水稻白叶枯病抗性QTL的挖掘与候选基因分析

doi:10.11983/CBB25059

植物学报 ›› 2025, Vol. 60 ›› Issue (5): 831-845.DOI: 10.11983/CBB25059 cstr: 32102.14.CBB25059

水稻白叶枯病抗性QTL的挖掘与候选基因分析

陈钧¹^,^†, 徐江民¹^,^†, 周逸楠¹, 江亚楠¹, 胡程翔¹, 金芊芸¹, 赵蓓蓓¹, 朱哲楠¹, 徐雨青¹, 张璐怡¹, 刘笑妍¹, 刘隽¹, 李三峰², 王跃星²^,^*(), 饶玉春¹^,^*()

¹浙江师范大学生命科学学院, 金华 321004
²中国水稻研究所水稻生物育种全国重点实验室, 杭州 310006

收稿日期:2025-04-08 接受日期:2025-06-03 出版日期:2025-09-10 发布日期:2025-06-10
通讯作者: *饶玉春, 博士/博士后, 教授, 博士生导师, “双龙学者”特聘教授, 浙江省“高校领军人才培养计划”高层次拔尖人才(2022年), 金华市青年拔尖人才(2023年), 浙江省发明协会理事、植物遗传专业委员会副主任, 中国作物学会会员, 浙江省遗传学会会员。主要从事水稻等禾谷类作物的分子遗传学研究。以第一作者或通讯作者身份在Science Bulletin和New Phytologist等权威期刊发表论文80余篇, 以合作者身份在Nature Plants、Proceedings of the National Academy of Sciences of the United States of America等杂志发表论文30余篇。主持转基因国家重大专项子课题、国家自然科学基金和浙江省自然科学基金等科研项目。授权国家发明专利25项(第一完成人)。ryc@zjnu.cn 王跃星, 博士, 研究员, 博士生导师, 中国水稻研究所超级稻育种创新团队首席科学家, 国家水稻改良中心副主任。入选国家高层次人才青年拔尖人才、浙江省高层次人才青年拔尖人才和“151”第二层次人才培养工程以及中国农业科学院“农科英才”杰出青年英才。主要从事水稻遗传育种工作, 已完成一系列水稻重要农艺性状基因的克隆和育种利用。以第一作者在Nature Genetics和Molecular Plant等国际著名期刊发表论文多篇。主持国家自然科学基金、浙江省自然科学基金杰出青年基金等项目。以第一或主要完成人选育水稻优质不育系和杂交水稻新品种7个, 获植物新品种权5项, 授权国家发明专利8项。荣获中国农学会青年科技奖。E-mail: wangyuexing@caas.cn
作者简介:^†共同第一作者
基金资助:
国家重点研发计划(2021YFA1300703);2025年国家级大学生创新创业训练计划支持项目(202510345055);2025年浙江省大学生科技创新活动计划暨新苗人才计划(2025R404A036)

Identification of Candidate Genes for Rice Resistance to Bacterial Blight via QTL Mapping and Gene Expression Analysis

Chen Jun¹^,^†, Xu Jiangmin¹^,^†, Zhou Yinan¹, Jiang Yanan¹, Hu Chengxiang¹, Jin Qianyun¹, Zhao Beibei¹, Zhu Zhenan¹, Xu Yuqing¹, Zhang Luyi¹, Liu Xiaoyan¹, Liu Jun¹, Li Sanfeng², Wang Yuexing²^,^*(), Rao Yuchun¹^,^*()

¹College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
²State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China

Received:2025-04-08 Accepted:2025-06-03 Online:2025-09-10 Published:2025-06-10
Contact: *E-mail: wangyuexing@caas.cn; ryc@zjnu.cn
About author:^†These authors contributed equally to this paper

摘要/Abstract

摘要： 水稻(Oryza sativa)白叶枯病是危害全球水稻生产的三大主要病害之一, 严重影响水稻的产量和品质。抗性基因的挖掘与利用是防治白叶枯病最有效的途径之一。为挖掘水稻白叶枯病抗性相关的数量性状位点(QTL), 以籼稻华占、粳稻热研2号及其构建的120个重组自交系(RILs)群体为实验材料, 在水稻分蘖盛期接种4种不同的白叶枯病致病小种并评价抗性表型。基于前期构建的高密度遗传图谱进行QTL定位, 共检测到19个QTLs, 其中最大LOD值为5.49。对检测到的QTL区间内候选基因进行筛选, 并利用qRT-PCR进行基因表达水平分析, 发现LOC_Os02g13270、LOC_Os02g13410、LOC_Os02g13420、LOC_Os02g13430和LOC_Os01g12130在双亲间的表达量差异显著, 且在接种白叶枯病菌后受诱导表达, 推测其为调控白叶枯病抗性的重点候选基因。研究结果为白叶枯病抗性相关基因的精细定位和克隆奠定了基础, 对于培育广谱抗病水稻品种有重要意义。

关键词: 水稻, 白叶枯病, QTL定位, 候选基因

Abstract: INTRODUCTION: Bacterial blight is one of the three major diseases that threaten global rice production, seriously damaging the yield and quality of rice. The utilization of resistance genes is one of the most effective ways to control bacterial blight. RATIONALE: To cultivate rice varieties with both resistance to bacterial blight and high-yield characteristics, stable and efficient resistance genes need to be identified and used. To identify quantitative trait locus (QTL) related to bacterial blight resistance in rice, this study used the indica rice HZ, the japonica rice Nekken2 and their 120 recombinant inbred lines (RILs) as experimental materials. Four different races of bacterial blight pathogens were inoculated at the tillering stage of rice and the resistance phenotypes were evaluated. RESULTS: Based on the high-density genetic map constructed previously, we identified 19 QTLs for resistance to rice bacterial blight, with the maximum limit of detection (LOD) value being 5.49. Candidate genes within the detected QTL intervals were screened based on their expression levels analyzed by qRT-PCR. LOC_Os04g01310 and LOC_ Os04g01320, which are related to the regulatory pathway of STK receptor protein, showed significant upregulated expression after inoculation treatment. Meanwhile, the expression levels of the MYB transcription factor family gene LOC_Os05g10690 and the gene LOC_Os01g12320 related to GDSL-like lipase/acylhydrolase showed an extremely significant increase after inoculation treatment. The expression levels of the candidate genes LOC_Os02g13270 (Mpv17/PMP22 family domain containing protein), LOC_Os02g13410 (leucine rich repeat family protein), LOC_ Os02g13420 (leucine rich repeat receptor protein kinase EXS precursor), LOC_Os02g13430 (receptor-like protein kinase 5 precursor) and LOC_Os01g12130 (enodulin MtN3 family protein) were significantly different between the two parents and were induced after inoculation with the bacterial blight pathogen. CONCLUSION: By QTL mapping and gene expression analysis, we identified several candidate genes related to rice bacterial blight resistance. These results provide clues for further fine mapping and cloning of new bacterial blight resistance genes for future breeding of rice varieties with strong resistance to bacterial blight.

QTL mapping of resistance to bacterial blight in recombinant inbred lines of rice. QTLs can be used to reveal the structure of complex quantitative traits and identify candidate genes. Based on a high-density genetic map, a total of 19 QTLs were co-located and multiple candidate genes were screened out. To further locate and clone the related genes and lay a theoretical foundation for breeding new high-yield and disease-resistant rice varieties.

Key words: Oryza sativa, bacterial blight, QTL mapping, candidate genes

陈钧, 徐江民, 周逸楠, 江亚楠, 胡程翔, 金芊芸, 赵蓓蓓, 朱哲楠, 徐雨青, 张璐怡, 刘笑妍, 刘隽, 李三峰, 王跃星, 饶玉春. 水稻白叶枯病抗性QTL的挖掘与候选基因分析. 植物学报, 2025, 60(5): 831-845.

Chen Jun, Xu Jiangmin, Zhou Yinan, Jiang Yanan, Hu Chengxiang, Jin Qianyun, Zhao Beibei, Zhu Zhenan, Xu Yuqing, Zhang Luyi, Liu Xiaoyan, Liu Jun, Li Sanfeng, Wang Yuexing, Rao Yuchun. Identification of Candidate Genes for Rice Resistance to Bacterial Blight via QTL Mapping and Gene Expression Analysis. Chinese Bulletin of Botany, 2025, 60(5): 831-845.

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Primer name	Forward primer (5'-3')	Reverse primer (5′-3′)
OsActin	TGGCATCTCAGCACATTCC	TGCACAATGGATGGGTCAGA
LOC_Os02g13270	TGGCCATTTCCTCCATAAAG	TTGGTATCCTTCTTCCCTTTGA
LOC_Os02g13350	AATGTCCATCGCACTGTTCA	GCTGCTTCAATCTCGGACTC
LOC_Os02g13410	TCAATTATCCGGCAGACTCC	TGCCTGTGCTACTGATCCTG
LOC_Os02g13420	TGCTCAGCTTTGGAGTTCCT	CCCAACGATAGCCTGTCAAT
LOC_Os02g13430	CCGATGAGTGATGTTCTCCA	CGCTATGTGTTCCGCTATGA
LOC_Os04g01310	TAATGGTACCAAGGGGGTGA	GAAGGCGATTCGTTGGATAA
LOC_Os04g01320	AGCCCGACTTCAAGCTAACA	ATGGATTCATTGGCATGGTT
LOC_Os01g12130	AATGGTGCTACCCGTTCTTG	CCGTGCGTATGAAACAGAAA
LOC_Os01g12160	CATCGCCTACTTCGAGTTCA	CATGCATGATGAGGACGAAC
LOC_Os01g12320	AGGTCCCGGAAAATACCACT	ATGGCATGAAGCCAATCATC
LOC_Os05g10690	TGGTGAAGGAGGAGGTTGTC	TAGCTCCAGGTCAGGCATCT

Primer name	Forward primer (5'-3')	Reverse primer (5′-3′)
OsActin	TGGCATCTCAGCACATTCC	TGCACAATGGATGGGTCAGA
LOC_Os02g13270	TGGCCATTTCCTCCATAAAG	TTGGTATCCTTCTTCCCTTTGA
LOC_Os02g13350	AATGTCCATCGCACTGTTCA	GCTGCTTCAATCTCGGACTC
LOC_Os02g13410	TCAATTATCCGGCAGACTCC	TGCCTGTGCTACTGATCCTG
LOC_Os02g13420	TGCTCAGCTTTGGAGTTCCT	CCCAACGATAGCCTGTCAAT
LOC_Os02g13430	CCGATGAGTGATGTTCTCCA	CGCTATGTGTTCCGCTATGA
LOC_Os04g01310	TAATGGTACCAAGGGGGTGA	GAAGGCGATTCGTTGGATAA
LOC_Os04g01320	AGCCCGACTTCAAGCTAACA	ATGGATTCATTGGCATGGTT
LOC_Os01g12130	AATGGTGCTACCCGTTCTTG	CCGTGCGTATGAAACAGAAA
LOC_Os01g12160	CATCGCCTACTTCGAGTTCA	CATGCATGATGAGGACGAAC
LOC_Os01g12320	AGGTCCCGGAAAATACCACT	ATGGCATGAAGCCAATCATC
LOC_Os05g10690	TGGTGAAGGAGGAGGTTGTC	TAGCTCCAGGTCAGGCATCT

Race	Significance test for all traits between their parents (t-test)			Variation for all traits tested in the RILs population
Race	HZ	Nekken2	P value	Means±SD	Range	Skewness	Kurtosis
P6	32.57±1.92	19.25±1.78	5.66E-08	22.01±7.71	0.50-46.83	0.33	1.54
P10	4.08±0.58	2.92±0.38	2.11E-03	4.43±2.47	0.50-17.08	2.27	7.93
C5	21.50±2.49	10.63±2.59	1.59E-04	14.89±5.98	0.45-32.40	0.19	0.62
T1	11.83±1.29	15.25±1.51	1.78E-03	12.03±6.61	0.60-30.25	0.47	-0.42

Race	Significance test for all traits between their parents (t-test)			Variation for all traits tested in the RILs population
Race	HZ	Nekken2	P value	Means±SD	Range	Skewness	Kurtosis
P6	32.57±1.92	19.25±1.78	5.66E-08	22.01±7.71	0.50-46.83	0.33	1.54
P10	4.08±0.58	2.92±0.38	2.11E-03	4.43±2.47	0.50-17.08	2.27	7.93
C5	21.50±2.49	10.63±2.59	1.59E-04	14.89±5.98	0.45-32.40	0.19	0.62
T1	11.83±1.29	15.25±1.51	1.78E-03	12.03±6.61	0.60-30.25	0.47	-0.42

Race	QTL locus	Chromo- some	Physical distance (bp)	Position of support (cM)	Limit of detection	Overlapped with known genes/QTL
P6	qP6-2	2	6987519-7215671	29.95-30.93	2.82	Novel
	qP6-6	6	22540408-24198880	96.62-103.73	2.10	Xa27 (Gu et al., 2004)
P10	qP10-4.1	4	46622-253174	0.20-1.09	4.09	Novel
	qP10-4.2	4	21662809-22843728	92.86-97.92	4.12	OsABA1 (Zhang et al., 2019)
	qP10-4.3	4	26889242-31662274	115.27-135.73	5.49	Xa1 (Yoshimura et al., 1998); Xa2 (He et al., 2006); Xa14 (Bao et al., 2010, in Chinese); Xa38 (Bhasin et al., 2012)
	qP10-5	5	5860546-5932385	25.12-25.43	2.17	Novel
	qP10-8	8	27210008-27435407	116.64-117.66	2.34	OsPDR1 (Zhang et al., 2020)
	qP10-9	9	11237877-11654883	48.17-49.96	2.50	Novel
	qP10-11	11	4880924-5893190	20.92-25.26	3.23	Novel
	qP10-12.1	12	3541703-5035843	15.18-21.59	3.52	OsSGS3a (Gu et al., 2023)
	qP10-12.2	12	9212254-11302449	39.49-48.45	3.47	ELL1 (Tian et al., 2020)
C5	qC5-1	1	6568005-6737416	28.16-28.88	2.41	Novel
	qC5-8	8	26765295-26912750	114.74-115.37	2.58	Xa-45(t) (Neelam et al., 2020)
T1	qT1-1.1	1	2317764-2649258	9.94-11.36	2.25	Novel
	qT1-1.2	1	5747788-6006625	24.64-25.75	2.17	TUT1 (Zhang et al., 2019)
	qT1-3	3	28465343-29876347	122.02-128.07	2.24	Xa11 (Goto et al., 2009); OsSLR1 (De Vleesschauwer et al., 2016)
	qT1-4	4	23759183-23831009	101.85-102.16	2.48	Novel
	qT1-5	5	5860546-5932385	25.12-25.43	2.51	Novel
	qT1-12	12	19717421-19889567	84.52-85.26	2.12	OsPR10a (Huang et al., 2016)

水稻白叶枯病抗性QTL的挖掘与候选基因分析

Identification of Candidate Genes for Rice Resistance to Bacterial Blight via QTL Mapping and Gene Expression Analysis

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QTL locus	Chromosome	Gene ID	Functional annotation
qP6-2	2	LOC_Os02g13270	Mpv17/PMP22 family domain containing protein
		LOC_Os02g13350	NUDIX family
		LOC_Os02g13410	Leucine-rich repeat family protein
		LOC_Os02g13420	Leucine-rich repeat receptor protein kinase EXS precursor
		LOC_Os02g13430	Receptor-like protein kinase 5 precursor
qP10-4.1	4	LOC_Os04g01310	Serine/threonine-protein kinase receptor precursor
		LOC_Os04g01320	Serine/threonine-protein kinase receptor precursor
qC5-1	1	LOC_Os01g12130	Enodulin MtN3 family protein
		LOC_Os01g12160	Ndole-3-acetic acid-amido synthetase
		LOC_Os01g12320	GDSL-like lipase/acylhydrolase
qT1-5	5	LOC_Os05g10690	Myb transcription factor

Gene ID	Length (bp)	Number of amino acids (aa)	Molecular weight (kDa)	Theoretical pI	Instabiliy index	Grand average of hydropathicity	Subcellular location
LOC_Os02g13270	3105	205	23.61	10.47	55.17	-0.063	Cytoplasmic
LOC_Os02g13350	2612	297	32.69	5.47	44.45	0.056	Nuclear
LOC_Os02g13410	2761	508	57.34	8.05	51.52	-0.406	Nuclear
LOC_Os02g13420	3070	611	66.79	5.75	29.68	0.077	Extracellular
LOC_Os02g13430	3541	1004	110.39	5.21	38.88	-0.049	Nuclear
LOC_Os04g01310	2758	828	91.62	6.01	40.39	-0.016	Endoplasmic reticulum
LOC_Os04g01320	2927	813	90.71	6.15	43.94	-0.170	Endoplasmic reticulum
LOC_Os01g12130	1563	252	28.17	9.25	36.00	0.538	Endoplasmic reticulum
LOC_Os01g12160	5501	591	64.19	5.90	39.85	-0.059	Cytoplasmic
LOC_Os01g12320	3688	379	40.97	5.13	41.35	0.061	Cytoplasmic
LOC_Os05g10690	3818	287	30.46	9.35	64.91	-0.298	Mitochondrial

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