Genotyping and Breeding Utilization of Parental Lines of japonica Hybrid Rice in Shanghai Based on High-Density SNP Chips

doi:10.16819/j.1001-7216.2026.260412

Abstract

Abstract:

【Objective】To elucidate the genetic characteristics of major parental lines of japonica hybrid rice in Shanghai at the genomic level, thereby providing a theoretical basis and germplasm resources for the molecular improvement of these parental lines and evaluation of new hybrid combinations.【Method】High-density rice whole-genome SNP chips were employed to analyze the genetic background, identify functional genes, and assess the breeding value of 20 major parental lines of japonica hybrid rice in Shanghai.【Result】The sterile lines of japonica hybrid rice generally exhibited a higher proportion of japonica components than the restorer lines. Among them, Shen 68A, Shen 01A, Shen 9A, Shen 10A, Shen 21A, Shen 46A, Shenwu 1A, Shenchang A, and Zixiang A showed a particularly high ratio of japonica genome segments and were classified as typical japonica types. A total of 19 and 35 functional genes controlling key traits such as yield, quality, and resistance to biotic and abiotic stresses were detected in the 11 sterile lines and 9 restorer lines, respectively. The major sterile lines of japonica hybrid rice in Shanghai exhibited favorable disease resistance. Several lines, including Shen 68A, Shen 9A, Shen 10A, Shen 21A, Shen 130A, and Shen 24A, carried the broad-spectrum blast resistance gene combination Pi2+Pita. The restorer lines featured large panicles and high spikelet numbers, harboring multiple yield-related genes (OsSPL16, Gn1a, CYP704A3, etc.). However, few restorer lines aggregated multiple major broad-spectrum blast resistance genes, indicating a need to strengthen molecular improvement for blast resistance in restorer lines.【Conclusion】This study clarifies the genetic backgrounds and functional gene profiles of major parental lines of japonica hybrid rice in Shanghai, laying a solid foundation for improving breeding efficiency and addressing genetic homogeneity in hybrid rice breeding.

Key words: parental lines, japonica hybrid rice, gene chip, breeding, genetic background, functional gene

摘要：

【目的】从基因组水平解析上海地区主要杂交粳稻亲本的遗传特性，为进一步开展杂交粳稻亲本分子改良和新组合测配提供理论依据与种质资源。【方法】利用高密度水稻全基因组SNP芯片对20个上海地区主要杂交粳稻亲本进行遗传背景分析、功能基因鉴定以及利用价值评价。【结果】杂交粳稻不育系粳型成分普遍高于恢复系，其中不育系申68A、申01A、申9A、申10A、申21A、申46A、申武1A、申长A和紫祥A粳型片段比例较高，属于典型粳稻类型。11个不育系和9个恢复系分别检测到控制产量、品质、抗生物和非生物逆境等重要性状功能基因19个和35个。上海地区主要杂交粳稻不育系抗病性好，申68A、申9A、申10A、申21A、申130A、申24A等多个不育系均含有广谱稻瘟病抗性基因组合“Pi2+Pita”。恢复系穗大粒多，含有较多的产量相关基因(OsSPL16、Gn1a和CYP704A3等)，但聚合多个广谱抗稻瘟病主效抗性基因的品种较少，需加强恢复系稻瘟病抗性的分子改良。【结论】本研究明确了上海地区主要杂交粳稻亲本的遗传背景和携带的功能基因，为提高杂交粳稻新品种选育效率以及解决杂交粳稻育种的同质化问题奠定了良好基础。

关键词: 亲本, 杂交粳稻, 基因芯片, 育种, 遗传背景, 功能基因

NIU Fuan, CHU Huangwei, ZHANG Anpeng, ZHOU Jihua, SUN Bin, DAI Yuting, XIE Kaizhen, SHI Fengzhen, YIN Zihui, HOU Cong, WANG Yi, LI Jing, CHENG Can, CAO Liming. Genotyping and Breeding Utilization of Parental Lines of japonica Hybrid Rice in Shanghai Based on High-Density SNP Chips[J]. Chinese Journal OF Rice Science, 2026, 40(6): 774-785.

牛付安, 储黄伟, 张安鹏, 周继华, 孙滨, 代雨婷, 谢开珍, 石凤珍, 尹子辉, 侯聪, 王奕, 李璟, 程灿, 曹黎明. 基于高密度基因芯片的上海杂交粳稻亲本基因型鉴定与育种利用[J]. 中国水稻科学, 2026, 40(6): 774-785.

Figures/Tables 6

References 35

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序号 Number	品种 Variety	籼型片段比例 indica segment ratio(%)	粳型片段比例 japonica segment ratio(%)	无法区分片段比例Unclassified segment ratio(%)	类型 Type
1	68A	3.37	90.57	6.06	典型粳稻 Typical japonica rice
2	N01A	2.43	91.91	5.66	典型粳稻 Typical japonica rice
3	S9A	3.37	90.97	5.66	典型粳稻 Typical japonica rice
4	N10A	3.23	92.05	4.72	典型粳稻 Typical japonica rice
5	S21A	3.77	90.30	5.93	典型粳稻 Typical japonica rice
6	N9746A	2.56	93.94	3.50	典型粳稻 Typical japonica rice
7	W1A	3.10	92.45	4.45	典型粳稻 Typical japonica rice
8	HA62	3.10	90.57	6.33	典型粳稻 Typical japonica rice
9	N87A	1.21	95.15	3.64	典型粳稻 Typical japonica rice
10	N04-130A	4.18	89.89	5.93	粳稻 japonica rice
11	D3A	5.39	88.01	6.60	粳稻 japonica rice
12	F7	9.70	84.91	5.39	粳稻 japonica rice
13	F14	12.94	78.57	8.49	粳稻 japonica rice
14	Th6	13.88	80.19	5.93	粳稻 japonica rice
15	F17	13.75	80.32	5.93	粳稻 japonica rice
16	F42	18.33	74.53	7.14	粳稻japonica rice
17	SCR1	15.77	75.61	8.62	粳稻 japonica rice
18	SH26	9.84	83.83	6.33	粳稻 japonica rice
19	F31	54.31	27.22	18.47	偏籼 indica-like rice
20	KH272	62.26	17.92	19.82	籼稻 indica rice

序号 Number	品种 Variety	籼型片段比例 indica segment ratio(%)	粳型片段比例 japonica segment ratio(%)	无法区分片段比例Unclassified segment ratio(%)	类型 Type
1	68A	3.37	90.57	6.06	典型粳稻 Typical japonica rice
2	N01A	2.43	91.91	5.66	典型粳稻 Typical japonica rice
3	S9A	3.37	90.97	5.66	典型粳稻 Typical japonica rice
4	N10A	3.23	92.05	4.72	典型粳稻 Typical japonica rice
5	S21A	3.77	90.30	5.93	典型粳稻 Typical japonica rice
6	N9746A	2.56	93.94	3.50	典型粳稻 Typical japonica rice
7	W1A	3.10	92.45	4.45	典型粳稻 Typical japonica rice
8	HA62	3.10	90.57	6.33	典型粳稻 Typical japonica rice
9	N87A	1.21	95.15	3.64	典型粳稻 Typical japonica rice
10	N04-130A	4.18	89.89	5.93	粳稻 japonica rice
11	D3A	5.39	88.01	6.60	粳稻 japonica rice
12	F7	9.70	84.91	5.39	粳稻 japonica rice
13	F14	12.94	78.57	8.49	粳稻 japonica rice
14	Th6	13.88	80.19	5.93	粳稻 japonica rice
15	F17	13.75	80.32	5.93	粳稻 japonica rice
16	F42	18.33	74.53	7.14	粳稻japonica rice
17	SCR1	15.77	75.61	8.62	粳稻 japonica rice
18	SH26	9.84	83.83	6.33	粳稻 japonica rice
19	F31	54.31	27.22	18.47	偏籼 indica-like rice
20	KH272	62.26	17.92	19.82	籼稻 indica rice

基因名称 Gene name	表型 Phenotype	代表品种 Representative variety	68A	N01A	S9A	N10A	S21A	N9746A	W1A	HA62	N87A	N04-130A	D3A
Wx^b	中等直链淀粉含量 Medium amylose content	日本晴Nipponbare	√	√	√	√	√	√	√	√	√	√	√
ALK	增加中长型支链淀粉含量 Increasing medium and long-chain amylopectin content	明恢63 Minghui 63		√				√	√	√	√	√	√
GW5	增加粒宽 Enhancing grain width	日本晴 Nipponbare	N	√	√	√	√	√	√		√	√	√
gs3	增加粒长 Increasing grain length	明恢63 Minghui 63								√
Pi2	增强稻瘟病抗性 Enhancing blast resistance	99SNP	√	√	√	√	√				√	√	√
Pita	增强稻瘟病抗性 Enhancing blast resistance	32SNP	√		√	√	√		√			√	√
Pid3	增强稻瘟病抗性 Enhancing blast resistance	64SNP										√
STV11	持久抗水稻条纹叶枯病 Durable resistance to rice stripe virus	卡萨拉斯 Kasalath	N		√	√	√	√
Rymv1	抗黄色斑驳病毒病 Resistance to yellow mottle virus disease	日本晴 Nipponbare	√	√	√	√	√	√	√	√	√	√	√
qLTG3-1	提高种子低温下发芽势 Improving seed germination potential under low temperature conditions	日本晴 Nipponbare		√			√	√	√	√	√		√
OsFRO1	铁耐受 Iron tolerance	茉莉香米 KDML105	N	√	√	√	√	√	√	√	√	√	√
qUVR-10	增强光修复活性 Enhancing photorepair activity	笹锦 Sasanishiki	√	√	√	√	√	√	√		√	√	√
OsHESO1	延迟抽穗 Late heading	单倍型B Haplotype B	√	√	√	√	√	√	√	√	√	√	√
Hd3a	促进抽穗 Promoting heading	日本晴 Nipponbare		√	√	√	√	√	√	√	√	√	√
OsGATA28	延迟抽穗 Late heading	单倍型C Haplotype C	N	√	√	√	√				√	√	√
Hd17	延迟抽穗 Late heading	越光 Koshihikari				√		√	√
SaF	广亲和(粳稻亲和) Wide compatibility (japonica-compatibility	日本晴 Nipponbare	N	√	√	√	√	√	√	√	√	√	√
Sdt97	半矮秆Semi-dwarf	Y98149	N	√	√	√	√	√	√	√	√	√	√
sh4	非落粒Non-shattering	日本晴 Nipponbare	N	√	√	√	√	√	√	√	√	√	√

基因名称 Gene name	表型 Phenotype	代表品种 Representative variety	68A	N01A	S9A	N10A	S21A	N9746A	W1A	HA62	N87A	N04-130A	D3A
Wx^b	中等直链淀粉含量 Medium amylose content	日本晴Nipponbare	√	√	√	√	√	√	√	√	√	√	√
ALK	增加中长型支链淀粉含量 Increasing medium and long-chain amylopectin content	明恢63 Minghui 63		√				√	√	√	√	√	√
GW5	增加粒宽 Enhancing grain width	日本晴 Nipponbare	N	√	√	√	√	√	√		√	√	√
gs3	增加粒长 Increasing grain length	明恢63 Minghui 63								√
Pi2	增强稻瘟病抗性 Enhancing blast resistance	99SNP	√	√	√	√	√				√	√	√
Pita	增强稻瘟病抗性 Enhancing blast resistance	32SNP	√		√	√	√		√			√	√
Pid3	增强稻瘟病抗性 Enhancing blast resistance	64SNP										√
STV11	持久抗水稻条纹叶枯病 Durable resistance to rice stripe virus	卡萨拉斯 Kasalath	N		√	√	√	√
Rymv1	抗黄色斑驳病毒病 Resistance to yellow mottle virus disease	日本晴 Nipponbare	√	√	√	√	√	√	√	√	√	√	√
qLTG3-1	提高种子低温下发芽势 Improving seed germination potential under low temperature conditions	日本晴 Nipponbare		√			√	√	√	√	√		√
OsFRO1	铁耐受 Iron tolerance	茉莉香米 KDML105	N	√	√	√	√	√	√	√	√	√	√
qUVR-10	增强光修复活性 Enhancing photorepair activity	笹锦 Sasanishiki	√	√	√	√	√	√	√		√	√	√
OsHESO1	延迟抽穗 Late heading	单倍型B Haplotype B	√	√	√	√	√	√	√	√	√	√	√
Hd3a	促进抽穗 Promoting heading	日本晴 Nipponbare		√	√	√	√	√	√	√	√	√	√
OsGATA28	延迟抽穗 Late heading	单倍型C Haplotype C	N	√	√	√	√				√	√	√
Hd17	延迟抽穗 Late heading	越光 Koshihikari				√		√	√
SaF	广亲和(粳稻亲和) Wide compatibility (japonica-compatibility	日本晴 Nipponbare	N	√	√	√	√	√	√	√	√	√	√
Sdt97	半矮秆Semi-dwarf	Y98149	N	√	√	√	√	√	√	√	√	√	√
sh4	非落粒Non-shattering	日本晴 Nipponbare	N	√	√	√	√	√	√	√	√	√	√

基因名称 Gene name	表型 Phenotype	代表品种 Representative variety	F7	F14	Th6	F17	F42	SCR1	SH26	F31	KH272
GW5	增加粒宽 Enhancing grain width	日本晴 Nipponbare	√	√		√		√	√
OsSPL16	高产High yield	华粳籼74 Huajingxian 74		√		√				√
Gn1a	增加穗粒数 Increasing grain number per panicle	哈巴达克, 9311 Habataki, 9311								√	√
CYP704A3	增加粒长 Increasing grain length	IR 24									√
Wx^b	中等直链淀粉含量 Medium amylose content	日本晴 Nipponbare Nipponbare	√	√	√	√	√	√	√	√	√
ALK	增加中长型支链淀粉含量 Increasing medium- and long- chain amylopectin content	明恢63 Minghui 63	√		√		√	√	√	√	√
OsAAP6	高蛋白 Increasing seed protein content	9311		√						√	√
BADH2	香味Aroma	苏御糯 Suyunuo						√
Chalk5	低垩白度Low chalkiness	H94								√
Pi2	增强稻瘟病抗性 Enhancing blast resistance	99SNP		√		√		√
Pi5	增强稻瘟病抗性 Enhancing blast resistance	33SNP								√
Pia	增强稻瘟病抗性 Enhancing blast resistance	13SNP								√
Pid2	增强稻瘟病抗性 Enhancing blast resistance	66SNP			√		√
Pid3	增强稻瘟病抗性 Enhancing blast resistance	64SNP								√	√
STV11	持久抗水稻条纹叶枯病 Durable resistance to rice stripe	卡萨拉斯 Kasalath		√		√				√	√
Xa21	增强白叶枯病抗性 Enhancing bacterial blight resistance	12SNP	√	√		√	√	√	√	√	√
Rymv1	抗黄色斑驳病毒病 Resistance to yellow mottle virus disease	日本晴 Nipponbare	√	√	√	√	√	√	√	√	√
NRT1.1B	提高氮利用效率 Improving nitrogen use efficiency (NUE)	9311	√		√	√				√	√
qLTG3-1	提高种子低温下发芽势 Improving seed germination potential under low temperature conditions	日本晴 Nipponbare	√	√	√	√	√	√	√
OsFRO1	铁耐受Iron tolerance	茉莉香米KDML105	√	√	√	√	√	√	√	√
qUVR-10	增强光修复活性 Enhancing photorepair activity	笹锦Sasanishiki	√			√	√		√
Cold1	冷敏感Cold-sensitive	9311								√	√
OsHESO1	延迟抽穗 Delayed heading	单倍型B Haplotype B	√	√	√	√	√	√	√	√	√
Hd3a	促进抽穗 Promoting heading	日本晴 Nipponbare	√	√	√	√	√	√	√	√	√
OsGATA28	延迟抽穗 Delayed heading	单倍型C Haplotype C			√
Hd6	延迟水稻抽穗 Delayed heading	日本晴 Nipponbare		√	√		√	√
Hd17	延迟抽穗 Delayed heading	越光 Koshihikari		√	√		√	√		√
Hd1	促进抽穗Promoting heading	卡萨拉斯Kasalath								√	√
Rf2	育性恢复Fertility restoration	卡萨拉斯Kasalath		√		√
SaF	广亲和(粳稻亲和) Wide compatibility (japonica-compatibility)	日本晴 Nipponbare	√	√	√	√	√	√	√	√
S5	广亲和(籼稻亲和) Wide compatibility (indica-compatibility)	南京11, 珍汕97 Nanjing 11, Zhenshan 97								√	√
Sd1	半矮秆Semi-dwarf	DGWG-type		√						√	√
Sdt97	半矮秆Semi-dwarf	Y98149		√		√		√			√
TAC1	分蘖角度增大 Reducing tiller angle	IR24								√	√
sh4	非落粒Non-shattering	日本晴 Nipponbare	√	√	√	√	√	√	√	√	√