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

Abstract

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

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

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

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