华南籼稻稻瘟病抗性QTL鉴定与候选基因挖掘

doi:10.3864/j.issn.0578-1752.2025.14.001

中国农业科学 ›› 2025, Vol. 58 ›› Issue (14): 2707-2719.doi: 10.3864/j.issn.0578-1752.2025.14.001

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

华南籼稻稻瘟病抗性QTL鉴定与候选基因挖掘

郑敏华¹^,²(), 陈洛¹^,²(), 邢甲乐¹, 谢月兰³, 姜先芽³, 聂帅¹, 蔡甫格⁴, 巫浩翔¹, 陆展华¹, 孙伟², 霍兴¹, 白嵩¹, 赵均良¹, 杨武¹^,^*()

¹ 广东省农业科学院水稻研究所/广东省水稻科学技术重点实验室/广东省水稻工程实验室/农业农村部华南优质稻遗传育种实验室（部省共建），广州 510640
² 仲恺农业工程学院农业与生物学院，广州 510225
³ 阳江市农业科学研究所，广东阳江 529500
⁴ 安顺市农业科学院，贵州安顺 562100

收稿日期:2025-01-24 接受日期:2025-03-24 出版日期:2025-07-16 发布日期:2025-07-17
通信作者:
杨武，E-mail：yangwu@gdaas.cn
联系方式: 郑敏华，E-mail：Zheng1802040210@163.com。陈洛，E-mail：13229416940@163.com。郑敏华和陈洛为同等贡献作者。
基金资助:
广东省重点领域研发计划(2022B0202060002); 科技创新战略（农业科研主力军建设）专项(R2023PY-JX001); 广东省农业科学院水稻研究所优谷计划(2022YG05); 广东省水稻科学技术重点实验室(2023B1212060042)

Genome-Wide Association Study and Genetic Improvement Study of Rice Blast Resistance

ZHENG MinHua¹^,²(), CHEN Luo¹^,²(), XING JiaLe¹, XIE YueLan³, JIANG XianYa³, NIE Shuai¹, CAI FuGe⁴, WU HaoXiang¹, LU ZhanHua¹, SUN Wei², HUO Xing¹, BAI Song¹, ZHAO JunLiang¹, YANG Wu¹^,^*()

¹ Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640
² College of Agriculture ＆ Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225
³ Yangjiang Institute of Agricultural Sciences, Yangjiang 529500, Guangdong
⁴ Anshun Academy of Agricultural Sciences, Anshun 562100, Guizhou

Received:2025-01-24 Accepted:2025-03-24 Published:2025-07-16 Online:2025-07-17

摘要/Abstract

摘要：

【目的】稻瘟病严重危害水稻的安全生产。由于稻瘟病菌的高度变异特性，以及当前水稻育种亲本的遗传背景狭窄，使得当前水稻稻瘟病抗性的遗传改良进展缓慢。利用种质资源鉴定稻瘟病抗性基因位点，有助于水稻稻瘟病抗性的遗传改良。【方法】利用已测序的265份籼稻品种（包括120份国际资源品种和145份华南地区栽培品种）进行田间稻瘟病抗性鉴定，通过全基因组关联分析鉴定稻瘟病抗性QTL，分析稻瘟病抗性QTL不同单倍型对稻瘟病抗性的效应，结合水稻基因组注释对新鉴定的稻瘟病抗性QTL进行候选基因分析。【结果】田间抗性评价筛选出穗瘟抗性和叶瘟抗性均高抗的材料47份，包括18份国际资源品种和29份华南地区栽培品种。全基因组关联分析共鉴定到9个稻瘟病抗性QTL，分布在水稻第1、5、6、11和12染色体上，其中，有4个QTL与前人研究报道的稻瘟病抗性基因共定位，有5个QTL为新鉴定位点。这9个QTL峰值SNP的等位变异衍生的不同单倍型材料的稻瘟病抗性存在差异，其中8个QTL的高抗性单倍型在华南地区栽培品种中的分布高于国际资源品种，只有qPB11的高抗性单倍型在华南地区栽培品种的分布频率（1%）低于其在国际资源品种的分布频率（16%）。在新鉴定QTL的候选基因分析中，挖掘到4个编码NBS-LRR抗病蛋白和4个编码NB-ARC结构域蛋白的候选基因，在第11染色体27.22—27.35 Mb的区间内成簇分布。【结论】华南地区栽培品种比国际资源品种具有更强的稻瘟病抗性。qPB1-1、qPB1-2、qPB1-3、qPB5、qPB6、qPB12-1和qLB12/qPB12-2的高抗性单倍型在华南地区栽培品种的遗传改良过程中受到选择。qPB11候选区间内有编码NBS-LRR抗病蛋白和NB-ARC结构域蛋白的基因，有可能为新的稻瘟病抗性基因。

关键词: 水稻, 稻瘟病, 种质资源, 全基因组关联分析, 数量性状位点, 遗传改良

Abstract:

【Objective】Rice blast critically compromises rice production. The genetic enhancement of blast resistance remains challenging due to pathogen variability and limited genetic diversity in breeding parents. This study seeks to accelerate resistance breeding by identifying novel resistance loci through systematic germplasm characterization. 【Method】A panel of 265 sequenced indica rice accessions (including 120 international germplasms and 145 cultivars from South China) underwent field-based blast resistance evaluation. Genome-wide association study (GWAS) was subsequently employed to identify blast resistance quantitative trait loci (QTL). Haplotype effects of these QTL on blast resistance were analyzed, and candidate genes within newly identified QTL regions were predicted using rice genome annotation. 【Result】Field resistance evaluation identified 47 accessions (18 international germplasms and 29 cultivars from South China) exhibiting high resistance to both panicle and leaf blast. GWAS detected nine blast resistance QTL distributed across chromosomes 1, 5, 6, 11, and 12, respectively. Among them, four QTL was co-localized with previously reported blast resistance genes and five QTL were newly identified. Haplotype analysis revealed significant resistance variations associated with peak SNP alleles, with eight QTL showing higher frequency of resistant haplotypes in cultivars from South China compared to international germplasms. Notably, the qPB11 locus demonstrated an inverse distribution pattern, where its resistant haplotype frequency was substantially lower in cultivars from South China (1%) than in international germplasm (16%). Candidate gene analysis within novel QTL regions identified four NBS-LRR disease resistance proteins and four NB-ARC domain-containing proteins, with eight candidate genes clustered within a 27.22-27.35 Mb interval on chromosome 11.【Conclusion】Cultivars from South China exhibit superior blast resistance compared to international germplasms. The high-resistance haplotypes of qPB1-1, qPB1-2, qPB1-3, qPB5, qPB6, qPB12-1, and qLB12/qPB12-2 have been preferentially selected during the genetic improvement of cultivars from South China. Furthermore, the qPB11 locus harbors genes encoding NBS-LRR disease-resistant proteins and NB-ARC domain-containing proteins, representing new potential resistance gene for rice blast disease.

Key words: rice, rice blast, germplasm, genome-wide association study, QTL (quantitative trait locis), genetic improvement

郑敏华, 陈洛, 邢甲乐, 谢月兰, 姜先芽, 聂帅, 蔡甫格, 巫浩翔, 陆展华, 孙伟, 霍兴, 白嵩, 赵均良, 杨武. 华南籼稻稻瘟病抗性QTL鉴定与候选基因挖掘[J]. 中国农业科学, 2025, 58(14): 2707-2719.

ZHENG MinHua, CHEN Luo, XING JiaLe, XIE YueLan, JIANG XianYa, NIE Shuai, CAI FuGe, WU HaoXiang, LU ZhanHua, SUN Wei, HUO Xing, BAI Song, ZHAO JunLiang, YANG Wu. Genome-Wide Association Study and Genetic Improvement Study of Rice Blast Resistance[J]. Scientia Agricultura Sinica, 2025, 58(14): 2707-2719.

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品种名称Variety name	穗瘟抗性级别Panicle blast resistance level	叶瘟抗性级别Leaf blast resistance level
IRGC121611	1.0	0.0
IRGC121434	1.0	0.0
IRGC121852	1.0	0.0
IRGC121759	1.0	0.0
IRGC120918	1.0	0.0
IRGC121705	1.0	0.0
IRGC121901	1.0	0.0
IRGC121920	1.0	0.0
IRGC121919	1.0	0.0
IRGC120977	1.0	0.0
IRGC121053	1.0	0.0
IRGC120903	1.0	0.0
IRGC121650	1.0	0.0
IRGC121002	1.0	0.0
IRGC120981	1.0	0.0
IRGC121001	1.0	0.7
IRGC120983	1.0	0.7
IRGC121778	1.0	0.7
香秀占Xiangxiuzhan	1.0	0.0
银湖香占2号Yinhuxiangzhan2	1.0	0.0
华占Huazhan	1.0	0.0
贵育9号Guiyu9	1.0	0.0
贵育12 Guiyu12	1.0	0.0
香丝苗Xiangsimiao	1.0	0.0
福香占Fuxiangzhan	1.0	0.0
红荔丝苗Honglisimiao	1.0	0.0
广恢1521 Guanghui1521	1.0	0.0
R290	1.0	0.0
R3301	1.0	0.0
深恢9516-1 Shenhui9516-1	1.0	0.0
五山丝苗Wushansimiao	1.0	0.0
V5230♂	1.0	0.0
粤农丝苗Yuenongsimiao	1.0	0.0
五乡B WuxiangB	1.0	0.0
吉丰B JifengB	1.0	0.0
莉丝Lisi	1.0	0.0
蒂占Dizhan	1.0	0.0
广恢736 Guanghui736	1.0	0.0
广恢138 Guanghui138	1.0	0.0
赣香占1号Ganxiangzhan1	1.0	0.0
粤美占Yuemeizhan	1.0	0.0
广恢792 Guanghui792	1.0	0.0
广恢7170 Guanghui7170	1.0	0.0
R390	1.0	0.7
黄广油占Huangguangyouzhan	1.0	0.7
野香B YexiangB	1.0	0.7
晶美丝苗Jingmeisimiao	1.0	1.0

稻瘟病抗性QTL Rice blast resistance QTL	数量性状基因座 Quantitative trait locus	染色体Chromosome	峰值SNP Peak SNP	BH P值 BH P value	等位变异 Allelic variation	共定位QTL/基因 Co-localized QTL/gene	参考文献Reference
穗瘟抗性QTL Panicle blast resistance QTL	qPB1-1	1	5475858	1.41E-06	C/T
	qPB1-2	1	33075256	2.69E-05	C/T	Pi64, Pi37, Pish, SDS2	[22-25]
	qPB1-3	1	35182780	3.45E-06	C/T	OsWRKY22, OsExo70B1	[26-27]
	qPB5	5	13708912	3.08E-06	A/G
	qPB6	6	10431287	1.34E-05	A/G	Pid4, Pizh	[4,28]
	qPB11	11	27184395	5.98E-06	C/T
	qPB12-1	12	10959080	1.64E-05	C/T	Pi-ta, Ptr	[29-30]
	qPB12-2	12	14158887	4.23E-07	G/T
叶瘟抗性QTL Leaf blast resistance QTL	qLB12	12	14158887	9.00E-06	G/T

华南籼稻稻瘟病抗性QTL鉴定与候选基因挖掘

Genome-Wide Association Study and Genetic Improvement Study of Rice Blast Resistance

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