利用东乡普通野生稻染色体片段置换系定位产量相关性状QTL

doi:10.3724/SP.J.1006.2021.02054

作物学报 ›› 2021, Vol. 47 ›› Issue (7): 1391-1401.doi: 10.3724/SP.J.1006.2021.02054

利用东乡普通野生稻染色体片段置换系定位产量相关性状QTL

罗兰¹, 雷丽霞¹, 刘进²^,³, 张瑞华⁴, 金桂秀⁴, 崔迪², 黎毛毛³, 马小定²^,^*(), 赵正武¹^,^*(), 韩龙植²^,^*()

¹重庆师范大学, 重庆 401331
²中国农业科学院作物科学研究所 / 农作物基因资源与基因改良国家重大科学工程, 北京 100081
³江西省农业科学院水稻研究所, 江西南昌 330200
⁴临沂市农业科学院, 山东临沂 276000

收稿日期:2020-08-13 接受日期:2020-11-13 出版日期:2021-07-12 网络出版日期:2020-12-29
通讯作者: 马小定,赵正武,韩龙植
作者简介:罗兰, E-mail: 1366730598@qq.com;|雷丽霞, E-mail: 2873804227@qq.com
基金资助:
本研究由国家重点研发计划项目(2016YFD0100101);本研究由国家重点研发计划项目(2016YFD0100301);国家自然科学基金项目(31671664);中国农业科学院科技创新工程项目, 国家农作物种质资源保护项目(2018NWB036-01);中国农业科学院科技创新工程项目, 国家农作物种质资源保护项目(2018NWB036-12-2);国家农作物种质资源平台项目资助(NICGR2018-001)

Mapping QTLs for yield-related traits using chromosome segment substitution lines of Dongxiang common wild rice (Oryza rufipogon Griff.) and Nipponbare (Oryza sativa L.)

LUO Lan¹, LEI Li-Xia¹, LIU Jin²^,³, ZHANG Rui-Hua⁴, JIN Gui-Xiu⁴, CUI Di², LI Mao-Mao³, MA Xiao-Ding²^,^*(), ZHAO Zheng-Wu¹^,^*(), HAN Long-Zhi²^,^*()

¹Chongqing Normal University, Chongqing 401331, China
²National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
³Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, Jiangxi, China
⁴Linyi Academy of Agricultural Sciences, Linyi 276000, Shandong, China

Received:2020-08-13 Accepted:2020-11-13 Published:2021-07-12 Published online:2020-12-29
Contact: MA Xiao-Ding,ZHAO Zheng-Wu,HAN Long-Zhi
Supported by:
This study was supported by the National Key Research and Development Program of China(2016YFD0100101);This study was supported by the National Key Research and Development Program of China(2016YFD0100301);the National Natural Science Foundation of China(31671664);the CAAS Science and Technology Innovation Program, Protective Program of Crop Germplasm of China(2018NWB036-01);the CAAS Science and Technology Innovation Program, Protective Program of Crop Germplasm of China(2018NWB036-12-2);the National Infrastructure for Crop Germplasm Resources(NICGR2018-001)

摘要/Abstract

摘要：

以东乡普通野生稻和日本晴为亲本构建的染色体片段置换系为研究材料, 2019年分别在北京、山东临沂和江西南昌对分蘖数、穗粒数和粒形等11个产量相关性状进行多环境鉴定, 结合染色体片段置换系基因型数据定位水稻产量相关性状QTL。3个环境共检测到68个QTL, 包括株高4个、穗长5个、分蘖数2个、一次枝梗数7个、一次枝梗粒数8个、二次枝梗数8个、二次枝梗粒数10个、每穗粒数6个、千粒重7个、粒长8个和粒宽3个; LOD值介于2.50~12.66之间, 贡献率变幅为4.67%~27.79%, 15个QTL的贡献率大于15%; 24个QTL与已报道位点/基因位置重叠, 44个QTL为新发现位点; 6个QTL在2个环境能被检测到, 1个QTL qTGW2能在3个环境检测到, 且是还未报道的新位点。最后, 利用BSA法验证了qPH7、qPBPP8-2和qGW10三个QTL的可靠性。本研究将为后续产量相关性状基因克隆以及进一步解析其遗传基础和分子调控机制奠定基础。

关键词: 普通野生稻, 染色体片段置换系, 产量相关性状, QTL分析

Abstract:

In former study, we constructed a chromosome segment substitution lines (CSSLs) of Dongxiang common wild rice (Oryza rufipogon Griff.) in the background of Nipponbare (Oryza sativa L.). In this study, in order to investigate 11 yield-related traits, such as tillering number, grains per panicle and grain shapes, the CSSLs were planted in Beijing, Linyi and Nanchang. The results of quantitative trait loci (QTLs) for yield-related traits showed that a total of 68 QTLs were detected, including 4 QTLs for plant height, 5 QTLs for panicle length, 2 QTLs for tillering number, 7 QTLs for primary branch grain number, 8 QTLs for primary branch grain number, 8 QTLs for secondary branch grain number, 10 QTLs for secondary branch grain number, 6 QTLs for grains per panicle, 7 QTLs for 1000-grain weight, 8 QTLs for grain length and 3 QTLs for grain width. LOD score of the detected QTLs ranged from 2.50 to 12.66. The phenotypic variation explained by these QTLs ranged from 4.67% to 27.79%. There were 15 QTLs with a contribution rate more than 15%, 24 QTLs overlapped with the reported loci or gene position, 44 QTLs newly detected loci. In addition, 6 QTLs were stably detected at two sites, and 1 QTL (qTGW2) as a novel QTL was detected at three sites. Finally, the reliability of the three QTLs of qPH7, qPBPP8-2 and qGW10 was verified by BSA. Our results will be helpful for the subsequent cloning of yield-related trait genes and further analysis of their genetic basis and molecular regulation mechanism.

Key words: common wild rice (Oryza rufipogon Griff.), chromosome segment substitution lines (CSSLs), yield-related traits, QTL analysis

罗兰, 雷丽霞, 刘进, 张瑞华, 金桂秀, 崔迪, 黎毛毛, 马小定, 赵正武, 韩龙植. 利用东乡普通野生稻染色体片段置换系定位产量相关性状QTL[J]. 作物学报, 2021, 47(7): 1391-1401.

LUO Lan, LEI Li-Xia, LIU Jin, ZHANG Rui-Hua, JIN Gui-Xiu, CUI Di, LI Mao-Mao, MA Xiao-Ding, ZHAO Zheng-Wu, HAN Long-Zhi. 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.

图/表 5

图1

表1

图2

表2

北京、临沂和南昌3地产量相关性状QTL分析"

性状 Trait	位点 QTL	染色体 Chr.	标记名称 Marker	北京Beijing						南昌Nanchang
性状 Trait	位点 QTL	染色体 Chr.	标记名称 Marker	阈值 LOD value	贡献率 PVE (%)	加性效应 Additive	阈值 LOD value		贡献率 PVE (%)	加性效应 Additive	阈值 LOD value	贡献率 PVE (%)	加性效应 Additive
株高PH	qPH2	2	DX-C2-13	5.87	20.74	6.06					2.63	10.90	4.17
	qPH5	5	DX-C5-10				3.54		11.80	6.54
	qPH7	7	Indel-c7-1	2.93	9.86	5.91
	qPH8	8	DX-C8-12				2.80		8.99	5.52
穗长PL	qPL1	1	01-009	3.06	9.17	0.61
	qPL2-1	2	DX-C2-13	5.48	17.36	0.86
	qPL2-2	2	02-067				3.26		12.87	1.06	3.37	11.88	1.07
	qPL5	5	05-028								3.39	10.42	2.08
	qPL10	10	DX-S10-1	2.66	8.06	0.94
分蘖数TN	qTN1-1	1	DX-C1-2				3.03		10.96	-1.31
分蘖数TN	qTN1-2	1	010-060				3.89		13.32	-1.70
一次枝梗数PBPP	qPBPP1-1	1	DX-C1-6				2.77		9.25	1.03
	qPBPP1-2	1	DX-C1-10				2.68		8.34	2.33
	qPBPP3	3	DX-C3-8	3.08	9.86	-0.69
	qPBPP5	5	DX-C5-3	3.48	11.23	1.05
	qPBPP8-1	8	DX-C8-11									4.23	6.79	-1.41
	qPBPP8-2	8	DX-C8-12									7.98	13.99	1.36
一次枝梗数PBPP	qPBPP8-3	8	DX-S8-14	5.43	18.54	1.23
一次枝梗粒数PBGN	qPBGN1-1	1	DX-C1-3	3.00	9.85	4.05
	qPBGN1-2	1	DX-C1-10	3.74	12.29	-17.18
	qPBGN1-3	1	01-046					4.10		17.32	4.94
	qPBGN3	3	DX-C3-28	2.61	8.18	-5.57
	qPBGN8-1	8	DX-C8-11									4.70	7.45	-10.34
	qPBGN8-2	8	DX-C8-12									9.27	16.35	10.25
	qPBGN8-3	8	DX-S8-14	2.90	9.33	6.36
	qPBGN11	11	DX-S11-10	3.11	9.86	6.12
二次枝梗数SBPP	qSBPP1	1	DX-C1-7					3.26		8.86	3.50
	qSBPP2-1	2	DX-C2-1					5.52		15.83	10.49
	qSBPP2-2	2	DX-C2-2	9.46	23.99	7.76
	qSBPP2-3	2	02-057	5.26	12.01	2.71
	qSBPP4-1	4	DX-C4-12	3.68	8.10	-1.51
	qSBPP4-2	4	S4-12-2					5.50		15.75	-5.73
	qSBPP6-1	6	DX-C6-2									3.17	13.08	2.93
二次枝梗数SBPP	qSBPP6-2	6	S6-9-1	3.09	6.71	2.27
二次枝梗粒数SBGN	qSBGN2-1	2	DX-C2-1					12.66		27.79	56.08
	qSBGN2-2	2	DX-C2-2	8.56	21.39	20.58
	qSBGN2-3	2	02-057	4.33	9.79	6.87
	qSBGN3-1	3	DX-S3-16					3.90		6.99	20.08
	qSBGN3-2	3	DX-S3-17									4.03	15.34	17.26
	qSBGN4-1	4	DX-C4-2					4.93		9.03	-15.61
	qSBGN4-2	4	DX-C4-8					2.68		4.67	-11.22
	qSBGN4-3	4	DX-C4-12	4.64	10.55	-4.84
	qSBGN6-1	6	DX-C6-2									2.85	10.56	9.59
	qSBGN6-2	6	S6-9-1	4.21	9.47	7.58
每穗粒数GPP	qGPP1	1	01-046					4.39		13.92	14.35
	qGPP2	2	DX-C2-1					4.02		14.43	37.54
	qGPP4	4	S4-12-2					3.55		12.58	-19.21
	qGPP6-1	6	06-013									3.26	13.45	20.53
	qGPP6-2	6	06-037	5.14	17.43	14.15
	qGPP11	11	DX-S11-10	3.08	9.96	10.70
千粒重TGW	qTGW2	2	02-008	4.39	14.36	-2.79		3.26		9.19	-1.98	4.21	10.96	-2.56
	qTGW3	3	DX-C3-1	3.27	10.64	1.31
	qTGW8-1	8	DX-C8-3					4.07		11.68	-3.14
	qTGW8-2	8	DX-S8-14					3.02		8.54	-1.12	3.07	7.86	-1.27
	qTGW9-1	9	DX-C9-4					2.90		8.12	1.33
	qTGW9-2	9	DX-C9-10									3.02	7.81	-2.15
	qTGW12	12	S12-6-3									5.28	14.11	-2.38
粒长GL	qGL1	1	DX-C1-18	5.29	16.65	0.42
粒长GL	qGL2	2	02-067					3.13		10.71	0.13	2.86	7.12	0.15
	qGL3-1	3	DX-C3-8					3.89		13.44	0.17
	qGL3-2	3	indel-c3-12	3.08	9.22	0.12
	qGL3-3	3	DX-S3-17									5.75	15.14	0.37
	qGL3-4	3	DX-C3-23	4.78	14.90	0.17						5.69	14.95	0.25
	qGL4	4	S4-12-2					3.14		10.68	0.18
	qGL10	10	DX-C10-8									3.55	8.88	0.20
粒宽GW	qGW3	3	DX-S3-17									2.50	10.06	-0.11
	qGW8	8	DX-C8-15	4.59	17.86	-0.07		3.53		14.49	-0.07
	qGW10	10	DX-C10-10									2.56	10.33	-0.08

表2

图3

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性状 Trait	北京Beijing				临沂Linyi				南昌Nanchang
性状 Trait	日本晴 Nip	平均值±标准差 Mean±SD	变异系数 CV (%)	幅度 Range	日本晴 Nip	平均值±标准差 Mean±SD	变异系数 CV (%)	幅度 Range	日本晴 Nip	平均值±标准差 Mean±SD	变异系数 CV (%)	幅度 Range
株高 PH (cm)	96.30	108.02±10.07	9.33	87.75-133.75	94.64	103.34±10.95	10.59	80.30-134.82	95.00	100.31±9.76	9.73	70.20-130.00
穗长 PL (cm)	19.68	19.97±1.53	7.68	15.07-24.94	21.59	22.29±2.03	9.10	16.64-26.96	21.74	22.32±2.01	9.01	17.78-28.03
分蘖数 TN	13.00	14.30±2.14	14.96	8.80-20.00	17.21	16.24±2.89	17.78	9.00-24.17	13.60	11.83±1.58	13.38	7.80-15.40
一次枝梗数 PBPP	10.23	10.72±1.42	13.27	7.17-15.17	10.69	10.99±1.56	14.18	8.42-19.67	9.63	10.52±1.50	14.27	6.38-15.75
一次枝梗粒数PBGN	63.42	62.50±11.28	18.04	30.50-00.17	60.60	61.79±8.65	14.00	42.50-84.83	57.38	62.79±10.57	16.84	35.38-111.75
二次枝梗数 SBPP	15.17	12.65±4.25	33.61	5.08-29.75	21.38	20.85±7.13	34.20	6.42-63.00	17.13	18.60±5.21	27.99	9.00-43.75
二次枝梗粒数 SBGN	41.79	33.97±12.04	35.46	11.08-75.17	63.02	59.58±24.91	41.80	13.92-208.17	45.75	53.05±19.48	36.72	20.75-181.63
每穗粒数 GPP	105.21	96.46±16.51	17.11	57.58-156.67	123.63	121.37±30.55	25.17	62.67-288.25	103.13	115.84±24.04	20.75	77.50-258.63
千粒重 TGW (g)	23.81	23.21±1.92	8.28	17.95-28.30	26.58	25.81±1.76	6.82	19.71-30.01	25.68	24.51±2.03	8.26	16.39-28.87
粒长 GL (mm)	6.60	6.74±0.29	4.36	6.21-7.57	6.94	7.04±0.29	4.17	6.34-7.89	6.93	7.07±0.40	5.66	6.27-8.85
粒宽 GW (mm)	3.20	3.22±0.10	3.09	2.92-3.44	3.39	3.34±0.11	3.34	2.97-3.60	3.37	3.31±0.15	4.64	2.49-3.60

利用东乡普通野生稻染色体片段置换系定位产量相关性状QTL

Mapping QTLs for yield-related traits using chromosome segment substitution lines of Dongxiang common wild rice (Oryza rufipogon Griff.) and Nipponbare (Oryza sativa L.)

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