Mapping Major QTLs for Panicle Traits Using CSSLs of Dongxiang Wild Rice (Oryza rufipogon Griff.)

doi:10.16819/j.1001-7216.2023.221205

Abstract

Abstract:

【Objective】 Panicles are the primary yield determinants in rice, making it essential to explore major QTL associated with panicle traits for subsequent fine mapping, cloning, and breeding purposes. 【Method】 We employed a population of Chromosome Segment Substitution Lines(CSSLs) generated by crossing Nipponbare (japonica) with C35 (Dongxiang wild rice) and conducted phenotypic evaluations and major QTL mapping across four distinct ecological environments. 【Result】 Significant variations in panicle traits were observed in the CSSL populations across different ecological environments. The introduction of Dongxiang wild rice chromosome segments brought about substantial changes in panicle traits, leading to a noticeable increase in production. A total of 64 QTLs controlling grain number per panicle and grain size were identified across early-season, mid-season, late-season in Jiangxi, and Hainan environments. Among these QTLs, qPL2, qSN1.2, qSN2, qFGN3, qTGW2, qTGW12.1, and qSL2 consistently expressed in three environments, and 21 QTLs were detected in two environments, while others were specific to a single environment. Major QTLs, including qSN1.1, qSN1.2, qSN2, qSN3, and qSN12, exhibited significant effects on grain number per panicle, suggesting that multiple QTL aggregations play a crucial role in regulating grain number. Major QTLs such as qSL2, qSL3.2, qSLW3.1, qSLW3.2, qTGW8.1, and qSLW10 had evident effects on grain size, influencing grain length, grain width, and the length-to-width ratio. Interactions between these loci jointly determined grain size. Additionally, we observed clusters of panicle trait QTLs on 10 chromosome segments. These major QTL clusters, qGNS1.1, qGNS1.3, qGNS2.1, qGNS3.1, qGNS9, qGNS10, and qGNS12, contained several QTLs that regulated grain number and grain size traits. These clusters exhibited stable expression across diverse environments, underscoring the regulatory role of alleles from Dongxiang wild rice in enhancing yield. 【Conclusion】 These findings not only serve as the foundation for uncovering valuable genes in Dongxiang wild rice but also provide new genetic resources for the rice molecular breeding.

Key words: Dongxiang wild rice, chromosome segment substitution line, panicle trait, QTL mapping

摘要：

【目的】 稻穗是水稻产量的主要承载者，发掘穗部性状相关的主效QTL对进一步精细定位、克隆和育种利用具有重要意义。【方法】 以粳稻日本晴为受体、东乡野生稻为供体构建的一套染色体片段置换系（chromosome segment substitution lines, CSSLs）群体为材料，在4个生态环境下进行穗部性状表型鉴定与主效QTL定位分析。【结果】 不同生态环境下CSSL群体穗部性状存在较大幅度变异，东乡野生稻染色体片段的导入显著改变背景亲本的穗部性状，具有明显的增产效应；早季、中季、晚季和海南环境下共检测到64个控制每穗颖花数和籽粒大小的QTL，其中qPL2、qSN1.2、qSN2、qFGN3、qTGW2、qTGW12.1和qSL2在3个环境下稳定表达，21个QTL在2个环境下被重复检测到，其余QTL仅在单一环境下被发现；主效QTL qSN1.1、qSN1.2、qSN2、qSN3和qSN12对每穗颖花数具有明显的影响，多个QTL聚合具有明显调控每穗颖花数的功能；主效QTL qSL2、qSL3.2、qSLW3.1、qSLW3.2、qTGW8.1和qSLW10对籽粒大小具有明显的影响。这些位点分别作用于粒长、粒宽和长宽比，相互作用、共同决定籽粒大小；同时，穗部性状QTL成簇分布于10个染色体区段，其中主效QTL簇qGNS1.1、qGNS1.3、qGNS2.1、qGNS3.1、qGNS9、qGNS10和qGNS12包含多个调控每穗颖花数及籽粒大小性状的QTL，可在不同环境下稳定表达。来自东乡野生稻的等位基因具有明显调控产量表型的功能。【结论】 研究结果不仅为东乡野生稻优异基因发掘奠定基础，也可为水稻穗部性状的分子育种提供新基因源。

关键词: 东乡野生稻, 染色体片段置换系, 穗部性状, QTL分析

HU Jiaxiao, LIU Jin, CUI Di, LE Si, ZHOU Huiying, HAN Bing, MENG Bingxin, YU Liqin, HAN Longzhi, MA Xiaoding, LI Maomao. Mapping Major QTLs for Panicle Traits Using CSSLs of Dongxiang Wild Rice (Oryza rufipogon Griff.)[J]. Chinese Journal OF Rice Science, 2023, 37(6): 597-608.

胡佳晓, 刘进, 崔迪, 勒思, 周慧颖, 韩冰, 孟冰欣, 余丽琴, 韩龙植, 马小定, 黎毛毛. 利用东乡野生稻染色体片段置换系鉴定穗部性状主效QTL[J]. 中国水稻科学, 2023, 37(6): 597-608.

Figures/Tables 8

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	Luo L, Lei L X, Liu J, Zhang R H, Jin G X, Cui D, Li M M, Ma X D, Zhao Z W, Han L Z. Mapping QTLs for yield-related traits using chromosome segment substitution lines of Dongxiang common wild rice (Oryza rufipogon Griff.) and Nipponbare (Oryza sativa L.)[J]. Acta Agronomica Sinica, 2021, 47(7): 1391-1401. (in Chinese with English abstract)

性状 Trait	环境 Environment	日本晴 Nipponbare	染色体置换系群体 CSSL population
性状 Trait	环境 Environment	日本晴 Nipponbare	均值±标准差 Mean±SD Mean±Sd	变幅Range Range	峰度Kurtosis Skewness	偏度Skewness Kurtosis
穗长	E1	22.37	21.80±1.74	15.68~27.78	−0.01	1.93
PL	E2	21.40	22.32±2.00	17.78~28.03	0.59	0.42
	E3	21.55	22.29±2.03	16.64~26.96	0.00	0.17
	E4	19.68	19.97±1.56	15.07~24.94	0.36	1.10
颖花数	E1	110.08	93.64±18.20	61.00~160.70	0.93	1.46
SN	E2	104.00	104.73±17.69	71.67~151.40	0.35	−0.14
	E3	75.71	72.90±17.54	41.00~158.00	1.63	1.94
	E4	54.90	58.06±14.23	34.93~124.47	1.97	2.44
实粒数	E1	90.42	80.39±17.95	20.10~121.70	−0.46	1.17
FGN	E2	84.30	80.03±16.83	22.00~119.40	−0.58	1.18
	E3	63.00	57.56±16.90	5.30~118.33	0.50	1.74
	E4	33.53	41.26±16.88	3.13~94.73	0.69	1.11
结实率	E1	82.00	85.63±10.48	28.76~96.01	−3.08	1.10
SF/%	E2	80.92	77.03±13.22	21.77~96.51	−1.81	1.15
	E3	83.21	78.50±12.12	9.23~96.64	−2.40	1.90
	E4	61.81	70.10±19.48	5.35~96.78	−0.93	0.61
千粒重	E1	25.57	23.03±2.88	15.42~31.12	−0.17	−0.21
TGW/g	E2	25.68	24.48±2.04	15.86~28.87	−1.12	2.64
	E3	26.58	25.81±1.77	19.71~30.01	−0.40	0.53
	E4	25.89	25.54±2.44	12.86~33.50	−1.41	2.23
粒长	E1	7.43	7.71±0.34	6.70~8.70	0.44	0.95
SL/mm	E2	6.93	7.06±0.39	6.27~8.82	1.76	1.22
	E3	7.30	7.46±0.30	6.70~8.25	0.30	−0.02
	E4	7.60	7.68±0.34	6.70~8.60	0.61	1.09
粒宽	E1	3.35	3.29±0.14	2.70~3.55	−0.98	2.01
SW/mm	E2	3.37	3.31±0.15	2.46~3.58	−2.49	1.34
	E3	3.00	3.10±0.12	2.80~3.50	0.34	0.38
	E4	3.38	3.27±0.12	2.87~3.51	−0.86	1.30
长宽比	E1	2.22	2.35±0.15	2.06~3.00	1.10	3.20
SLW	E2	2.06	2.15±0.22	1.87~3.55	1.15	1.97
	E3	2.43	2.41±0.13	2.12~2.78	0.34	0.25
	E4	2.25	2.35±0.14	2.04~2.79	0.60	1.02

性状 Trait	环境 Environment	日本晴 Nipponbare	染色体置换系群体 CSSL population
性状 Trait	环境 Environment	日本晴 Nipponbare	均值±标准差 Mean±SD Mean±Sd	变幅Range Range	峰度Kurtosis Skewness	偏度Skewness Kurtosis
穗长	E1	22.37	21.80±1.74	15.68~27.78	−0.01	1.93
PL	E2	21.40	22.32±2.00	17.78~28.03	0.59	0.42
	E3	21.55	22.29±2.03	16.64~26.96	0.00	0.17
	E4	19.68	19.97±1.56	15.07~24.94	0.36	1.10
颖花数	E1	110.08	93.64±18.20	61.00~160.70	0.93	1.46
SN	E2	104.00	104.73±17.69	71.67~151.40	0.35	−0.14
	E3	75.71	72.90±17.54	41.00~158.00	1.63	1.94
	E4	54.90	58.06±14.23	34.93~124.47	1.97	2.44
实粒数	E1	90.42	80.39±17.95	20.10~121.70	−0.46	1.17
FGN	E2	84.30	80.03±16.83	22.00~119.40	−0.58	1.18
	E3	63.00	57.56±16.90	5.30~118.33	0.50	1.74
	E4	33.53	41.26±16.88	3.13~94.73	0.69	1.11
结实率	E1	82.00	85.63±10.48	28.76~96.01	−3.08	1.10
SF/%	E2	80.92	77.03±13.22	21.77~96.51	−1.81	1.15
	E3	83.21	78.50±12.12	9.23~96.64	−2.40	1.90
	E4	61.81	70.10±19.48	5.35~96.78	−0.93	0.61
千粒重	E1	25.57	23.03±2.88	15.42~31.12	−0.17	−0.21
TGW/g	E2	25.68	24.48±2.04	15.86~28.87	−1.12	2.64
	E3	26.58	25.81±1.77	19.71~30.01	−0.40	0.53
	E4	25.89	25.54±2.44	12.86~33.50	−1.41	2.23
粒长	E1	7.43	7.71±0.34	6.70~8.70	0.44	0.95
SL/mm	E2	6.93	7.06±0.39	6.27~8.82	1.76	1.22
	E3	7.30	7.46±0.30	6.70~8.25	0.30	−0.02
	E4	7.60	7.68±0.34	6.70~8.60	0.61	1.09
粒宽	E1	3.35	3.29±0.14	2.70~3.55	−0.98	2.01
SW/mm	E2	3.37	3.31±0.15	2.46~3.58	−2.49	1.34
	E3	3.00	3.10±0.12	2.80~3.50	0.34	0.38
	E4	3.38	3.27±0.12	2.87~3.51	−0.86	1.30
长宽比	E1	2.22	2.35±0.15	2.06~3.00	1.10	3.20
SLW	E2	2.06	2.15±0.22	1.87~3.55	1.15	1.97
	E3	2.43	2.41±0.13	2.12~2.78	0.34	0.25
	E4	2.25	2.35±0.14	2.04~2.79	0.60	1.02

位点 Locus	标记 Marker	LOD值 LOD value				贡献率PVE /%				加性效应Additive effect
位点 Locus	标记 Marker	E1	E2	E3	E4	E1	E2	E3	E4	E1	E2	E3	E4
穗长 Panicle length
qPL1	DX-C1-9				2.63				9.64				0.66
qPL2	DX-C2-13		3.39	3.26	3.20		13.35	12.88	11.91		0.91	1.06	0.65
qPL5.1	DX-C5-8		2.48				9.56				2.16
qPL5.2	05-041				4.16				14.34				−0.98
qPL7	DX-C7-2	3.75				14.19				1.13
qPL8	DX-C8-3	2.93				10.04				−3.09
qPL10	DX-S10-1				2.78				10.43				0.93
qPL12	DX-C12-12	2.83				10.39				−0.74
颖花数 Spikelet number
qSN1.1	DX-C1-3		2.49	2.52			11.38	9.05			7.57	6.71
qSN1.2	DX-C1-16	3.28		3.13	6.14	13.38		10.93	17.85	−24.24		−21.27	−21.72
qSN2	DX-C2-2	7.38		4.72	10.69	23.38		18.37	29.90	34.07		25.93	29.37
qSN3	indel-c3-12	2.62				7.44				−7.31
qSN12	DX-S12-3			2.97	5.06			9.14	12.98			−15.88	−19.53
实粒数 Filled grain number
qFGN1.1	DX-C1-2		2.10	3.50			6.96	11.08			6.01	8.37
qFGN1.2	DX-C1-16				5.58				5.83				18.19
qFGN2.1	DX-C2-2			2.58				7.45				18.61
qFGN2.2	DX-S2-14				5.76				6.05				22.59
qFGN3	DX-C3-8	5.03	5.42	2.39		16.14	19.12	6.68		−10.69	−12.18	−7.94
qFGN4	DX-C4-12	2.76			5.57	9.78			5.83	20.99			7.33
qFGN5	DX-C5-4	3.02				10.74				30.95
qFGN6	06-037				3.03				2.99				8.19
qFGN11	DX-C11-8				14.00				17.84				−54.59
qFGN12	DX-C12-2				10.89				12.89				23.54
结实率 Seed fertility
qSF1	DX-C1-7	4.28				14.28				−5.61
qSF2.1	DX-C2-1		2.53				4.42				−10.92
qSF2.2	indel-c2-3		3.38				6.02				−7.51
qSF3.1	indel-c3-2	5.64				19.40				−20.64
qSF3.2	DX-S3-12-2	6.60				19.59				5.88
qSF4	DX-C4-12				3.48				14.17				8.82
qSF5	DX-C5-4	7.93				24.08				24.02
qSF6	06-013	4.11				13.66				−7.90
qSF9.1	DX-C9-4		11.83				25.63				−18.78
qSF9.2	DX-C9-10		6.42	3.86			12.20	12.01			−18.07	−17.42
qSF12	DX-C12-10		3.72				6.67				−5.57

位点 Locus	标记 Marker	LOD值 LOD value				贡献率PVE /%				加性效应Additive effect
位点 Locus	标记 Marker	E1	E2	E3	E4	E1	E2	E3	E4	E1	E2	E3	E4
穗长 Panicle length
qPL1	DX-C1-9				2.63				9.64				0.66
qPL2	DX-C2-13		3.39	3.26	3.20		13.35	12.88	11.91		0.91	1.06	0.65
qPL5.1	DX-C5-8		2.48				9.56				2.16
qPL5.2	05-041				4.16				14.34				−0.98
qPL7	DX-C7-2	3.75				14.19				1.13
qPL8	DX-C8-3	2.93				10.04				−3.09
qPL10	DX-S10-1				2.78				10.43				0.93
qPL12	DX-C12-12	2.83				10.39				−0.74
颖花数 Spikelet number
qSN1.1	DX-C1-3		2.49	2.52			11.38	9.05			7.57	6.71
qSN1.2	DX-C1-16	3.28		3.13	6.14	13.38		10.93	17.85	−24.24		−21.27	−21.72
qSN2	DX-C2-2	7.38		4.72	10.69	23.38		18.37	29.90	34.07		25.93	29.37
qSN3	indel-c3-12	2.62				7.44				−7.31
qSN12	DX-S12-3			2.97	5.06			9.14	12.98			−15.88	−19.53
实粒数 Filled grain number
qFGN1.1	DX-C1-2		2.10	3.50			6.96	11.08			6.01	8.37
qFGN1.2	DX-C1-16				5.58				5.83				18.19
qFGN2.1	DX-C2-2			2.58				7.45				18.61
qFGN2.2	DX-S2-14				5.76				6.05				22.59
qFGN3	DX-C3-8	5.03	5.42	2.39		16.14	19.12	6.68		−10.69	−12.18	−7.94
qFGN4	DX-C4-12	2.76			5.57	9.78			5.83	20.99			7.33
qFGN5	DX-C5-4	3.02				10.74				30.95
qFGN6	06-037				3.03				2.99				8.19
qFGN11	DX-C11-8				14.00				17.84				−54.59
qFGN12	DX-C12-2				10.89				12.89				23.54
结实率 Seed fertility
qSF1	DX-C1-7	4.28				14.28				−5.61
qSF2.1	DX-C2-1		2.53				4.42				−10.92
qSF2.2	indel-c2-3		3.38				6.02				−7.51
qSF3.1	indel-c3-2	5.64				19.40				−20.64
qSF3.2	DX-S3-12-2	6.60				19.59				5.88
qSF4	DX-C4-12				3.48				14.17				8.82
qSF5	DX-C5-4	7.93				24.08				24.02
qSF6	06-013	4.11				13.66				−7.90
qSF9.1	DX-C9-4		11.83				25.63				−18.78
qSF9.2	DX-C9-10		6.42	3.86			12.20	12.01			−18.07	−17.42
qSF12	DX-C12-10		3.72				6.67				−5.57

性状 Trait	位点 Locus	标记 Marker	LOD值 LOD value				贡献率PVE/%				加性效应Additive effect
性状 Trait	位点 Locus	标记 Marker	E1	E2	E3	E4	E1	E2	E3	E4	E1	E2	E3	E4
千粒重	qTGW1	DX-C1-16	2.50				10.37				−2.78
TGW	qTGW2	02-008		4.09	3.20	2.44		10.62	9.04	10.01		−2.54	−1.97	−2.83
	qTGW8.1	DX-S8-14		2.93	3.05			7.50	8.65			−1.25	−1.13
	qTGW8.2	DX-C8-3			4.00	2.03			11.52	7.55			−3.13	−3.47
	qTGW9.1	DX-C9-4			2.90	2.30			8.15	8.49			1.34	1.54
	qTGW9.2	DX-C9-10		3.27				8.50				−2.26
	qTGW12.1	S12-6-3		5.13	4.50	2.45		13.63	15.54	9.32		−2.36	−3.20	−1.50
	qTGW12.2	DX-C12-9		3.50				6.80				−1.37
粒长	qSL1.1	DX-S1-20	7.56	3.04			21.24	10.95			−0.27	−0.20
SL	qSL1.2	DX-S1-5			3.32				13.59				−0.19
	qSL2	02-067		3.11	2.73	2.64		7.45	11.29	7.84		0.15	0.14	0.14
	qSL3.1	DX-S3-17	3.80	6.13			10.39	15.60			0.28	0.37
	qSL3.2	DX-C3-23	8.06	6.26			24.28	16.00			0.26	0.25
	qSL7	07-041			2.56				10.62				0.09
	qSL10	DX-C10-8		3.44		2.87		8.24		8.44		0.19		0.16
	qSL11	DX-S11-10	3.96				10.84				−0.20
	qSL12	S12-6-3	2.80			3.30	7.06			6.50	0.30			0.28
粒宽	qSW3.1	DX-S3-14-1		3.31	2.49			13.22	9.73			0.10
SW	qSW3.2	DX-S3-17		2.51				7.84				−0.11
	qSW6	DX-C6-4				2.69				8.82
	qSW7	indel-c7-9	2.33		2.74		8.93		8.02		−0.08		−0.07
	qSW10	DX-C10-10		2.70		2.74		9.84		11.31		−0.09		−0.07
	qSW11	DX-S11-13	2.78				11.47				0.09
长宽比	qSLW1.1	DX-S1-20	4.51				15.66				−0.09
SLW	qSLW1.2	DX-C1-18			2.71	2.62			11.20	9.20			0.16	0.14
	qSLW3.1	DX-C3-1	4.52	2.78			16.73	8.12			0.12	0.12
	qSLW3.2	DX-S3-17	3.68	4.81			12.54	14.70			−0.09	0.20
	qSLW3.3	DX-C3-32				3.07				10.88				0.10
	qSLW9	DX-C9-8		3.69		2.16		13.98		6.98		−0.20		0.07
	qSLW10	DX-C10-8		3.84		2.39		11.48		8.36		0.12		0.06