QTL Mapping and Pyramiding Effect Analysis of Diurnal Floret Opening Time Traits in japonica Rice

doi:10.16819/j.1001-7216.2026.250112

Abstract

Abstract:

【Objective】Diurnal flowering time (FT) of rice is an important trait that affects the outcrossing rate and seed production yield of japonica rice sterile lines. This study aims to locate QTLs related to diurnal-floret-opening-time (DFOT) in japonica rice and analyze the pyramiding effects to clarify the main effect loci for DFOT traits.【Method】Recombinant inbred line populations consisting of 221 lines were constructed using japonica maintainer line J65B with early floret-opening-time and J139B with late floret-opening-time. The floret-opening-time was investigated in three years. QTL mapping analysis was conducted using genetic mapping and BSA-seq methods.【Result】A total of 30 DFOT QTLs were detected using complete interval mapping (ICIM) method on chromosomes 2−12. qFT5.2, qFT5.3, qFT5.5, qFT10.2, and qFT10.3 were major and stable QTLs which were detected simultaneously in more than eight environments, with an additive effect range of 13.04−50.93. Based on floret-opening time, extreme individuals were pooled for BSA-seq analysis. Association intervals related to floret-opening-time were detected in the regions of qFT5.3, qFT5.5, qFT6.2, and qFT10.2. According to the genotyping results, different progenies were divided into J139B type and J65B type in each QTL interval. QTL pyramiding effect analysis showed that QTLs derived from J65B would advance diurnal-floret-opening-time. The loci of qFT5.3 and qFT6.2 were essential for achieving early diurnal- floret-opening-time. The loci of qFT5.5 and qFT10.2 could further advance the diurnal-floret-opening-time.【Conclusion】Genetic mapping and BSA-seq analysis successfully identified four major stable QTLs related to rice diurnal-floret-opening-time. The localization of qFT5.3, qFT5.5, qFT6.2, and qFT10.2 establishes a foundation for further fine mapping and gene cloning and genetic improvement of diurnal-floret-opening-time in japonica rice.

Key words: japonica rice, diurnal-floret-opening-time, recombinant inbred line, BSA-seq, QTL mapping

摘要：

【目的】水稻日开花时间是影响粳稻不育系异交率及制繁种产量的重要性状。本研究旨在定位粳稻花时调控相关的QTL并对其聚合效应加以分析，明确早花时QTL的主效位点。【方法】利用早花时粳稻保持系粳65B(J65B)和晚花时粳稻保持系粳139B（J139B）构建包含221个家系的重组自交系群体。连续3年调查群体花时性状，采用遗传图谱和BSA-seq两种方法进行花时QTL定位分析。【结果】利用完备区间作图法共检测到30个花时性状QTL，分布于2~12号染色体上，其中qFT5.2、qFT5.3、qFT5.5、qFT10.2、qFT10.3在8个以上环境中被同时检测到，加性效应范围13.04~50.93，是稳定表达的主效位点；选取花时极端早和极端晚家系构建混池，利用BSA-seq方法在qFT5.3、qFT5.5、qFT6.2、qFT10.2位点检测到花时关联区域；选取两种方法共同定位到的稳定表达位点进行QTL聚合分析，J65B类型的QTL均会提早花时，qFT5.3和qFT6.2是早花时改良的基础位点，qFT5.5、qFT10.2是进一步提早花时的重要位点。【结论】采用两种方法定位到4个稳定表达主效花时QTL qFT5.3、qFT5.5、qFT6.2和qFT10.2，为早花时基因进一步精细定位、基因克隆和粳稻花时性状改良奠定了基础。

关键词: 粳稻, 花时, 重组自交系, BSA-seq, QTL定位

ZHANG Cheng, SHAO Guojun, ZHANG Xue, TIAN Shujun, SUN Chi, GUO Yanying, ZHOU Ran, HAN Yong, ZHENG Wenjing, SUN Lianping. QTL Mapping and Pyramiding Effect Analysis of Diurnal Floret Opening Time Traits in japonica Rice[J]. Chinese Journal OF Rice Science, 2026, 40(1): 106-117.

张城, 邵国军, 张雪, 田书军, 孙驰, 郭艳颖, 周燃, 韩勇, 郑文静, 孙廉平. 粳稻花时性状QTL定位与聚合效应分析[J]. 中国水稻科学, 2026, 40(1): 106-117.

Figures/Tables 11

References 21

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环境 Environment	天气 Weather		注 Note
2022-08-04	阴转多云Overcast to cloudy	23~29
2022-08-05	阴转阵雨Overcast with showers later	21~26	部分晚花时株系受降雨影响未开花 Some late-FT lines failed to bloom due to rainfall
2022-08-07	阴转晴Overcast to clear	19~30
2022-08-08	晴Clear	19~32
2022-08-09	阴转阵雨Overcast with showers later	20~30	部分晚花时株系受降雨影响未开花 Some late-FT lines failed to bloom due to rainfall
2022-08-10	阴转阵雨Overcast with showers later	19~27	雨后花时异常 Abnormal FT after rain
2022-08-14	多云转晴 Cloudy to clear	17~27	群体开花末期 Flowering end period of the population
2023-08-10	多云 Cloudy	20~30	群体开花始期 Flowering initiation period of the population‌
2023-08-11	多云 Cloudy	20~29
2023-08-12	阴转阵雨 Overcast with showers later	19~27
2023-08-14	多云转阵雨Cloudy with showers later	20~27
2023-08-17	多云转晴Cloudy to clear	19~31
2024-08-02	多云Cloudy	26~32	闷热，开花早 Hot and stuffy, early FT
2024-08-03	多云转阵雨Cloudy with showers later	27~32	闷热，开花早，部分晚花时株系受降雨影响未开花 Hot and stuffy, early FT. Some late-FT lines failed to bloom due to the rainfall

环境 Environment	天气 Weather		注 Note
2022-08-04	阴转多云Overcast to cloudy	23~29
2022-08-05	阴转阵雨Overcast with showers later	21~26	部分晚花时株系受降雨影响未开花 Some late-FT lines failed to bloom due to rainfall
2022-08-07	阴转晴Overcast to clear	19~30
2022-08-08	晴Clear	19~32
2022-08-09	阴转阵雨Overcast with showers later	20~30	部分晚花时株系受降雨影响未开花 Some late-FT lines failed to bloom due to rainfall
2022-08-10	阴转阵雨Overcast with showers later	19~27	雨后花时异常 Abnormal FT after rain
2022-08-14	多云转晴 Cloudy to clear	17~27	群体开花末期 Flowering end period of the population
2023-08-10	多云 Cloudy	20~30	群体开花始期 Flowering initiation period of the population‌
2023-08-11	多云 Cloudy	20~29
2023-08-12	阴转阵雨 Overcast with showers later	19~27
2023-08-14	多云转阵雨Cloudy with showers later	20~27
2023-08-17	多云转晴Cloudy to clear	19~31
2024-08-02	多云Cloudy	26~32	闷热，开花早 Hot and stuffy, early FT
2024-08-03	多云转阵雨Cloudy with showers later	27~32	闷热，开花早，部分晚花时株系受降雨影响未开花 Hot and stuffy, early FT. Some late-FT lines failed to bloom due to the rainfall

环境 Environment	J139B (min)	J65B (min)	群体均值 Mean(min)	幅度 FT difference(min)	标准误 Standard error	偏度 Skewness	峰度 Kurtosis	KS检验 KS-test	P值 P-value
2022-08-04	358 b B	277.9 bc C	328.0	130.0	21.9	−1.527	2.840	2.29	0.000
2022-08-05	360 b AB	278 bc C	348.2	141.0	43.2	−0.704	−0.884	1.61	0.011
2022-08-07	338 c CD	280.1 bc BC	318.0	126.0	17.1	−1.524	5.989	1.91	0.001
2022-08-08	333.6 cd D	248.4 d D	304.5	125.0	24.3	−1.453	2.103	2.26	0.000
2022-08-09	354 b BC	242.8 d D	307.8	140.0	33.4	−0.349	−0.699	1.07	0.203
2022-08-10	272.9 h H	266.8 c C	267.5	80.0	16.9	0.109	−0.552	0.83	0.489
2022-08-14	322.1 de DE	306.5 a A	312.9	91.0	13.8	0.434	1.271	1.03	0.236
2023-08-10	301.4 fg FG	274.4 bc C	283.2	135.0	27.3	−2.179	6.351	1.07	0.200
2023-08-11	366.4 ab AB	297.7 a AB	337.5	206.6	30.0	−1.560	4.279	1.55	0.017
2023-08-12	313.1 ef EF	275.9 bc C	305.2	130.9	28.0	−0.813	0.191	1.49	0.024
2023-08-14	376.6 a A	282.7 b BC	344.3	192.6	32.1	−1.524	2.691	2.66	0.000
2023-08-17	333.9 cd D	272.5 bc C	304.0	102.9	19.3	−0.840	1.138	1.09	0.189
2024-08-02	293.1 g G	115.5 e E	237.1	220.0	53.3	−0.952	−0.162	2.57	0.000
2024-08-03	358.3 b B	85.4 f F	238.5	281.2	84.4	−0.322	−1.188	1.60	0.012
均值Mean	334.4	250.3
标准差 SD	30.6	65.8
变异系数 CV	9.1	26.3

环境 Environment	J139B (min)	J65B (min)	群体均值 Mean(min)	幅度 FT difference(min)	标准误 Standard error	偏度 Skewness	峰度 Kurtosis	KS检验 KS-test	P值 P-value
2022-08-04	358 b B	277.9 bc C	328.0	130.0	21.9	−1.527	2.840	2.29	0.000
2022-08-05	360 b AB	278 bc C	348.2	141.0	43.2	−0.704	−0.884	1.61	0.011
2022-08-07	338 c CD	280.1 bc BC	318.0	126.0	17.1	−1.524	5.989	1.91	0.001
2022-08-08	333.6 cd D	248.4 d D	304.5	125.0	24.3	−1.453	2.103	2.26	0.000
2022-08-09	354 b BC	242.8 d D	307.8	140.0	33.4	−0.349	−0.699	1.07	0.203
2022-08-10	272.9 h H	266.8 c C	267.5	80.0	16.9	0.109	−0.552	0.83	0.489
2022-08-14	322.1 de DE	306.5 a A	312.9	91.0	13.8	0.434	1.271	1.03	0.236
2023-08-10	301.4 fg FG	274.4 bc C	283.2	135.0	27.3	−2.179	6.351	1.07	0.200
2023-08-11	366.4 ab AB	297.7 a AB	337.5	206.6	30.0	−1.560	4.279	1.55	0.017
2023-08-12	313.1 ef EF	275.9 bc C	305.2	130.9	28.0	−0.813	0.191	1.49	0.024
2023-08-14	376.6 a A	282.7 b BC	344.3	192.6	32.1	−1.524	2.691	2.66	0.000
2023-08-17	333.9 cd D	272.5 bc C	304.0	102.9	19.3	−0.840	1.138	1.09	0.189
2024-08-02	293.1 g G	115.5 e E	237.1	220.0	53.3	−0.952	−0.162	2.57	0.000
2024-08-03	358.3 b B	85.4 f F	238.5	281.2	84.4	−0.322	−1.188	1.60	0.012
均值Mean	334.4	250.3
标准差 SD	30.6	65.8
变异系数 CV	9.1	26.3

QTL	环境 Environment	染色体 Chr.	位置 Position	标记区间 Marker interval	LOD	表型贡献率 Phenotypic variance explained(%)	加性效应 Additive effect
qFT2.1	1	2	32	3548115−5120420	3.69	13.511	15.93
qFT2.2	1	2	160	5211026−10870893	2.50	0.721	14.08
qFT2.3	3	2	174-181	10870893−15640124	2.94-7.67	1.673-3.905	26.8-38.06
qFT3.1	2	3	2-3	1276817−6232373	4.28-5.10	0.993-3.874	3.76-6.51
qFT3.2	2	3	66-68	11778351−15589648	3.11-6.14	0.442-1.631	10.23-24.27
qFT3.3	1	3	133	15589648−15963860	3.65	3.867	35.89
qFT3.4	4	3	157-161	15963860−19173865	2.56-3.36	1.679-3.841	15.65-37.13
qFT3.5	2	3	180-180	21059861−22120274	3.06-3.56	0.512-0.672	10.78-15.3
qFT4	1	4	96	20657255−20765327	2.97	0.183	5.43
qFT5.1	1	5	23	1178896−2313820	3.48	0.895	6.13
qFT5.2	8	5	89-102	3512365−3770562	4.60-16.46	0.271-5.459	18.09-50.52
qFT5.3	10	5	107-119	3770562−5289420	3.11-18.94	0.271-8.945	13.04-50.47
qFT5.4	3	5	211-212	10410805−10847593	2.87-4.59	1.223-3.273	20.33-34.22
qFT5.5	9	5	217-232	11057325−20726014	3.87-13.67	0.271-5.636	16.81-48.85
qFT6.1	1	6	10	1632003−3338507	3.00	0.449	4.09
qFT6.2	3	6	129	26902414−29897327	3.28-7.15	0.555-1.644	6.71-24.23
qFT7.1	1	7	84	10497568−13804874	4.57	3.267	-22.95
qFT7.2	2	7	91-92	13804874−17673544	5.15-6.00	2.731-3.429	-22.09--17.81
qFT8.1	1	8	161	15987810−17697658	2.65	2.313	2.91
qFT8.2	1	8	227	21632760−24890652	3.03	1.061	7.32
qFT9.1	1	9	83	15336683−16946239	10.50	1.399	-10.86
qFT9.2	1	9	94	17736891−19018118	6.09	0.718	8.02
qFT10.1	1	10	22	2340168−2526630	2.95	0.566	6.72
qFT10.2	8	10	97-108	10550006−14355797	2.83-12.27	0.239-5.465	16.27-50.37
qFT10.3	8	10	117-127	14355797−17930367	2.64-11.99	0.236-5.428	16.41-50.93
qFT11.1	1	11	1	5768520−6510910	3.92	3.699	8.52
qFT11.2	1	11	37	8759552−8972803	4.16	0.594	4.73
qFT11.3	1	11	163	23361525−23613051	9.30	1.855	8.82
qFT12.1	1	11	81	19422618−22520720	2.65	0.805	5.81
qFT12.2	2	12	136-148	22520720−25953139	4.35-5.47	3.854-5.540	35.39-46.63