Allele Mining and Breeding Application of Grain Number per Panicle Gene Gn1a in Rice

doi:10.16819/j.1001-7216.2025.240105

Chinese Journal OF Rice Science ›› 2025, Vol. 39 ›› Issue (2): 220-230.DOI: 10.16819/j.1001-7216.2025.240105

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Allele Mining and Breeding Application of Grain Number per Panicle Gene Gn1a in Rice

LIU Zhichao¹^,²^,^#, CHANG Longxue¹^,²^,^#, AI Xin², JIN Long², ZHANG Fengyong², LI Zhiyong², WANG Yifeng², TONG Xiaohong², HUANG Jie², ZHANG Jian², JIN Jian¹^,^*(), YING Jiezheng²^,^*()

¹State Key Laboratory for Conservation and Utilization of Subtropical Agricultural Resources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
²State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311401, China

Received:2024-01-09 Revised:2024-02-06 Online:2025-03-10 Published:2025-03-19
Contact: JIN Jian, YING Jiezheng
About author:
^#These authors contributed equally to this paper

水稻穗粒数基因Gn1a的等位基因挖掘与育种应用

刘智超¹^,²^,^#, 常龙学¹^,²^,^#, 艾鑫², 金龙², 张丰勇², 李志永², 王以锋², 童晓红², 黄捷², 张健², 金健¹^,^*(), 应杰政²^,^*()

¹广西大学生命科学与技术学院/亚热带农业生物资源保护与利用国家重点实验室，南宁 530004
²中国水稻研究所水稻生物育种全国重点实验室，杭州 311401

通讯作者: 金健,应杰政
作者简介:
^#共同第一作者
基金资助:
国家自然科学基金资助项目(32072050);浙江省自然科学基金重大项目(LD24C130001);宁波江北区公益类科技项目(2022B02);广西自然科学基金面上项目(2020GXNSFAA297236)

Abstract

Abstract:

【Objective】Based on advances in rice functional genomics, this study aimed to screen favorable alleles of the Gn1a gene controlling grain number per panicle, providing technical support for modern rice variety improvement. 【Method】Advanced genetic populations were developed through backcrossing and self-crossing for QTL mapping. Near-isogenic lines (NILs) were constructed to validate QTL effects. Target gene sequences were amplified and aligned, followed by designing functional markers for genotyping. 【Result】A major quantitative trait locus (QTL) controlling secondary branch number and grains per panicle was co-localized with the Gn1a locus on chromosome 1 short arm. This mapping utilized four BC₃F₃ populations derived from crosses between the japonica donor parent Jizi 1560 and recurrent parents, including early indica varieties (Zhongjiazao 17, Zhongzao 39) and three-line restorer lines (Huazhan, R173). Sequence analysis revealed an unreported indica-specific allele (Gn1a-i) in Zhongjiazao 17 and Zhongzao 39, characterized by a ‌16-bp deletion in the 5' UTR‌ compared to the japonica allele (Gn1a-j). Comparative analyses of four near-isogenic line (NIL) populations confirmed that Gn1a-i significantly increased grains per panicle and yield. A functional marker (ZC51) targeting the 16-bp deletion was developed to genotype 39 rice materials, which were categorized into nine types: conventional early/late indica varieties, three-line maintainers/restorers, two-line sterile lines, northern/southern japonica varieties, landraces, and wild rice. All modern indica materials (cultivars and hybrid parents) carried Gn1a-i, whereas landraces and wild rice retained Gn1a-j. Notably, both southern and northern japonica varieties exhibited biallelic Gn1a-i and Gn1a-j‌. 【Conclusion】It was confirmed that Gn1a-i allele increased grain yield by increasing number of primary branches, secondary branches and grains per panicle. The favorable allele of Gn1a-i has great potentials in the improvement of japonica rice varieties, and the functional gene marker of ZC51 can be directly used in the marker-assisted selection of Gn1a.

Key words: grain number per panicle, allele, quantitative trait loci, molecular marker-assisted selection

摘要：

【目的】基于水稻功能基因组学的快速发展，通过全基因组关联分析和等位基因挖掘，鉴定出调控每穗粒数的关键基因Gn1a的优异等位变异，为现代水稻高产分子育种策略提供了理论依据与靶点资源。【方法】通过‌构建高世代回交自交系遗传群体‌开展QTL精细定位；基于近等基因系（NILs）‌验证目标QTL的遗传效应‌；结合目标基因的‌PCR扩增、高通量测序及多序列比对‌解析功能变异位点；进一步‌开发功能分子标记‌并应用于水稻种质资源的‌基因型精准鉴定‌。【结果】在中嘉早17、中早39（常规早籼主推品种）、华占、R173（杂交晚籼核心恢复系）4个背景与粳稻吉资1560‌构建的BC₃F₃群体中，1号染色体短臂Gn1a位点共同定位到控制穗粒数与二次枝梗数的QTL。Gn1a测序分析揭示,中嘉早17与中早39携带新型Gn1a等位变异（命名为Gn1a-i），与粳型等位基因Gn1a-j相比，在5' UTR区存在16-bp缺失。4套近等基因系的分析结果表明Gn1a-i增加每穗粒数和籽粒产量。基于该InDel位点开发的共显性功能标记ZC51‌，对‌9类39份水稻材料（涵盖常规早籼、常规晚籼、三系保持系、两系不育系、三系恢复系、北方粳稻、南方粳稻、农家品种及野生稻）进行Gn1a等位基因分型检测，结果显示：‌籼型群体（常规早/晚籼、三系保持系、两系不育系、三系恢复系）100%携带Gn1a-i等位基因；‌野生稻与农家品种携带Gn1a-j等位基因；‌粳稻群体（南/北方）携带Gn1a-i和Gn1a-j双等位基因。【结论】明确了Gn1a-i等位基因通过增加二次枝梗数和每穗粒数来提高籽粒产量，Gn1a-i有利等位基因在当前粳稻品种的改良中具有较大利用潜力，Gn1a功能基因标记ZC51能直接用于分子标记辅助选择育种。

关键词: 每穗粒数, 等位基因, 数量性状座位, 分子标记辅助选择

LIU Zhichao, CHANG Longxue, AI Xin, JIN Long, ZHANG Fengyong, LI Zhiyong, WANG Yifeng, TONG Xiaohong, HUANG Jie, ZHANG Jian, JIN Jian, YING Jiezheng. Allele Mining and Breeding Application of Grain Number per Panicle Gene Gn1a in Rice[J]. Chinese Journal OF Rice Science, 2025, 39(2): 220-230.

刘智超, 常龙学, 艾鑫, 金龙, 张丰勇, 李志永, 王以锋, 童晓红, 黄捷, 张健, 金健, 应杰政. 水稻穗粒数基因Gn1a的等位基因挖掘与育种应用[J]. 中国水稻科学, 2025, 39(2): 220-230.

Figures/Tables 7

References 36

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群体 Population	性状 Trait	区间 Interval	LOD值 LOD value	加性效应 Additive effect	显性效应 Dominance effect	贡献率 Variation explained (%)
C1	一次枝梗数NPB		ns
	二次枝梗数NSB	JD1037−ZC51	4.01	−3.40	−0.04	12.70
	每穗粒数NGPP	JD1037−ZC51	4.00	−13.94	−0.12	12.70
C2	一次枝梗数NPB	ZC51−ZC100	3.12	−0.45	−0.09	10.20
	二次枝梗数NSB	ZC51−ZC100	5.22	−3.87	−3.02	16.50
	每穗粒数NGPP	ZC51−ZC100	4.89	−18.52	−13.97	15.60
C3	一次枝梗数NPB		ns
	二次枝梗数NSB	JD1037−ZC51	4.04	−3.68	−1.31	13.70
	每穗粒数NGPP	JD1037−ZC51	2.99	−11.39	−4.77	10.40
C4	一次枝梗数NPB		ns
	二次枝梗数NSB	ZC51−ZC100	5.63	−3.08	−0.37	18.70
	每穗粒数NGPP	ZC51−ZC100	5.10	−10.71	−2.03	17.10

群体 Population	性状 Trait	区间 Interval	LOD值 LOD value	加性效应 Additive effect	显性效应 Dominance effect	贡献率 Variation explained (%)
C1	一次枝梗数NPB		ns
	二次枝梗数NSB	JD1037−ZC51	4.01	−3.40	−0.04	12.70
	每穗粒数NGPP	JD1037−ZC51	4.00	−13.94	−0.12	12.70
C2	一次枝梗数NPB	ZC51−ZC100	3.12	−0.45	−0.09	10.20
	二次枝梗数NSB	ZC51−ZC100	5.22	−3.87	−3.02	16.50
	每穗粒数NGPP	ZC51−ZC100	4.89	−18.52	−13.97	15.60
C3	一次枝梗数NPB		ns
	二次枝梗数NSB	JD1037−ZC51	4.04	−3.68	−1.31	13.70
	每穗粒数NGPP	JD1037−ZC51	2.99	−11.39	−4.77	10.40
C4	一次枝梗数NPB		ns
	二次枝梗数NSB	ZC51−ZC100	5.63	−3.08	−0.37	18.70
	每穗粒数NGPP	ZC51−ZC100	5.10	−10.71	−2.03	17.10

序号 No.		类型 Type	等位基因 Allele	序号 No.		类型 Type	等位基因 Allele
1	吉资1560 Jizi 1560	供体亲本 Donor parent	Gn1a-j	21	明恢 63 Minghui 63	三系恢复系 Three-line restorer line	Gn1a-i
2	中早39 Zhongzao 39	常规早籼 Conventional early indica rice	Gn1a-i	22	南粳 44 Nanjing 44	南方粳稻 Southern japonica rice	Gn1a-i
3	中嘉早17 Zhongjiazao 17	常规早籼 Conventional early indica rice	Gn1a-i	23	镇稻 88 Zhendao 88	南方粳稻 Southern japonica rice	Gn1a-i
4	中鉴100 Zhongjian 100	常规早籼 Conventional early indica rice	Gn1a-i	24	浙禾香 2 号 Zhehexiang 2	南方粳稻 Southern japonica rice	Gn1a-j
5	舟903 Zhou 903	常规早籼 Conventional early indica rice	Gn1a-i	25	春江糯 6 号 Chunjiangnuo 6	南方粳稻 Southern japonica rice	Gn1a-j
6	黄华占 Huanghuazhan	常规晚籼 Conventional late indica rice	Gn1a-i	26	沈农 265 Shennong 265	北方粳稻 Northern japonica rice	Gn1a-j
7	扬稻6号 Yangdao 6	常规晚籼 Conventional late indica rice	Gn1a-i	27	吉粳 88 Jijing 88	北方粳稻 Northern japonica rice	Gn1a-i
8	中籼2503 Zhongxian 2503	常规晚籼 Conventional late indica rice	Gn1a-i	28	盐丰 47 Yanfeng 47	北方粳稻 Northern japonica rice	Gn1a-i
9	湘晚籼3号 Xiangwanxian 3	常规晚籼 Conventional late indica rice	Gn1a-i	29	空育131 Kongyu 131	北方粳稻 Northern japonica rice	Gn1a-i
10	天丰B Tianfeng B	三系保持系 Three-line maintainer line	Gn1a-i	30	大量稻 Daliangdao	农家品种 Farmhouse variety	Gn1a-j
11	II 32B	三系保持系 Three-line maintainer line	Gn1a-i	31	鸡吓稻 Jixiadao	农家品种 Farmhouse variety	Gn1a-j
12	协青早B Xieqingzao B	三系保持系 Three-line maintainer line	Gn1a-i	32	黑嘴稻 Heizuidao	农家品种 Farmhouse variety	Gn1a-j
13	ZS97B	三系保持系 Three-line maintainer line	Gn1a-i	33	木樨球 Muxiqiu	农家品种 Farmhouse variety	Gn1a-j
14	贡877S Gong 877S	两系不育系 Two-line male sterile line	Gn1a-i	34	贩牛种 Fanniuzhong	农家品种 Farmhouse variety	Gn1a-j
15	中0S Zhong 0S	两系不育系 Two-line male sterile line	Gn1a-i	35	麦节青 Maijieqing	农家品种 Farmhouse variety	Gn1a-j
16	武香S Wuxiang S	两系不育系 Two-line male sterile line	Gn1a-i	36	茶陵野生稻 Chaling wild rice	普通野生稻 Common wild rice	Gn1a-j
17	C815S	两系不育系 Two-line male sterile line	Gn1a-i	37	广西野生稻 Guangxi wild rice	普通野生稻 Common wild rice	Gn1a-j
18	华占 Huazhan	三系恢复系 Three-line restorer line	Gn1a-i	38	东乡野生稻 Dongxiang wild rice	普通野生稻 Common wild rice	Gn1a-j
19	R173	三系恢复系 Three-line restorer line	Gn1a-i	39	长雄野生稻 Oryza longistaminata	长雄野生稻 Oryza longistaminata	Gn1a-j
20	绵恢725 Mianhui 725	三系恢复系 Three-line restorer line	Gn1a-i

序号 No.		类型 Type	等位基因 Allele	序号 No.		类型 Type	等位基因 Allele
1	吉资1560 Jizi 1560	供体亲本 Donor parent	Gn1a-j	21	明恢 63 Minghui 63	三系恢复系 Three-line restorer line	Gn1a-i
2	中早39 Zhongzao 39	常规早籼 Conventional early indica rice	Gn1a-i	22	南粳 44 Nanjing 44	南方粳稻 Southern japonica rice	Gn1a-i
3	中嘉早17 Zhongjiazao 17	常规早籼 Conventional early indica rice	Gn1a-i	23	镇稻 88 Zhendao 88	南方粳稻 Southern japonica rice	Gn1a-i
4	中鉴100 Zhongjian 100	常规早籼 Conventional early indica rice	Gn1a-i	24	浙禾香 2 号 Zhehexiang 2	南方粳稻 Southern japonica rice	Gn1a-j
5	舟903 Zhou 903	常规早籼 Conventional early indica rice	Gn1a-i	25	春江糯 6 号 Chunjiangnuo 6	南方粳稻 Southern japonica rice	Gn1a-j
6	黄华占 Huanghuazhan	常规晚籼 Conventional late indica rice	Gn1a-i	26	沈农 265 Shennong 265	北方粳稻 Northern japonica rice	Gn1a-j
7	扬稻6号 Yangdao 6	常规晚籼 Conventional late indica rice	Gn1a-i	27	吉粳 88 Jijing 88	北方粳稻 Northern japonica rice	Gn1a-i
8	中籼2503 Zhongxian 2503	常规晚籼 Conventional late indica rice	Gn1a-i	28	盐丰 47 Yanfeng 47	北方粳稻 Northern japonica rice	Gn1a-i
9	湘晚籼3号 Xiangwanxian 3	常规晚籼 Conventional late indica rice	Gn1a-i	29	空育131 Kongyu 131	北方粳稻 Northern japonica rice	Gn1a-i
10	天丰B Tianfeng B	三系保持系 Three-line maintainer line	Gn1a-i	30	大量稻 Daliangdao	农家品种 Farmhouse variety	Gn1a-j
11	II 32B	三系保持系 Three-line maintainer line	Gn1a-i	31	鸡吓稻 Jixiadao	农家品种 Farmhouse variety	Gn1a-j
12	协青早B Xieqingzao B	三系保持系 Three-line maintainer line	Gn1a-i	32	黑嘴稻 Heizuidao	农家品种 Farmhouse variety	Gn1a-j
13	ZS97B	三系保持系 Three-line maintainer line	Gn1a-i	33	木樨球 Muxiqiu	农家品种 Farmhouse variety	Gn1a-j
14	贡877S Gong 877S	两系不育系 Two-line male sterile line	Gn1a-i	34	贩牛种 Fanniuzhong	农家品种 Farmhouse variety	Gn1a-j
15	中0S Zhong 0S	两系不育系 Two-line male sterile line	Gn1a-i	35	麦节青 Maijieqing	农家品种 Farmhouse variety	Gn1a-j
16	武香S Wuxiang S	两系不育系 Two-line male sterile line	Gn1a-i	36	茶陵野生稻 Chaling wild rice	普通野生稻 Common wild rice	Gn1a-j
17	C815S	两系不育系 Two-line male sterile line	Gn1a-i	37	广西野生稻 Guangxi wild rice	普通野生稻 Common wild rice	Gn1a-j
18	华占 Huazhan	三系恢复系 Three-line restorer line	Gn1a-i	38	东乡野生稻 Dongxiang wild rice	普通野生稻 Common wild rice	Gn1a-j
19	R173	三系恢复系 Three-line restorer line	Gn1a-i	39	长雄野生稻 Oryza longistaminata	长雄野生稻 Oryza longistaminata	Gn1a-j
20	绵恢725 Mianhui 725	三系恢复系 Three-line restorer line	Gn1a-i

Allele Mining and Breeding Application of Grain Number per Panicle Gene Gn1a in Rice

水稻穗粒数基因Gn1a的等位基因挖掘与育种应用

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