水稻耐厌氧萌发QTL鉴定及候选基因挖掘

doi:10.3864/j.issn.0578-1752.2026.19.002

中国农业科学 ›› 2026, Vol. 59 ›› Issue (19): 4208-4220.doi: 10.3864/j.issn.0578-1752.2026.19.002

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

水稻耐厌氧萌发QTL鉴定及候选基因挖掘

杨惠娟¹^,²(), 刘祎凡², 余晓蔓², 黄丹霖², 陈丹丹², 舒亚洲², 魏华², 贺慧英², 商连光²(), 袁巧玲²()

¹ 青岛农业大学，山东青岛 266000
² 中国农业科学院（深圳）农业基因组研究所/农业农村部基因组数据分析重点实验室/岭南现代农业科学与技术广东省实验室深圳分中心/基因组多维解析技术全国重点实验室，广东深圳 518120

收稿日期:2026-02-10 接受日期:2026-04-07 出版日期:2026-10-01 发布日期:2026-10-10
通信作者:
袁巧玲，E-mail：yuanqiaoling@caas.cn。
商连光，E-mail：shanglianguang@caas.cn
联系方式: 杨惠娟，E-mail：18304892416@163.com。
基金资助:
国家重点研发计划(2024YFF1000400); 中国农业科学院科技创新工程(CAAS-CSIAF-202303)

Identification of QTLs and Exploration of Candidate Genes Conferring Anaerobic Germination Tolerance in Rice

YANG HuiJuan¹^,²(), LIU YiFan², YU XiaoMan², HUANG DanLin², CHEN DanDan², SHU YaZhou², WEI Hua², HE HuiYing², SHANG LianGuang²(), YUAN QiaoLing²()

¹ Qingdao Agricultural University, Qingdao 266000, Shandong
² Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences/Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs/Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture/State Key Laboratory of Genome and Multi-omics Technologies, Shenzhen 518120, Guangdong

Received:2026-02-10 Accepted:2026-04-07 Published:2026-10-01 Online:2026-10-10

摘要/Abstract

摘要：

【目的】直播稻生产中，种子在厌氧条件下萌发率低、出苗不齐，制约其稳产性和推广面积。解析水稻厌氧萌发的遗传调控机制，发掘控制胚芽鞘伸长能力的关键基因，为耐淹直播稻品种选育提供基因资源。【方法】从237份供试材料中筛选出69份材料进行厌氧胚芽鞘长度和厌氧成苗率检测，发现2个性状呈显著正相关，厌氧胚芽鞘长度可作为该群体厌氧成苗率潜力的表型鉴定指标；通过厌氧萌发处理，获得237份水稻泛基因组群体材料的厌氧胚芽鞘长度表型，将表型与高密度SNP标记进行全基因组关联分析（GWAS），挖掘控制水稻耐厌氧萌发的关键遗传位点；通过基因功能注释、转录组分析和基因单倍型分析，筛选候选基因。【结果】对69份材料进行厌氧胚芽鞘长度和厌氧成苗率检测，结果显示，胚芽鞘长度与田间模拟直播淹水成苗率呈极显著正相关（r²=0.4533），证实胚芽鞘伸长能力可作为耐厌氧萌发筛选的有效指标。对237份水稻泛基因组群体材料的厌氧胚芽鞘和高密度SNP进行GWAS分析，在水稻第8和第12染色体上分别鉴定到1个新的显著关联位点，均为未见报道的新位点。将位点命名为qAG8和qAG12，在qAG8和qAG12位点区间分别检测到46和48个基因，利用基因功能注释分别在qAG8和qAG12位点筛选出29和14个具有功能注释的基因。整合转录组分析与单倍型分析，进一步筛选出4个可能与水稻耐厌氧萌发相关的候选基因：LOC_Os08g39210（编码细胞壁相关激酶OsWAK74，定位于细胞壁，负调控细胞增殖）、LOC_Os08g39290（含EF-hand结构域，可能参与钙信号转导）、LOC_Os08g39550（编码多聚半乳糖醛酸酶抑制蛋白，定位于细胞壁）和LOC_Os12g39830（水稻细胞周期蛋白CycD5;2，参与细胞周期调控）。【结论】成功在第8和第12染色体上鉴定到2个新的耐厌氧萌发遗传位点；并通过转录组和单倍型分析，获得4个水稻厌氧萌发候选新基因。

关键词: 水稻, 耐厌氧萌发, 胚芽鞘长度, 成苗率, 全基因组关联分析

Abstract:

【Objective】In direct-seeded rice production, low germination rates and uneven emergence under anaerobic conditions are major bottlenecks limiting yield stability and cultivation area. This study aims to elucidate the genetic regulation of anaerobic germination in rice and identify key genes controlling coleoptile elongation, thereby providing genetic resources for breeding submergence-tolerant direct-seeded rice varieties.【Method】Sixty-nine of 237 accessions were selected to measure anaerobic coleoptile length and seedling establishment rate, and the correlation between the two traits was evaluated. After anaerobic germination treatment, coleoptile length data was collected from all 237-rice pan-genome accessions. A genome-wide association study (GWAS) was performed using these phenotypic data together with high-density SNP markers to identify genetic loci underlying tolerance to anaerobic germination. Candidate genes were further screened through functional annotation, transcriptome analysis, and haplotype analysis.【Result】Coleoptile length was highly significantly correlated with seedling establishment rate (r²=0.4533), confirming that coleoptile elongation is a reliable indicator for anaerobic germination tolerance. GWAS identified two novel significant association loci on chromosomes 8 and 12, named qAG8 and qAG12, neither of which has been reported previously. Within these intervals, 46 and 48 genes were detected, respectively; after functional annotation, 29 genes from qAG8 and 14 from qAG12 were retained. Integration of transcriptome and haplotype analyses revealed four candidate genes potentially involved in anaerobic germination: LOC_Os08g39210 (encoding a cell wall-associated kinase OsWAK74, localized to the cell wall and negatively regulating cell proliferation), LOC_Os08g39290 (containing an EF-hand domain, possibly involved in calcium signaling), LOC_Os08g39550 (encoding a polygalacturonase inhibitor protein, localized to the cell wall), and LOC_Os12g39830 (a rice cyclin CycD5;2, involved in cell cycle regulation).【Conclusion】Two novel loci (qAG8 and qAG12) conferring tolerance to anaerobic germination were identified on chromosomes 8 and 12, and four candidate genes were uncovered through transcriptome and haplotype analyses. These findings provide new insights into the genetic basis of anaerobic germination and offer potential molecular targets for marker-assisted breeding of direct-seeded rice.

Key words: rice, anaerobic germination tolerance, coleoptile length, seedling establishment rate, genome-wide association study (GWAS)

杨惠娟, 刘祎凡, 余晓蔓, 黄丹霖, 陈丹丹, 舒亚洲, 魏华, 贺慧英, 商连光, 袁巧玲. 水稻耐厌氧萌发QTL鉴定及候选基因挖掘[J]. 中国农业科学, 2026, 59(19): 4208-4220.

YANG HuiJuan, LIU YiFan, YU XiaoMan, HUANG DanLin, CHEN DanDan, SHU YaZhou, WEI Hua, HE HuiYing, SHANG LianGuang, YUAN QiaoLing. Identification of QTLs and Exploration of Candidate Genes Conferring Anaerobic Germination Tolerance in Rice[J]. Scientia Agricultura Sinica, 2026, 59(19): 4208-4220.

图/表 8

图1

图2

表1

图3

图4

表2

qAG8与qAG12候选基因"

基因登录号 Accession	基因注释 Gene annotation	厌氧响应 Anaerobic response
LOC_Os08g39140	热激蛋白Heat shock protein	—
LOC_Os08g39160	甲酰基转移酶Formyl transferase, putative, expressed	—
LOC_Os08g39174	Ty1-copia反转录转座子蛋白Retrotransposon protein, putative, Ty1-copia subclass, expressed	—
LOC_Os08g39180	OsWAK受体样蛋白激酶OsWAK73 OsWAK receptor-like protein kinase OsWAK73, expressed	—
LOC_Os08g39210	壁相关激酶；类受体蛋白激酶 Wall-associated kinase 74; GRAIN WEIGHT AND NUMBER 1; receptor-like protein kinase	下调Down regulation
LOC_Os08g39220	OsWAK受体样蛋白激酶OsWAK75 OsWAK receptor-like protein kinase OsWAK75, expressed	—
LOC_Os08g39240	OsWAK受体样细胞质激酶OsWAK76 OsWAK receptor-like cytoplasmic kinase OsWAK76, expressed	—
LOC_Os08g39250	N6-腺嘌呤甲基转移酶样蛋白 ENHANCED DOWNY MILDEW 2-LIKE; N6-adenine methyltransferase-like (MTL) domain-containing protein	—
LOC_Os08g39270	细胞壁相关蛋白Fasciclin domain containing protein, expressed	—
LOC_Os08g39290	EF手型结构域蛋白家族EF hand family protein, expressed	上调Up regulation
LOC_Os08g39300	丝氨酸:乙醛酸氨基转移酶Serine: glyoxylate aminotransferase	—
LOC_Os08g39310	SWIB/MDM2结构域蛋白SWIB/MDM2 domain containing protein, expressed	—
LOC_Os08g39330	皮肤分泌蛋xP2前体Skin secretory protein xP2 precursor, putative, expressed	上调Up regulation
LOC_Os08g39350	甘油磷酸二酯磷酸二酯酶家族蛋白 Glycerophosphoryl diester phosphodiesterase family protein, putative, expressed	—
LOC_Os08g39370	柠檬酸转运蛋白Citrate transporter, putative, expressed	—
LOC_Os08g39380	β-1,2-木糖基转移酶β-1,2-xylT β-1,2-xylosyltransferase, β-1,2-xylT, reduced culm number11	—
LOC_Os08g39390	ZOS8-10:C2H2锌指蛋白ZOS8-10:C2H2 zinc finger protein, expressed	—
LOC_Os08g39420	假尿苷-5′-磷酸糖苷酶 Pseudouridine-5′-phosphate glycosidase; Ψ-5′-phosphate glycosidase; homologous to both yeiN and PUMY	—
LOC_Os08g39430	叶绿体前体类囊体腔19 kDa蛋白Thylakoid lumenal 19 kDa protein, chloroplast precursor, putative, expressed	—
LOC_Os08g39440	RNA结合蛋白RNA recognition motif containing protein, putative, expressed	—
LOC_Os08g39450	A20/AN1型锌指蛋白A20/AN1 zinc-finger protein; Zinc-finger containing stress-associated protein	—
LOC_Os08g39460	AGC激酶家族AGC_PVPK_like_CDK8.2-ACG kinases include homologs to PKA, PKG and PKC, expressed	—
LOC_Os08g39500	60S核糖体蛋白L31 60S ribosomal protein L31, putative, expressed	—
LOC_Os08g39540	锌指关节结构域蛋白Zinc knuckle domain containing protein, expressed	—
LOC_Os08g39550	多聚半乳糖醛酸酶抑制蛋白Polygalacturonase-inhibiting protein	上调Up regulation
LOC_Os08g39560	半胱氨酸蛋白酶家族蛋白OTU-like cysteine protease family protein, putative, expressed	—
LOC_Os08g39570	LRR结构域蛋白Leucine rich repeat family protein, expressed	—
LOC_Os08g39580	锌指关节结构域蛋白Zinc knuckle family protein, expressed	—
LOC_Os12g39750	保守假设蛋白Conserved hypothetical protein	—
LOC_Os12g39830	细胞周期蛋白Rice cyclin gene	下调Down regulation
LOC_Os12g39850	bHLH转录因子Root Hair Defective-Six Like (RSL) Class Ⅱ family of transcription factor; bHLH transcription factor; basic helix-loop-helix (bHLH) transcription factor	—
LOC_Os12g39860	磷酸核糖基转移酶Phosphoribosyl transferase, putative, expressed	—
LOC_Os12g39980	含驱动蛋白马达结构域蛋白Kinesin motor domain containing protein, putative, expressed	下调Down regulation
LOC_Os12g39990	Dof转录因子；单锌指蛋白Dof transcription factor; DNA binding with one finger protein	—
LOC_Os12g40070	B3 DNA结合结构域蛋白B3 DNA binding domain containing protein, expressed	—
LOC_Os12g40080	B3 DNA结合结构域蛋白B3 DNA binding domain containing protein, expressed	—
LOC_Os12g40090	B3 DNA结合结构域蛋白B3 DNA binding domain containing protein, expressed	—
LOC_Os12g40120	B3 DNA结合结构域蛋白 B3 DNA binding domain containing protein, expressed	—
LOC_Os12g40130	磷酸核糖基转移酶Phosphoribosyl transferase, putative, expressed	—
LOC_Os12g40140	含F-box结构域蛋白OsFBX457 F-box domain containing protein OsFBX457, expressed	—
LOC_Os12g40170	假设蛋白Hypothetical protein	—
LOC_Os12g40190	超大GTP结合蛋白Extra-large GTP-binding protein	—

表2

图5

图6

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品种 Accession	编号 No.	亚群 Subpopulation	有氧胚芽鞘长度 Aerobic coleoptile length (cm)	厌氧胚芽鞘长度 Anaerobic coleoptile length (cm)
9311	NH231	籼稻Indica	2.10	3.34
Taidongludao	NH168	粳稻Japonica	2.12	3.46
NCS 458::IRGC 62290-1	TG52	籼稻Indica	3.18	3.48
Zinuo	NH082	籼稻Indica	0.18	3.50
Nanoay P.A	NH033	粳稻Japonica	1.78	3.56
L 301B	NH133	籼稻Indica	1.90	3.58
2037(Rajahamsal)	NH011	籼稻Indica	1.52	3.62
RY2	NH232	粳稻Japonica	2.88	3.78
J34	NH045	籼稻Indica	1.66	3.82
LJ	TG7	粳稻Japonica	0.40	4.92

水稻耐厌氧萌发QTL鉴定及候选基因挖掘

Identification of QTLs and Exploration of Candidate Genes Conferring Anaerobic Germination Tolerance in Rice

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