.54±0.07B	43.13±0.05A	44.98	4.04~71.45	37.80	26.81	0.06		1.88	5.49~74.29	39.77	21.65	-0.29	3.31
单株产量/g SYPP	42.05±4.78B	191.08±15.61A	131.37	3.43~331.28	105.73	48.88	0.83		1.15	6.16~303.41	135.34	43.34	0.27	-0.22
生物量/g GB	195.20±33.86B	451.12±76.53A	302.67	55.00~585.00	278.16	40.17	0.42		-0.23	15.00~825.00	338.76	42.47	0.42	0.33
根质量/g RW	43.90±12.20B	110.30±46.11A	79.98	5.00~80.00	24.51	49.52	1.04		1.78	5.00~85.00	27.96	50.88	1.09	1.44
单株结实率/% SRPP	87.00±0.02A	83.18±0.03B	85.51	27.98~98.81	69.98	24.44	-0.27		-0.74	26.73~99.55	79.15	18.47	-0.91	0.79
单株蒴果数 CNPP	141.00±18.74B	209.00±20.84A	289.00	14.00~496.00	219.00	46.66	0.57		-0.18	14.00~594.00	284.00	42.22	0.09	-0.61
单株粒数 SNPP	368.00±51.74B	521.00±45.74A	740.00	0.00~551.00	222.00	47.36	0.40		-0.12	31.00~597.00	237.00	37.10	0.39	0.72
单株有效穗数 ESNPP	5.00±0.50A	4.00±0.50B	9.00	1.00~20.00	6.00	45.05	0.76		1.15	1.00~18.00	9.00	37.50	-0.02	-0.30

性状 Trait	亲本 Parent		F₁	F₂群体 F₂ population						BC₁群体 BC₁ population
性状 Trait	16-201	9048	F₁	范围 Range	平均值 Mean	变异系数/% CV	偏度 Skewness	峰度 Kurtosis		范围 Range	平均值 Mean	变异系数% CV	偏度 Skewness	峰度 Kurtosis
收获指数/% HI	21.54±0.07B	43.13±0.05A	44.98	4.04~71.45	37.80	26.81	0.06		1.88	5.49~74.29	39.77	21.65	-0.29	3.31
单株产量/g SYPP	42.05±4.78B	191.08±15.61A	131.37	3.43~331.28	105.73	48.88	0.83		1.15	6.16~303.41	135.34	43.34	0.27	-0.22
生物量/g GB	195.20±33.86B	451.12±76.53A	302.67	55.00~585.00	278.16	40.17	0.42		-0.23	15.00~825.00	338.76	42.47	0.42	0.33
根质量/g RW	43.90±12.20B	110.30±46.11A	79.98	5.00~80.00	24.51	49.52	1.04		1.78	5.00~85.00	27.96	50.88	1.09	1.44
单株结实率/% SRPP	87.00±0.02A	83.18±0.03B	85.51	27.98~98.81	69.98	24.44	-0.27		-0.74	26.73~99.55	79.15	18.47	-0.91	0.79
单株蒴果数 CNPP	141.00±18.74B	209.00±20.84A	289.00	14.00~496.00	219.00	46.66	0.57		-0.18	14.00~594.00	284.00	42.22	0.09	-0.61
单株粒数 SNPP	368.00±51.74B	521.00±45.74A	740.00	0.00~551.00	222.00	47.36	0.40		-0.12	31.00~597.00	237.00	37.10	0.39	0.72
单株有效穗数 ESNPP	5.00±0.50A	4.00±0.50B	9.00	1.00~20.00	6.00	45.05	0.76		1.15	1.00~18.00	9.00	37.50	-0.02	-0.30

性状 Trait	QTL	染色体 Chr	连锁群 LG	位置 Position	LOD	贡献率/% PVE	加性效应 Add	显性效应 Dom	置信区间 CI	标记区间 MI
收获指数	FqHI3-1	3	9	47	2.82	5.37	-0.03	-0.02	37.5~52.5	RCM915~RCM917
HI	BqHI3-1	3	4	9	6.10	0.90	0.23		0.0~19.4	RCM297~RCM74
	BqHI5-1	5	2	15	2.71	1.00	0.24		5.0~26.3	RCM83~RCM67
单株产量	FqSYPP3-1	3	9	102	2.60	6.19	23.94	-0.67	93.6~111.8	RCM931~RCM922
SYPP	FqSYPP5-1	5	3	27	2.78	1.64	14.45	9.18	12.6~44.8	RCM1212~RCM523
	FqSYPP6-1	6	7	5	2.54	3.26	2.33	-22.45	0.0~14.5	RCM1556~RCM1521
	FqSYPP9-1	9	1	10	3.37	5.84	-20.43	-2.68	3.5~18.0	RCM1335~RCM1336
	BqSYPP4-1	4	3	289	2.32	4.20	33.14		273.5~305.5	RCM912~RCM101
生物量	FqGB1-1	1	8	12	2.75	2.06	0.79	-53.63	4.3~14.0	RCM150~RCM1824
GB	FqGB9-1	9	1	18	2.27	4.04	-26.17	-25.91	16.5~18.0	RCM1336~RCM1338
根质量 RW	FqRW6-1	6	5	17	2.54	7.42	7.37	-14.32	12.5~22.5	RCM581~RCM71
单株结实率	FqSRPP3-1	3	6	20	4.94	9.61	-0.07	0.02	12.9~26.6	RCM520~RCM76
SRPP	FqSRPP3-2	3	6	30	4.98	9.00	-0.06	0.02	26.6~30.6	RCM76~RCM74
	FqSRPP3-3	3	9	49	5.49	7.23	-0.07	-0.01	39.5~52.5	RCM915~RCM917
	FqSRPP3-4	3	9	65	4.41	6.16	-0.07	0.00	52.8~67.1	RCM917~RCM933
	FqSRPP5-1	5	3	32	3.20	5.35	0.06	-0.02	11.5~44.5	RCM1212~RCM523
	BqSRPP3-1	3	3	66	3.48	6.37	-0.08		58.5~73.5	RCM933~RCM950
主穗结实率	FqSRPS3-1	3	6	29	4.61	3.75	-0.05	0.04	26.5~30.0	RCM76~RCM74
SRPS	FqSRPS3-2	3	6	23	3.68	9.08	-0.04	0.05	15.2~26.6	RCM520~RCM76
	FqSRPS3-3	3	9	59	4.82	10.10	-0.06	0.02	31.6~64.8	RCM917~RCM950
	FqSRPS5-1	5	3	41	2.04	1.86	0.04	0.01	25.5~55.5	RCM1212~RCM523
	FqSRPS7-1	7	2	179	3.01	12.85	-0.14	0.19	172.5~184.5	RCM550~RCM1848
	FqSRPS10-1	10	4	87	2.19	1.67	0.04	0.00	75.5~87.0	RCM226~RCM945
	BqSRPS3-1	3	3	85	3.32	6.72	-0.07		77.5~95.5	RCM917~RCM931
	BqSRPS3-2	3	4	6	4.39	1.07	-0.16		0.0~9.4	RCM297~RCM522
	BqSRPS3-3	3	4	17	4.65	1.05	-0.16		9.4~34.7	RCM522~RCM76
	BqSRPS4-1	4	3	293	10.84	1.04	-0.27		284.8~297.8	RCM912~RCM101
	BqSRPS7-1	7	1	22	7.57	0.95	-0.21		5.5~30.1	RCM1846~RCM1778
	BqSRPS7-2	7	1	42	3.15	1.12	-0.28		40.8~44.5	RCM264~RCM1772
	BqSRPS7-3	7	1	48	3.03	1.12	-0.28		46.4~49.7	RCM1624~RCM1772
	BqSRPS7-4	7	1	53	3.13	1.12	-0.29		52.5~55.3	RCM1772~RCM1838
	BqSRPS7-5	7	1	59	3.24	1.08	-0.27		58.1~61.9	RCM1838~RCM1842
一级分枝穗结实率	FqSRPBS3-1	3	6	9	4.07	5.61	-0.08	0.04	4.5~12.5	RCM521~RCM520
SRPBS	FqSRPBS3-2	3	6	16	3.90	8.08	-0.08	0.04	5.6~23.3	RCM520~RCM76
	FqSRPBS3-3	3	9	60	9.69	15.40	-0.15	-0.03	53.5~64.5	RCM917~RCM950
	BqSRPBS3-1	3	3	67	4.20	4.37	-0.10		62.5~73.5	RCM950~RCM920
	BqSRPBS3-2	3	3	251	3.33	2.14	-0.27		247.9~259.2	RCM926~RCM945
	BqSRPBS3-3	3	3	261	2.83	2.46	-0.35		260.2~281.2	RCM945~RCM912
	BqSRPBS3-4	3	4	16	4.41	2.07	-0.24		9.4~27.3	RCM522~RCM74
	BqSRPBS3-5	3	4	3	4.32	2.04	-0.24		0.0~6.0	RCM297~RCM520
二级分枝穗结实率	FqSRSBS7-1	7	2	9	2.89	19.96	-0.24	-0.09	0.0~17.5	RCM1769~RCM1843
SRSBS	BqSRSBS3-1	3	3	86	3.96	11.51	-0.18		81.5~96.5	RCM931~RCM922
单株粒数	FqSNPP3-1	3	6	29	3.10	3.59	-29.53	8.15	26.5~30.0	RCM76~RCM74
SNPP	FqSNPP3-2	3	6	29	3.47	5.91	-31.97	8.18	16.9~29.6	RCM520~RCM74
	FqSNPP5-1	5	3	91	2.48	3.22	17.84	31.74	77.5~112.5	RCM67~RCM23
	FqSNPP5-2	5	3	36	4.56	8.29	45.58	-1.86	24.7~60.9	RCM1212~RCM523
	FqSNPP9-1	9	1	15	4.67	5.89	-38.47	-9.42	5.5~18.0	RCM1335~RCM1336
单株蒴果数	FqCNPP6-1	6	7	3	2.94	2.18	-12.98	-47.83	0.0~11.5	RCM1556~RCM1521
CNPP	FqCNPP7-1	7	2	176	2.06	6.81	64.05	-86.29	168.5~189.5	RCM550~RCM1848
	FqCNPP9-1	9	1	12	2.81	2.24	-32.22	-28.81	3.5~15.5	RCM1335~RCM1336
	BqCNPP3-1	3	3	76	3.39	5.20	-60.40		73.5~83.5	RCM920~RCM917
	BqCNPP4-1	4	3	289	2.44	4.63	69.06		274.5~299.5	RCM912~RCM101

性状 Trait	QTL	染色体 Chr	连锁群 LG	位置 Position	LOD	贡献率/% PVE	加性效应 Add	显性效应 Dom	置信区间 CI	标记区间 MI
收获指数	FqHI3-1	3	9	47	2.82	5.37	-0.03	-0.02	37.5~52.5	RCM915~RCM917
HI	BqHI3-1	3	4	9	6.10	0.90	0.23		0.0~19.4	RCM297~RCM74
	BqHI5-1	5	2	15	2.71	1.00	0.24		5.0~26.3	RCM83~RCM67
单株产量	FqSYPP3-1	3	9	102	2.60	6.19	23.94	-0.67	93.6~111.8	RCM931~RCM922
SYPP	FqSYPP5-1	5	3	27	2.78	1.64	14.45	9.18	12.6~44.8	RCM1212~RCM523
	FqSYPP6-1	6	7	5	2.54	3.26	2.33	-22.45	0.0~14.5	RCM1556~RCM1521
	FqSYPP9-1	9	1	10	3.37	5.84	-20.43	-2.68	3.5~18.0	RCM1335~RCM1336
	BqSYPP4-1	4	3	289	2.32	4.20	33.14		273.5~305.5	RCM912~RCM101
生物量	FqGB1-1	1	8	12	2.75	2.06	0.79	-53.63	4.3~14.0	RCM150~RCM1824
GB	FqGB9-1	9	1	18	2.27	4.04	-26.17	-25.91	16.5~18.0	RCM1336~RCM1338
根质量 RW	FqRW6-1	6	5	17	2.54	7.42	7.37	-14.32	12.5~22.5	RCM581~RCM71
单株结实率	FqSRPP3-1	3	6	20	4.94	9.61	-0.07	0.02	12.9~26.6	RCM520~RCM76
SRPP	FqSRPP3-2	3	6	30	4.98	9.00	-0.06	0.02	26.6~30.6	RCM76~RCM74
	FqSRPP3-3	3	9	49	5.49	7.23	-0.07	-0.01	39.5~52.5	RCM915~RCM917
	FqSRPP3-4	3	9	65	4.41	6.16	-0.07	0.00	52.8~67.1	RCM917~RCM933
	FqSRPP5-1	5	3	32	3.20	5.35	0.06	-0.02	11.5~44.5	RCM1212~RCM523
	BqSRPP3-1	3	3	66	3.48	6.37	-0.08		58.5~73.5	RCM933~RCM950
主穗结实率	FqSRPS3-1	3	6	29	4.61	3.75	-0.05	0.04	26.5~30.0	RCM76~RCM74
SRPS	FqSRPS3-2	3	6	23	3.68	9.08	-0.04	0.05	15.2~26.6	RCM520~RCM76
	FqSRPS3-3	3	9	59	4.82	10.10	-0.06	0.02	31.6~64.8	RCM917~RCM950
	FqSRPS5-1	5	3	41	2.04	1.86	0.04	0.01	25.5~55.5	RCM1212~RCM523
	FqSRPS7-1	7	2	179	3.01	12.85	-0.14	0.19	172.5~184.5	RCM550~RCM1848
	FqSRPS10-1	10	4	87	2.19	1.67	0.04	0.00	75.5~87.0	RCM226~RCM945
	BqSRPS3-1	3	3	85	3.32	6.72	-0.07		77.5~95.5	RCM917~RCM931
	BqSRPS3-2	3	4	6	4.39	1.07	-0.16		0.0~9.4	RCM297~RCM522
	BqSRPS3-3	3	4	17	4.65	1.05	-0.16		9.4~34.7	RCM522~RCM76
	BqSRPS4-1	4	3	293	10.84	1.04	-0.27		284.8~297.8	RCM912~RCM101
	BqSRPS7-1	7	1	22	7.57	0.95	-0.21		5.5~30.1	RCM1846~RCM1778
	BqSRPS7-2	7	1	42	3.15	1.12	-0.28		40.8~44.5	RCM264~RCM1772
	BqSRPS7-3	7	1	48	3.03	1.12	-0.28		46.4~49.7	RCM1624~RCM1772
	BqSRPS7-4	7	1	53	3.13	1.12	-0.29		52.5~55.3	RCM1772~RCM1838
	BqSRPS7-5	7	1	59	3.24	1.08	-0.27		58.1~61.9	RCM1838~RCM1842
一级分枝穗结实率	FqSRPBS3-1	3	6	9	4.07	5.61	-0.08	0.04	4.5~12.5	RCM521~RCM520
SRPBS	FqSRPBS3-2	3	6	16	3.90	8.08	-0.08	0.04	5.6~23.3	RCM520~RCM76
	FqSRPBS3-3	3	9	60	9.69	15.40	-0.15	-0.03	53.5~64.5	RCM917~RCM950
	BqSRPBS3-1	3	3	67	4.20	4.37	-0.10		62.5~73.5	RCM950~RCM920
	BqSRPBS3-2	3	3	251	3.33	2.14	-0.27		247.9~259.2	RCM926~RCM945
	BqSRPBS3-3	3	3	261	2.83	2.46	-0.35		260.2~281.2	RCM945~RCM912
	BqSRPBS3-4	3	4	16	4.41	2.07	-0.24		9.4~27.3	RCM522~RCM74
	BqSRPBS3-5	3	4	3	4.32	2.04	-0.24		0.0~6.0	RCM297~RCM520
二级分枝穗结实率	FqSRSBS7-1	7	2	9	2.89	19.96	-0.24	-0.09	0.0~17.5	RCM1769~RCM1843
SRSBS	BqSRSBS3-1	3	3	86	3.96	11.51	-0.18		81.5~96.5	RCM931~RCM922
单株粒数	FqSNPP3-1	3	6	29	3.10	3.59	-29.53	8.15	26.5~30.0	RCM76~RCM74
SNPP	FqSNPP3-2	3	6	29	3.47	5.91	-31.97	8.18	16.9~29.6	RCM520~RCM74
	FqSNPP5-1	5	3	91	2.48	3.22	17.84	31.74	77.5~112.5	RCM67~RCM23
	FqSNPP5-2	5	3	36	4.56	8.29	45.58	-1.86	24.7~60.9	RCM1212~RCM523
	FqSNPP9-1	9	1	15	4.67	5.89	-38.47	-9.42	5.5~18.0	RCM1335~RCM1336
单株蒴果数	FqCNPP6-1	6	7	3	2.94	2.18	-12.98	-47.83	0.0~11.5	RCM1556~RCM1521
CNPP	FqCNPP7-1	7	2	176	2.06	6.81	64.05	-86.29	168.5~189.5	RCM550~RCM1848
	FqCNPP9-1	9	1	12	2.81	2.24	-32.22	-28.81	3.5~15.5	RCM1335~RCM1336
	BqCNPP3-1	3	3	76	3.39	5.20	-60.40		73.5~83.5	RCM920~RCM917
	BqCNPP4-1	4	3	289	2.44	4.63	69.06		274.5~299.5	RCM912~RCM101

性状 Trait	QTLs	染色体 Chr	连锁群 LG	位置 Position	LOD	贡献率/% PVE	加性效应 Add	显性效应 Dom	置信区间 CI	标记区间 MI
单株产量 SYPP	qSYPP2-1	3	1	83	3.21	4.96	-20.91	-57.78	67.5~108.5	RCM926~RCM931
生物量 GB	qGB2-2	3	1	156	3.55	4.46	144.72	-160.27	151.5~160.5	RCM918~RCM933
	qGB2-3	3	1	68	7.05	2.90	-186.00	-213.03	67.4~73.1	RCM926~RCM931
	qGB2-4	3	1	104	3.42	5.72	18.08	-89.44	91.0~113.8	RCM926~RCM918
根质量 RW	qRW2-1	3	1	62	5.32	2.33	-41.48	-47.58	52.5~72.5	RCM926~RCM931
单株结实率 SRPP	qSRPP2-1	3	1	46	3.99	1.58	-0.02	-0.24	40.5~52.5	RCM926~RCM931
单株蒴果数 CNPP	qCNPP2-1	3	1	67	6.87	6.12	-90.78	-126.56	55.5~81.5	RCM926~RCM931
单株粒数 SNPP	qSNPP2-1	3	1	65	7.29	6.01	-252.84	-308.16	53.5~78.5	RCM926~RCM931

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