Development and Application of a Functional Marker for Heading Date Gene Hd6 in Rice

doi:10.16819/j.1001-7216.2025.231009

Chinese Journal OF Rice Science ›› 2025, Vol. 39 ›› Issue (1): 47-54.DOI: 10.16819/j.1001-7216.2025.231009

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Development and Application of a Functional Marker for Heading Date Gene Hd6 in Rice

CHEN Zhihui¹^,²^,³, TAO Yajun¹^,²^,³, FAN Fangjun¹^,²^,³, XU Yang¹^,²^,³^,⁴, WANG Fangquan¹^,²^,³, LI Wenqi¹^,²^,³, GULINAER·Bahetibieke ⁵, JIANG Yanjie¹^,²^,³, ZHU Jianping¹^,²^,³, LI Xia¹^,²^,³, YANG Jie¹^,²^,³^,⁴^,^*()

¹Key Laboratory of Germplasm Innovation in Downstream of Huaihe River, Ministry of Agriculture and Rural Affairs /Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
²Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
³Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
⁴Institute of Life Science, Jiangsu University, Zhenjiang 212013, China
⁵Institate of Agricultural Sciences of Ili Prefecture, Ili Kazakh 835000, China

Received:2023-10-24 Revised:2023-11-30 Online:2025-01-10 Published:2025-01-14
Contact: YANG Jie

水稻抽穗期调控基因Hd6功能标记的开发及应用

陈智慧¹^,²^,³, 陶亚军¹^,²^,³, 范方军¹^,²^,³, 许扬¹^,²^,³^,⁴, 王芳权¹^,²^,³, 李文奇¹^,²^,³, 古丽娜尔·巴合提别克⁵, 蒋彦婕¹^,²^,³, 朱建平¹^,²^,³, 李霞¹^,²^,³, 杨杰¹^,²^,³^,⁴^,^*()

¹江苏省农业科学院农业农村部淮河下游种质创制重点实验室/粮食作物研究所，南京 210014
²生物育种中山实验室，南京 210014
³扬州大学江苏省粮食作物现代化产业协同创新中心，扬州 225009
⁴江苏大学生命科学学院，镇江 212013
⁵伊犁哈萨克自治州农业科学研究所，伊宁 835000

通讯作者: 杨杰
基金资助:
江苏省种业振兴“揭榜挂帅”项目(JBGS〔2021〕039);江苏省重点研发计划（现代农业）资助项目(BE2021374);江苏省重点研发计划（现代农业）资助项目(BE2022382);江苏省重点研发计划（现代农业）资助项目(1002);生物育种钟山实验室项目(BM2022008-03)

1. .xlsx(18KB)

Abstract

Abstract:

【Objective】This study aims to explore the distribution of Hd6 alleles in japonica rice and indica rice from Jiangsu Province, and to enhance the application value and selection efficiency of Hd6 alleles in the genetic improvement of rice heading date. 【Method】We designed and screened various types of gene functional markers based on the single nucleotide polymorphisms in the functional regions of the Hd6 alleles in Kasalath and hd6 in Nipponbare. Through PCR amplification and sequencing, we selected the gene markers K-Hd6-21F/Hd6-1R and N-Hd6-22F/Hd6-1R to genotype japonica rice varieties from different ecological types in Jiangsu Province and indica rice varieties from various sources.【Result】We found that K-Hd6-21F/Hd6-1R and N-Hd6-22F/Hd6-1R could effectively distinguish different genotypes at the Hd6 locus. The results indicated that 42% of the 48 medium-maturing japonica rice varieties carried the Hd6 allele, 50% of the 30 late-maturing japonica rice varieties carried Hd6, and 77.5% of the 48 early-maturing japonica rice varieties carried Hd6. The two alleles of Hd6 were distributed among varieties from three different ecological regions in Jiangsu Province, and the genotype frequency of functional Hd6 alleles increased with the heading date. The Hd6 gene is highly conserved in indica rice and was tested in all 62 indica varieties.【Conclusion】This study lays a foundation for the utilization of the Hd6 gene and molecular marker-assisted selection in rice breeding, providing a new basis and effective approach for the breeding of early-maturing varieties in indica rice.

Key words: rice, heading date, Hd6, functional marker, allele-specific PCR

摘要：

【目的】探究Hd6等位基因型在江苏粳稻和籼稻中的分布，提高Hd6等位基因型在水稻抽穗期遗传改良中的应用价值和选择效率。【方法】根据籼稻品种Kasalath中有功能的等位基因Hd6与粳稻品种日本晴中无功能的等位基因hd6在功能区域存在的单核苷酸差异，设计和筛选出Hd6基因功能标记K-Hd6-21F/Hd6-1R和N-Hd6-22F/Hd6-1R，并测序分析验证；利用K-Hd6-21F/Hd6-1R和N-Hd6-22F/Hd6-1R对江苏省不同生态类型的粳稻品种和不同来源的籼稻品种的Hd6基因型进行检测。【结果】该功能标记可准确鉴定出Hd6的不同基因型；48份中熟中粳水稻品种中，携带Hd6的水稻品种占42%；30份迟熟中粳水稻品种中携带Hd6的占50%；48份早熟晚粳水稻品种中，携带Hd6的占77.5%。Hd6的2种等位基因型在江苏省3个不同生态区域粳稻品种中均有分布，但有功能的Hd6等位基因型在3个区域粳稻品种中的分布随着抽穗期变长，基因型频率增加；而Hd6基因在籼稻中表现出高度保守性，检测的62个籼稻品种均携带有功能的Hd6等位基因型。【结论】本研究为Hd6基因的育种利用和分子标记辅助选择奠定了基础，也为籼稻早熟品种的选育提供新依据和有效途径。

关键词: 水稻, 抽穗期, Hd6, 功能标记, 等位基因特异性PCR

CHEN Zhihui, TAO Yajun, FAN Fangjun, XU Yang, WANG Fangquan, LI Wenqi, GULINAER·Bahetibieke , JIANG Yanjie, ZHU Jianping, LI Xia, YANG Jie. Development and Application of a Functional Marker for Heading Date Gene Hd6 in Rice[J]. Chinese Journal OF Rice Science, 2025, 39(1): 47-54.

陈智慧, 陶亚军, 范方军, 许扬, 王芳权, 李文奇, 古丽娜尔·巴合提别克, 蒋彦婕, 朱建平, 李霞, 杨杰. 水稻抽穗期调控基因Hd6功能标记的开发及应用[J]. 中国水稻科学, 2025, 39(1): 47-54.

Figures/Tables 8

References 32

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引物名称 Primer	引物序列 Primer sequence(5’-3’)	PCR产物大小PCR product size(bp)
K-Hd6-11F	GTGGAGGTCCAAACATTGTGA	348
N-Hd6-12F	GTGGAGGTCCAAACATTGTGT	348
K-Hd6-21F	GTGGAGGTCCAAACATTGTAA	348
N-Hd6-22F	GTGGAGGTCCAAACATTGTAT	348
Hd6-1R	AAGCAGTGAGAATGGTGATATTTG	348
Hd6-KF1	GTGAGCAGGATGACTATGA	504
Hd6-KR1	TAGGGATGACAATGAAGG	504

引物名称 Primer	引物序列 Primer sequence(5’-3’)	PCR产物大小PCR product size(bp)
K-Hd6-11F	GTGGAGGTCCAAACATTGTGA	348
N-Hd6-12F	GTGGAGGTCCAAACATTGTGT	348
K-Hd6-21F	GTGGAGGTCCAAACATTGTAA	348
N-Hd6-22F	GTGGAGGTCCAAACATTGTAT	348
Hd6-1R	AAGCAGTGAGAATGGTGATATTTG	348
Hd6-KF1	GTGAGCAGGATGACTATGA	504
Hd6-KR1	TAGGGATGACAATGAAGG	504

编号 Code	品种名称 Name	类型 Type		SNP	K-Hd6-21F /Hd6-1R	N-Hd6-22F /Hd6-1R	Hd6功能 Function
1	南粳505 Nanjing 505	中熟中粳	Medium-maturity middle-season japonica rice	A	1	0	1
2	金粳818 Jinjing 818	中熟中粳	Medium-maturity middle-season japonica rice	A	1	0	1
3	南粳45 Nanjing 45	中熟中粳	Late-maturity middle-season japonica rice	A	1	0	1
4	南粳49 Nanjing 49	迟熟中粳	Late-maturity middle-season japonica rice	A	1	0	1
5	淮稻5 号 Huaidao 5	迟熟中粳	Late-maturity middle-season japonica rice	A	1	0	1
6	苏垦118 Suken 118	迟熟中粳	Late-maturity middle-season japonica rice	A	1	0	1
7	南粳5055 Nanjing 5055	迟熟中粳	Early-maturity late-season japonica rice	A	1	0	1
8	南粳46 Nanjing 46	早熟晚粳	Early-maturity late-season japonica rice	A	1	0	1
9	南粳47 Nanjing 47	早熟晚粳	Early-maturity late-season japonica rice	A	1	0	1
10	苏秀867 Suxiu 867	早熟晚粳	Medium-maturity middle-season japonica rice	A	1	0	1
11	南粳59 Nanjing 59	中熟中粳	Early-maturity late-season japonica rice	T	0	1	0
12	常农粳8号 Changnongjing 8	早熟晚粳	Early-maturity late-season japonica rice	A	1	0	1
13	南粳93093 Nanjing 93093	早熟晚粳	Medium-maturity middle-season japonica rice	A	1	0	1
14	徐稻9号 Xudao 9	中熟中粳	Medium-maturity middle-season japonica rice	A	1	0	1
15	连粳11号 Lianjing 11	中熟中粳	Medium-maturity middle-season japonica rice	A	1	0	1
16	徐稻3号 Xudao 3	中熟中粳	Medium-maturity middle-season japonica rice	T	0	1	0
17	宁粳1号 Ningjing 1	中熟中粳	Medium-maturity middle-season japonica rice	T	0	1	0
18	南粳9108 Nanjing 9108	早熟晚粳	Early-maturity late-season japonica rice	A	1	0	1
19	武运粳7号 Wuyunjing 7	迟熟中粳	Late-maturity middle-season japonica rice	T	0	1	0
20	金香玉1号 Jinxiangyu 1	早熟晚粳	Early-maturity late-season japonica rice	A	1	0	1
21	华粳8号 Huajing 8	迟熟中粳	Late-maturity middle-season japonica rice	T	0	1	0
22	南粳505 Nanjing 505	中熟中粳	Medium-maturity middle-season japonica rice	T	0	1	0
23	Kasalath	印度籼稻	Indian indica rice	A	1	0	1
24	日本晴Nipponbare	日本粳稻	Japanese japonica rice	T	0	1	0

编号 Code	品种名称 Name	类型 Type		SNP	K-Hd6-21F /Hd6-1R	N-Hd6-22F /Hd6-1R	Hd6功能 Function
1	南粳505 Nanjing 505	中熟中粳	Medium-maturity middle-season japonica rice	A	1	0	1
2	金粳818 Jinjing 818	中熟中粳	Medium-maturity middle-season japonica rice	A	1	0	1
3	南粳45 Nanjing 45	中熟中粳	Late-maturity middle-season japonica rice	A	1	0	1
4	南粳49 Nanjing 49	迟熟中粳	Late-maturity middle-season japonica rice	A	1	0	1
5	淮稻5 号 Huaidao 5	迟熟中粳	Late-maturity middle-season japonica rice	A	1	0	1
6	苏垦118 Suken 118	迟熟中粳	Late-maturity middle-season japonica rice	A	1	0	1
7	南粳5055 Nanjing 5055	迟熟中粳	Early-maturity late-season japonica rice	A	1	0	1
8	南粳46 Nanjing 46	早熟晚粳	Early-maturity late-season japonica rice	A	1	0	1
9	南粳47 Nanjing 47	早熟晚粳	Early-maturity late-season japonica rice	A	1	0	1
10	苏秀867 Suxiu 867	早熟晚粳	Medium-maturity middle-season japonica rice	A	1	0	1
11	南粳59 Nanjing 59	中熟中粳	Early-maturity late-season japonica rice	T	0	1	0
12	常农粳8号 Changnongjing 8	早熟晚粳	Early-maturity late-season japonica rice	A	1	0	1
13	南粳93093 Nanjing 93093	早熟晚粳	Medium-maturity middle-season japonica rice	A	1	0	1
14	徐稻9号 Xudao 9	中熟中粳	Medium-maturity middle-season japonica rice	A	1	0	1
15	连粳11号 Lianjing 11	中熟中粳	Medium-maturity middle-season japonica rice	A	1	0	1
16	徐稻3号 Xudao 3	中熟中粳	Medium-maturity middle-season japonica rice	T	0	1	0
17	宁粳1号 Ningjing 1	中熟中粳	Medium-maturity middle-season japonica rice	T	0	1	0
18	南粳9108 Nanjing 9108	早熟晚粳	Early-maturity late-season japonica rice	A	1	0	1
19	武运粳7号 Wuyunjing 7	迟熟中粳	Late-maturity middle-season japonica rice	T	0	1	0
20	金香玉1号 Jinxiangyu 1	早熟晚粳	Early-maturity late-season japonica rice	A	1	0	1
21	华粳8号 Huajing 8	迟熟中粳	Late-maturity middle-season japonica rice	T	0	1	0
22	南粳505 Nanjing 505	中熟中粳	Medium-maturity middle-season japonica rice	T	0	1	0
23	Kasalath	印度籼稻	Indian indica rice	A	1	0	1
24	日本晴Nipponbare	日本粳稻	Japanese japonica rice	T	0	1	0

Development and Application of a Functional Marker for Heading Date Gene Hd6 in Rice

水稻抽穗期调控基因Hd6功能标记的开发及应用

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[11]	SUI Jingjing, ZHAO Guilong, JIN Xin, BU Qingyun, TANG Jiaqi. Advances in Molecular and Physiological Mechanisms of Cold Tolerance Regulation of Rice at the Booting Stage [J]. Chinese Journal OF Rice Science, 2025, 39(1): 1-10.
[12]	REN Ningning, SUN Yongjian, SHEN Congcong, ZHU Shuangbing, LI Huiju, ZHANG Zhiyuan, CHEN Kai. Research Progress in Rice Mesocotyl [J]. Chinese Journal OF Rice Science, 2025, 39(1): 11-23.
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[15]	YANG Chuanming, WANG Lizhi, ZHANG Xijuan, YANG Xianli, WANG Yangyang, HOU Benfu, CUI Shize, LI Qingchao, LIU Kai, MA Rui, FENG Yanjiang, LAI Yongcai, LI Hongyu, JIANG Shukun. Analysis of QTL Controlling Cold Tolerance at Seedling Stage by Using a High-Density SNP Linkage Map in japonica Rice [J]. Chinese Journal OF Rice Science, 2025, 39(1): 82-91.