QTL Mapping and Analysis of Tiller Angle Based on High Density Genetic Map in Rice

doi:10.16819/j.1001-7216.2026.241103

Abstract

Abstract:

【Objective】Tiller angle is an important component of rice plant type, which directly affects rice planting density and ultimately influences rice yield. Exploring and studying new QTLs/genes that regulate rice tiller angle and applying them to plant type improvement is one of the effective ways to improve rice yield. 【Method】The recombinant inbred lines (RILs) derived from the crossing and selfing of the Indian japonica rice variety M494 and indica rice variety Zhong 9B were used as experimental materials. They were planted at Fuyang and Lingshui experimental bases of China National Rice Research Institute in Zhejiang and Hainan Province from 2021 to 2023. QTL mapping and analysis of rice tiller angle were conducted based on the high-density Bin map constructed by resequencing method. 【Result】A total of nine QTLs were detected in three years, distributed on chromosomes 1, 3, 9, 11 and 12. The phenotypic variation explained by each QTL ranged from 2.54% to 57.00%, and the additive effects were all derived from the large tiller angle parent M494. Among them, the major QTL qTA9-1 for tiller angle was located in the range of 20.71−20.80 Mb on chromosome 9, with a physical map interval of 86.36 kb region. Moreover, it was repeatedly detected in 2021 and 2022, and the highest contribution rate could reach 57.00%. This region overlapped with the cloned tiller angle gene TAC1. The RT-PCR results showed that the expression level of TAC1 in the large tiller angle genotype line M109 was significantly higher than that in the small tiller angle genotype line M67. Further sequencing analysis revealed that compared with the qta9-1 genotype line M67, the qTA9-1 genotype line M109 had a C to T mutation at the 3' splice site of intron 4 of the reported TAC1, which is the TAC1 functional SNP, and we speculate that qTA9-1 is TAC1. In 2021 and 2022, a novel QTL controlling tiller angle was repeatedly detected in the 15.20−16.00 Mb interval of chromosome 3, which exhibited epistatic interaction with the major tiller angle QTL qTA9-1. A minor QTL locus regulating tillering angle was repeatedly detected in the 21.10−22.02 Mb interval of chromosome 12. 【Conclusion】Nine QTLs for tiller angle were detected using the RIL population constructed by crossing M494 with Zhong 9B combining with the high-density genetic map, including the cloned gene TAC1, and a novel QTL for tiller angle was detected on chromosome 3. The above results provide a theoretical basis and genetic resources for further fine mapping of rice tiller angle genes and genetic improvement of plant type of rice varieties.

Key words: rice, tiller angle, high-density genetic map, QTL mapping analysis

摘要：

【目的】分蘖角度是水稻株型的重要组成部分，直接影响水稻的种植密度并最终影响水稻产量。挖掘和研究新的调控水稻分蘖角度QTL/基因并应用于株型改良，是提高水稻产量的有效方式之一。【方法】本研究利用印度粳稻品种M494和籼稻品种中9B杂交并自交衍生的重组自交系(Recombinant inbred lines，RILs)群体为试验材料，于2021至2023年在中国水稻研究所浙江省富阳与海南省陵水试验基地种植，基于重测序法构建的高密度Bin图谱进行水稻分蘖角度QTL定位与分析。【结果】3年共检测到9个QTL，分布于1、3、9、11和12号染色体上，单个QTL可解释的表型贡献率介于2.54%~57.00%，加性效应均来源于大分蘖角度亲本M494。其中主效分蘖角度QTL qTA9-1定位在9号染色体的20.71−20.80 Mb区间，物理图谱区间为86.36 kb，且在2021与2022年重复被检测到，贡献率最高可达57.00%，该区间覆盖已克隆分蘖角度基因TAC1。RT-PCR结果表明TAC1在大分蘖角度株系M109中的表达量显著高于小分蘖角度株系M67。进一步测序分析发现，与qta9-1基因型株系M67相比，qTA9-1基因型株系M109中TAC1在第4内含子的3’剪接位点发生了C到T的突变，为已报道的TAC1功能性SNP位点，推测qTA9-1即为TAC1。2021和2022年在3号染色体15.20−16.00 Mb区间重复检测到1个新的控制分蘖角度的QTL，其与主效分蘖角度QTL qTA9-1存在上位性互作；在12号染色体21.10−22.02 Mb区间重复检测到1个调控水稻分蘖角度的微效QTL位点。【结论】本研究利用M494和Z9B杂交构建的RIL群体，结合高密度遗传图谱，共检测到9个分蘖角度相关QTL，包括已克隆基因TAC1，在3号染色体检测到1个新的分蘖角度QTL。上述结果为进一步开展水稻分蘖角度基因的精细定位和水稻品种株型的遗传改良提供了理论基础和基因资源。

关键词: 水稻, 分蘖角度, 高密度遗传图谱, QTL定位分析

WANG Zhaojun, HE Yuxuan, LIU Junrong, XU Qun, ZHANG Mengchen, WANG Shan, SUN Yanfei, WEI Xinghua, YANG Yaolong, GUO Xiaohong, FENG Yue. QTL Mapping and Analysis of Tiller Angle Based on High Density Genetic Map in Rice[J]. Chinese Journal OF Rice Science, 2026, 40(3): 341-350.

王召君, 何雨宣, 刘浚蓉, 徐群, 章孟臣, 王珊, 孙燕飞, 魏兴华, 杨窑龙, 郭晓红, 冯跃. 基于高密度遗传图谱的水稻分蘖角度QTL定位与分析[J]. 中国水稻科学, 2026, 40(3): 341-350.

Figures/Tables 10

References 31

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基因名 Gene name	正向引物(5'→3') Forward primer (5'→3')	反向引物（5'→3'） Reverse primer (5'→3')
TAC1	GTGCAAGTGTGACTGAGCAA	AGCGTGCCAATTGCAAGTAT
Actin	TGCTATGTACGTCGCCATCCAG	AATGAGTAACCACGCTCCGTCA

基因名 Gene name	正向引物(5'→3') Forward primer (5'→3')	反向引物（5'→3'） Reverse primer (5'→3')
TAC1	GTGCAAGTGTGACTGAGCAA	AGCGTGCCAATTGCAAGTAT
Actin	TGCTATGTACGTCGCCATCCAG	AATGAGTAACCACGCTCCGTCA

年份 Year	RIL群体RIL population					亲本Parent
年份 Year	平均值 Mean	变幅 Range	偏度 Skewness	峰度 Kurtosis	标准差 Standard deviation	M494	Z9B
2021 2022 2023	11.4	7.5~22.5	0.77	−0.17	3.97	16.2	7.0
2022	11.5	5.8~22.0	0.74	−0.27	3.67
2023	12.6	5.5~27.2	1.07	2.07	3.79

年份 Year	RIL群体RIL population					亲本Parent
年份 Year	平均值 Mean	变幅 Range	偏度 Skewness	峰度 Kurtosis	标准差 Standard deviation	M494	Z9B
2021 2022 2023	11.4	7.5~22.5	0.77	−0.17	3.97	16.2	7.0
2022	11.5	5.8~22.0	0.74	−0.27	3.67
2023	12.6	5.5~27.2	1.07	2.07	3.79

年份 Year	染色体 Chromosome	位点 Locus	峰值标记 Peak marker	LOD值 LOD value	表型贡献率 Variation explained(%)	加性效应 Additive effect	物理位置 Position (Mb)	定位区间 Location interval (kb)
2021	3	qTA3-1	Bin03-96	3.69	5.08	0.93	15.70−16.00	299.52
2021/2022	9	qTA9-1	Bin09-21	24.70/34.60	49.27/57.00	2.90/2.92	20.71−20.80	86.36
2021	12	qTA12-1	Bin12-107	3.36	4.57	0.88	21.80−22.02	222.59
2022	3	qTA3-2	Bin03-101	2.77	2.54	0.61	15.20−15.40	201.72
2022	11	qTA11-1	Bin11-75	4.99	4.92	0.86	9.90−12.60	2702.55
2022	12	qTA12-2	Bin12-108	3.47	3.21	0.69	21.10−21.20	98.76
2023	1	qTA1-1	Bin01-168	4.56	8.34	1.23	42.10−42.87	772.47
2023	3	qTA3-3	Bin03-235	2.86	4.96	0.93	26.60−27.70	908.32
2023	9	qTA9-2	Bin09-22	9.95	19.07	1.83	20.10−20.40	298.66