Mapping of Grain Shape QTLs Using RIL Population from Longdao 5/Zhongyouzao 8

doi:10.16819/j.1001-7216.2024.230602

Chinese Journal OF Rice Science ›› 2024, Vol. 38 ›› Issue (1): 13-24.DOI: 10.16819/j.1001-7216.2024.230602

• Research Papers • Previous Articles Next Articles

Mapping of Grain Shape QTLs Using RIL Population from Longdao 5/Zhongyouzao 8

HOU Benfu¹^,²^,³, YANG Chuanming¹^,²^,³, ZHANG Xijuan²^,⁵, YANG Xianli²^,⁵, WANG Lizhi²^,⁵, WANG Jiayu⁴, LI Hongyu¹^,^*(), JIANG Shukun²^,³^,⁵^,^*()

¹Agricultural College, Heilongjiang Bayi Agricultural University, Daqing 163319, China
²Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences/Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region/Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China
³Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences/Heilongjiang Provincial Engineering Technology Research Center of Crop Germplasm Resources Innovation and Utilization in Songnen Plain, Qiqihar 161006, China
⁴Rice Research Institute, Shenyang Agricultural University, Shenyang 110161, China
⁵Northeast Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin 150086, China

Received:2023-05-13 Revised:2023-07-14 Online:2024-01-10 Published:2024-01-16
Contact: * email: shukunjiang@haas.cn; ndrice@163.com

利用龙稻5号/中优早8号RIL群体定位粒形QTL

侯本福¹^,²^,³, 杨传铭¹^,²^,³, 张喜娟²^,⁵, 杨贤莉²^,⁵, 王立志²^,⁵, 王嘉宇⁴, 李红宇¹^,^*(), 姜树坤²^,³^,⁵^,^*()

¹黑龙江八一农垦大学农学院, 黑龙江大庆 163319
²黑龙江省农业科学院耕作栽培研究所/黑龙江省寒地作物生理生态重点实验室/黑龙江省农作物低温冷害工程技术研究中心, 哈尔滨 150086
³黑龙江省农业科学院齐齐哈尔分院/黑龙江省松嫩平原西部作物种质资源创新与利用工程技术研究中心, 黑龙江齐齐哈尔 161006
⁴沈阳农业大学水稻研究所, 沈阳 110161
⁵国家耐盐碱水稻技术创新中心东北中心, 哈尔滨 150086

通讯作者: * email: shukunjiang@haas.cn; ndrice@163.com
基金资助:
黑龙江省属科研院所科研业务费资助项目(CZKYF2022-1-B004);国家自然科学基金资助项目(32071889)

Abstract

Abstract:

【Objective】Grain shape significantly influences the yield, quality, and commercial value of rice. This study aimed to identify Quantitative Trait Loci (QTLs) controlling grain shape using a rice recombinant inbred line population, thereby facilitating the mining of rice grain shape genes and the breeding of long-grain japonica rice. 【Method】 A population of 176 recombinant inbred lines was developed by crossing the japonica super rice variety Longdao 5 (LD5) with short round grain and the early maturing indica rice variety Zhongyouzao 8(ZYZ8) with long slender grain. Grain shape traits, including grain length(GL), grain width(GW), grain length to width ratio(LWR), and grain thickness(GT), were measured for three years using Smart Grain software, and the interrelationship between these traits was analyzed. Complete Interval Mapping (CIM) and Multi-Environment Trials (MET) were employed for QTL mapping and comparative analysis. 【Result】 Eight QTLs, comprising three for grain length (qGL3, qGL7, and qGL11), two for grain width (qGW3 and qGW5), two for grain thickness (qGT3 and qGT6), and one for grain length to width ratio (qLWR3), were identified on chromosomes 3, 5, 6, 7, and 11 using the CIM method. These QTLs explained 4.69%−18.89% of the phenotypic variation, with an LOD range from 2.52 to 8.74. Additionally, qGL3, qGL7, qGW3, qGW5, and qLWR3 were consistently detected over three years. Fourteen QTLs, including four for grain length, two for grain width, three for grain thickness, and five for grain length to width ratio, were detected on chromosomes 2, 3, 5, 6, 7, and 11 using the MET method. These QTLs explained 2.28%−15.78% of the phenotypic variation, with an LOD range from 4.20 to 20.90. Comparison with cloned grain shape genes revealed the proximity of qGL3/qLWR3a to GL3.1, qGW5 to GW5, and qLWR3b/qGT3 to TGW3. 【Conclusion】 A total of 8 and 14 grain shape QTLs were identified using the CIM and MET methods, respectively, including three cloned grain shape genes (GL3.1, TGW3, and GW5).

Key words: rice, panicle shape, QTL mapping, molecular-marker assisted breeding

摘要：

【目的】粒形是决定稻米产量、品质和商品价值的重要数量性状之一。本研究旨在利用水稻重组自交系群体鉴定控制粒形的QTL，为水稻粒形基因的挖掘和长粒形粳稻育种应用奠定基础。【方法】以短圆粒形的粳型超级稻品种龙稻5号（LD5）为母本和细长粒形的早熟籼稻品种中优早8号（ZYZ8）为父本构建包含176个家系的重组自交系群体测定粒长、粒宽、长宽比和粒厚等粒形性状，分析粒形性状间的关系并进行QTL定位和比较分析。【结果】利用区间作图法共检测到8个粒形QTL，分布在3、5、6、7和11号染色体上，表型贡献率范围为4.69%~18.89%，LOD值范围为2.52~8.74。这8个QTL包括3个粒长QTL qGL3、qGL7和qGL11，2个粒宽QTL qGW3和qGW5，2个粒厚QTL qGT3和qGT6，1个长宽比QTL qLWR3。其中，qGL3、qGL7、qGW3、qGW5和qLWR3可以在3个年份稳定检测到。利用多环境联合分析共检测到14个粒形QTL，包括qGL2、qGL3、qGL7和qGL11共4个粒长QTL；qGW3和qGW5共2个粒宽QTL；qGT3、qGT5和qGT6共3个粒厚QTL；qLWR3a、qLWR3b、qLWR5、qLWR7和qLWR11共5个长宽比QTL，分布在2、3、5、6、7和11号染色体上，表型贡献率范围为2.28%~15.78%，LOD值范围为4.20~20.90。与已克隆的粒形基因进行染色体位置比较发现，qGL3/qLWR3区间包含已克隆的GL3.1；qGW5区间包含已克隆的GW5；qLWR3b/qGT3区间包含已克隆的TGW3。【结论】利用区间作图法和多环境联合分析的方法从龙稻5号和中优早8号的重组自交系群体中共鉴定了14个粒形QTL，其中8个QTL是两种方法重复检测到的。这些QTL定位区间内包含已克隆的GL3.1、TGW3和GW5等粒形基因。

关键词: 水稻, 粒形, QTL定位, 分子辅助育种

HOU Benfu, YANG Chuanming, ZHANG Xijuan, YANG Xianli, WANG Lizhi, WANG Jiayu, LI Hongyu, JIANG Shukun. Mapping of Grain Shape QTLs Using RIL Population from Longdao 5/Zhongyouzao 8[J]. Chinese Journal OF Rice Science, 2024, 38(1): 13-24.

侯本福, 杨传铭, 张喜娟, 杨贤莉, 王立志, 王嘉宇, 李红宇, 姜树坤. 利用龙稻5号/中优早8号RIL群体定位粒形QTL[J]. 中国水稻科学, 2024, 38(1): 13-24.

Figures/Tables 8

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年份Year	性状 Trait	亲本 Parents		群体 Population
年份Year	性状 Trait	龙稻5号 Longdao 5	中优早8号 Zhongyouzao 8	平均值 Mean	群体区间 Range	偏度 Skewness	峰度 Kurtosis
2020	粒长 Grain length /mm	6.81±0.33	8.98±0.38**	8.18±0.62	6.43~9.65	0.11	−0.45
	粒宽 Grain width /mm	3.43±0.21	3.24±0.13**	3.30±0.25	2.65~3.94	0.05	−0.26
	粒厚 Grain thickness/mm	2.13±0.07	1.96±0.18*	1.98±0.15	1.53~2.33	−0.07	0.16
	长宽比 Length to width ratio	1.99±0.14	2.78±0.16**	2.50±0.26	1.91~3.38	0.48	0.33
2021	粒长 Grain length /mm	6.53±0.30	8.67±0.30**	7.73±0.59	6.24~9.30	0.08	−0.31
	粒宽 Grain width/mm	3.50±0.10	3.20±0.13**	3.28±0.26	2.68~3.89	0.02	−0.48
	粒厚 Grain thickness	2.10±0.04	1.93±0.22*	1.96±0.14	1.54~2.36	−0.11	0.03
	长宽比 Length to width ratio	1.86±0.08	2.72±0.13**	2.37±0.24	1.80~3.41	0.56	1.27
2022	粒长 Grain length/mm	6.86±0.27	9.04±0.24**	8.08±0.64	6.35~9.67	0.09	−0.53
	粒宽 Grain width /mm	3.48±0.15	3.22±0.17**	3.29±0.24	2.71~3.88	0.00	−0.53
	粒厚 Grain thickness /mm	2.08±0.08	1.92±0.06**	1.95±0.14	1.60~2.29	−0.01	−0.25
	长宽比 Length to width ratio	1.98±0.12	2.82±0.15**	2.48±0.26	1.87~3.48	0.53	0.94

年份Year	性状 Trait	亲本 Parents		群体 Population
年份Year	性状 Trait	龙稻5号 Longdao 5	中优早8号 Zhongyouzao 8	平均值 Mean	群体区间 Range	偏度 Skewness	峰度 Kurtosis
2020	粒长 Grain length /mm	6.81±0.33	8.98±0.38**	8.18±0.62	6.43~9.65	0.11	−0.45
	粒宽 Grain width /mm	3.43±0.21	3.24±0.13**	3.30±0.25	2.65~3.94	0.05	−0.26
	粒厚 Grain thickness/mm	2.13±0.07	1.96±0.18*	1.98±0.15	1.53~2.33	−0.07	0.16
	长宽比 Length to width ratio	1.99±0.14	2.78±0.16**	2.50±0.26	1.91~3.38	0.48	0.33
2021	粒长 Grain length /mm	6.53±0.30	8.67±0.30**	7.73±0.59	6.24~9.30	0.08	−0.31
	粒宽 Grain width/mm	3.50±0.10	3.20±0.13**	3.28±0.26	2.68~3.89	0.02	−0.48
	粒厚 Grain thickness	2.10±0.04	1.93±0.22*	1.96±0.14	1.54~2.36	−0.11	0.03
	长宽比 Length to width ratio	1.86±0.08	2.72±0.13**	2.37±0.24	1.80~3.41	0.56	1.27
2022	粒长 Grain length/mm	6.86±0.27	9.04±0.24**	8.08±0.64	6.35~9.67	0.09	−0.53
	粒宽 Grain width /mm	3.48±0.15	3.22±0.17**	3.29±0.24	2.71~3.88	0.00	−0.53
	粒厚 Grain thickness /mm	2.08±0.08	1.92±0.06**	1.95±0.14	1.60~2.29	−0.01	−0.25
	长宽比 Length to width ratio	1.98±0.12	2.82±0.15**	2.48±0.26	1.87~3.48	0.53	0.94

QTL	Chr.	标记区间 Marker interval	2020			2021						增效等位基因来源 Positive allele
QTL	Chr.	标记区间 Marker interval	LOD	表型贡献率Var./%	加性效应Add.	LOD	表型贡献率Var./%	加性效应 Add.	LOD	表型贡献率Var./%	加性效应 Add.	增效等位基因来源 Positive allele
qGL3	3	R3M30−RM3513	8.05	18.52	0.28	7.69	16.52	0.28	8.74	18.89	0.31	ZYZ8
qGL7	7	RM3404−RM11	2.90	5.37	0.16	3.33	5.73	0.16	2.90	5.30	0.16	ZYZ8
qGL11	11	RM1124−STS11.1	2.52	4.69	0.14							ZYZ8
qGW3	3	STS3.10−RM3684	4.46	9.53	−0.09	4.44	9.13	−0.09	4.03	8.54	−0.08	LD5
qGW5	5	R5M13−RM3476	3.20	7.48	−0.08	3.94	9.22	−0.09	3.21	7.8	−0.08	LD5
qGT3	3	RM503−RM700	3.21	8.05	−0.05	3.70	9.34	−0.04	2.76	6.36	−0.04	LD5
qGT6	6	RM3827−RM1340				2.53	6.09	0.04				ZYZ8
qLWR3a	3	R3M30−RM3513	5.34	12.46	0.10	5.76	13.33	0.10	6.10	14.33	0.11	ZYZ8

QTL	Chr.	标记区间 Marker interval	2020			2021						增效等位基因来源 Positive allele
QTL	Chr.	标记区间 Marker interval	LOD	表型贡献率Var./%	加性效应Add.	LOD	表型贡献率Var./%	加性效应 Add.	LOD	表型贡献率Var./%	加性效应 Add.	增效等位基因来源 Positive allele
qGL3	3	R3M30−RM3513	8.05	18.52	0.28	7.69	16.52	0.28	8.74	18.89	0.31	ZYZ8
qGL7	7	RM3404−RM11	2.90	5.37	0.16	3.33	5.73	0.16	2.90	5.30	0.16	ZYZ8
qGL11	11	RM1124−STS11.1	2.52	4.69	0.14							ZYZ8
qGW3	3	STS3.10−RM3684	4.46	9.53	−0.09	4.44	9.13	−0.09	4.03	8.54	−0.08	LD5
qGW5	5	R5M13−RM3476	3.20	7.48	−0.08	3.94	9.22	−0.09	3.21	7.8	−0.08	LD5
qGT3	3	RM503−RM700	3.21	8.05	−0.05	3.70	9.34	−0.04	2.76	6.36	−0.04	LD5
qGT6	6	RM3827−RM1340				2.53	6.09	0.04				ZYZ8
qLWR3a	3	R3M30−RM3513	5.34	12.46	0.10	5.76	13.33	0.10	6.10	14.33	0.11	ZYZ8

数量性状基因	染色体	标记区间	LOD值	表型贡献率	加性效应
QTL	Chr.	Marker interval	LOD value	Var./%	Add.
qGL2	2	RM6933―ID2	4.20	3.14	0.12
qGL3	3	R3M30―RM3513	20.90	15.78	0.26
qGL7	7	RM3404―RM11	8.26	5.02	0.15
qGL11	11	RM1124―STS11.1	8.51	5.85	0.16
qGW3	3	STS3.10―RM3684	6.20	4.55	―0.06
qGW5	5	STS5.2―RM3476	10.85	9.43	―0.08
qGT3	3	RM503―RM7000	6.83	5.26	―0.34
qGT5	5	R5M13―RM3476	4.84	4.37	―0.31
qGT6	6	RM3827―RM1340	5.07	3.85	0.29
qLWR3a	3	R3M30―RM3513	16.61	8.71	0.10
qLWR3b	3	STS3.10―RM3684	14.77	9.96	0.11
qLWR5	5	STS5.2―RM3476	4.64	2.01	0.05
qLWR7	7	RM3404―RM11	6.97	3.40	0.06
qLWR11	11	RM1124―STS11.1	4.99	2.28	0.05

Mapping of Grain Shape QTLs Using RIL Population from Longdao 5/Zhongyouzao 8

利用龙稻5号/中优早8号RIL群体定位粒形QTL

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