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

Abstract

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)

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.

Figures/Tables 8

Fig. 1

Fig. 2

Table 1

Fig. 3

Fig. 4

Table 2

Candidate genes located in the qAG8 and qAG12 QTL region"

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	—

Table 2

Fig. 5

Fig. 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

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

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