Identification of New Resistance Loci Against Sheath Blight Disease in Rice Through Genome-Wide Association Study

doi:10.1016/j.rsci.2018.12.002

Abstract

Abstract:

Sheath blight (SB) caused by the soil borne pathogen Rhizoctonia solani is one of the most serious global rice diseases. Breeding resistant cultivar is the most economical and effective strategy to control the disease. However, no rice varieties are completely resistant to SB, and only a few reliable quantitative trait loci (QTLs) linked with SB resistance have been identified to date. In this study, we conducted a genome-wide association study (GWAS) of SB resistance using 299 varieties from the rice diversity panel 1 (RDP1) that were genotyped using 44 000 high-density single nucleotide polymorphism (SNP) markers. Through artificial inoculation, we found that only 36.5% of the tested varieties displayed resistance or moderate resistance to SB. In particular, the aromatic and aus sub-populations displayed higher SB resistance than the tropical japonica (TRJ), indica and temperate japonica sub-populations. Seven varieties showed similar resistance levels to the resistant control YSBR1. GWAS identified at least 11 SNP loci significantly associated with SB resistance in the three independent trials, leading to the identification of two reliable QTLs, qSB-3 and qSB-6, on chromosomes 3 and 6. Using favorable alleles or haplotypes of significantly associated SNP loci, we estimated that both QTLs had obvious effects on reducing SB disease severity and can be used for enhancing SB resistance, especially in improving SB resistance of TRJ sub-population rice varieties. These results provided important information and genetic materials for developing SB resistant varieties through breeding.

Key words: genome-wide association study, quantitative trait locus, rice, sheath blight, plant height

Zongxiang Chen, Zhiming Feng, Houxiang Kang, Jianhua Zhao, Tianxiao Chen, Qianqian Li, Hongbing Gong, Yafang Zhang, Xijun Chen, Xuebiao Pan, Wende Liu, Guoliang Wang, Shimin Zuo. Identification of New Resistance Loci Against Sheath Blight Disease in Rice Through Genome-Wide Association Study[J]. Rice Science, 2019, 26(1): 21-31.

Figures/Tables 13

References 63

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Source of variance	df	SS	MS	F-value	P-value
Replication	1	0.182	0.182	3.801	0.123
Cultivar	4	5.352	1.338	27.905	0.004
Error	4	0.192	0.048
Total	9	5.726

Source of variance	df	SS	MS	F-value	P-value
Replication	1	0.182	0.182	3.801	0.123
Cultivar	4	5.352	1.338	27.905	0.004
Error	4	0.192	0.048
Total	9	5.726

Source of variance	df	SS	MS	F-value	P-value
Replication	2	3.707	1.853	1.418	0.243
Cultivar	298	1426.529	4.919	3.763	0
Error	580	758.17	1.307
Total	880	2188.405

Source of variance	df	SS	MS	F-value	P-value
Replication	2	3.707	1.853	1.418	0.243
Cultivar	298	1426.529	4.919	3.763	0
Error	580	758.17	1.307
Total	880	2188.405

Cultivars	Means of sheath blight disease scores	Significant difference on 5% level
Lemont	8.29 ±0.79	a
WYJ3	5.49 ±0.13	b
Jasmine85	4.26 ±0.08	c
C418	3.84 ±0.09	c
YSBR1	2.86 ±0.10	d