水稻种质资源稻瘟病抗性全基因组关联分析

doi:10.3724/SP.J.1006.2023.22024

Abstract

Abstract:

Rice blast is one of the major fungal diseases that threaten rice production worldwide. To improve rice blast resistance, identifying blast resistant genes and introgressing them into elite rice varieties is an effective way. In this study, a panel of 212 xian accessions and 235 geng accessions collected worldwide were evaluated for resistance against five blast isolates at seedling stage. All of them showed large variations in resistance against five isolates, and 8 xian and 12 geng accessions were detected to present resistance to all five blast isolates. Using genome-wide association strategy, a total of 43 QTLs were identified for resistance to five isolates in mix population (xian subpopulation and geng subpopulation), including 9, 4, 14, 14, and 2 QTLs for GD00-193, GD08-T19, GD17-CQ16, HB1708, and HLJ13-856, respectively. Among them, 12 resistant QTLs were detected only in xian rice sub-population, 7 only detected in geng rice sub-population, and 1 simultaneously detected in both sub-populations, indicating that blast resistance was generally better in xian than in geng rice, and there was obvious differentiation in blast resistance between xian and geng rice. A total of 11 QTLs affected resistance to two or more trains or were simultaneously identified in two or more populations, and 23 candidate genes were identified by candidate interval association analysis and haplotype analysis. Different resistance candidate genes had different frequencies in xian and geng populations. The results provide germplasm resources and favorable genes information for molecular improvement of blast resistance in rice varieties and the breeding and utilization strategies of different resistance genes.

Key words: blast resistance, germplasm, genome-wide association study, quantitative trait locus (QTLs), favorable allele

ZHOU Hai-Ping, ZHANG Fan, CHEN Kai, SHEN Cong-Cong, ZHU Shuang-Bing, QIU Xian-Jin, XU Jian-Long. Identification of rice blast resistance in xian and geng germplasms by genome- wide association study[J].Acta Agronomica Sinica, 2023, 49(5): 1170-1183.

Figures/Tables 7

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稻瘟病菌株 Blast isolate	混合群体 Mix population			籼稻 Xian rice			粳稻 Geng rice			P ^a
稻瘟病菌株 Blast isolate	平均值± 标准差 Mean ± SD	变幅 Range	变异系数 CV (%)	平均值± 标准差 Mean ± SD	变幅 Range	变异系数 CV (%)	平均值± 标准差 Mean ± SD	变幅 Range	变异系数 CV (%)	P ^a
GD00-193	4.13±1.98	1-8	47.96	4.61±1.97	1-8	42.75	3.69±1.98	1-8	53.64	1.51×10^-6
GD08-T19	2.87±1.33	1-7	46.29	2.87±1.39	1-7	48.39	2.83±1.23	1-6	43.43	0.76
GD17-CQ16	4.58±2.02	1-8	44.18	4.72±1.98	1-8	42.07	4.35±2.05	1-8	47.10	0.058
HB1708	4.21±2.00	1-7	47.48	4.41±1.93	1-7	43.90	4.08±1.96	1-7	48.17	0.076
HLJ13-856	3.27±1.42	1-7	43.39	3.02±1.35	1-6	44.66	3.52±1.45	1-7	41.26	2.02×10^-4

	GD00-193	GD08-T19	GD17-CQ16	HB1708
GD08-T19	0.09
	0.08
	0.11
GD17-CQ16	0.49^**	0.08
	0.46^**	0.09
	0.51^**	0.15^*
HB1708	0.62^**	0.12^*	0.46^**
	0.65^**	0.09	0.45^**
	0.60^**	0.11	0.49^**
HLJ13-856	-0.03	0.07	0.01	0.07
	-0.04	0.08	0.05	-0.06
	0.16^*	0.08	0.09	0.21^**

稻瘟病菌株 Blast isolate	QTL	混合群体/Mix population				籼稻 Xian rice				粳稻 Geng rice				前人克隆的基因 Previously cloned genes
稻瘟病菌株 Blast isolate	QTL	染色体 Chr.	峰值SNP Peak SNP	P值 P-value	贡献率 R²(%)	染色体 Chr.	峰值SNP Peak SNP	P值 P-value	贡献率 R²(%)	染色体 Chr.	峰值SNP Peak SNP	P值 P-value	贡献率 R²(%)	前人克隆的基因 Previously cloned genes
GD00-193	qGD001-1	1	1,552,373	4.69E-07	4.48
	qGD001-2	1	29,020,467	1.48E-08	17.94
	qGD001-3	1	33,145,916	9.94E-08	11.23									Pish/ Pi37 ^[27,28]
	qGD003	3	16,012,660	1.68E-06	2.78
	qGD004	4	34,840,786	2.41E-06	1.72
	qGD006					6	10,380,192	3.32E-06	13.49					Piz-t/Pi2/Pi9/Pi50/Pi-gm ^[23]
	qGD008	8	17,498,650	2.32E-07	15.86					8	17,465,932	3.67E-06	15.90
	qGD009	9	10,969,346	3.77E-07	2.89
	qGD011	11	15,664,938	2.18E-06	13.78
GD17-CQ16	qGD171-1					1	1,302,057	3.67E-07	19.43
	qGD171-2	1	1,568,573	8.78E-10	6.25
	qGD171-3	1	28,986,912	1.35E-07	9.70									pitp(t) ^[26]
	qGD173-1					3	14,041,426	2.36E-07	5.97
	qGD173-2	3	25,260,390	6.15E-07	7.27
	qGD176-1	6	11,067,689	5.83E-08	9.18
	qGD176-2	6	22,491,478	1.68E-06	3.58
	qGD177	7	4,852,217	1.34E-06	4.93					7	4,852,217	3.96E-06	4.23	qDI₁₄-7 ^[31]
	qGD178	8	20,759,700	7.36E-09	3.56									GF14c ^[39]
	qGD179	9	10,755,714	2.91E-07	9.00
	qGD1710	10	19,198,827	8.20E-08	3.03
	qGD1711-1	11	7,018,865	7.34E-07	1.95	11	7,086,996	1.93E-06	10.64					Pia/RGA4/Os11gRGA4 /RGA5/Os11gRGA5 ^[32,33]
	qGD1711-2	11	27,821,721	1.63E-08	6.76	11	27,724,695	6.15E-06	7.79	11	27,821,721	2.36E-08	3.69	Pik ^[34]
	qGD1712	12	17,657,476	1.75E-07	7.32

稻瘟病菌株 Blast isolate	QTL	混合群体/Mix population				籼稻/Xian				粳稻/Geng				前人克隆的基因 Previously cloned genes
稻瘟病菌株 Blast isolate	QTL	染色体 Chr.	峰值SNP Peak SNP	P值 P-value	贡献率 R²(%)	染色体 Chr.	峰值SNP Peak SNP	P值 P-value	贡献率 R²(%)	染色体 Chr.	峰值SNP Peak SNP	P值 P-value	贡献率 R²(%)	前人克隆的基因 Previously cloned genes
GD08-T19	qGD086					6	6,535,818	2.41E-06	12.44					Pi27(t) ^[30]
	qGD0811					11	22,027,592	1.14E-06	9.24
	qGD0812-1					12	10,118,034	4.36E-06	8.19
	qGD0812-2	12	12,070,327	7.84E-07	5.89
HB1708	qHB171-1	1	1,523,579	1.12E-06	3.39
	qHB171-2									1	2,388,489	2.94E-06	3.70	Pit ^[25]
	qHB171-3	1	33,005,596	1.32E-10	1.08					1	33,092,697	1.52E-07	1.09	Pish/ Pi37 ^[27,28]
	qHB173	3	10,681,409	3.64E-06	10.87
	qHB174					4	17,870,237	4.80E-07	17.50
	qHB175-1	5	3,738,799	2.47E-06	7.80									Pi25(t)^[30]
	qHB175-2	5	28,480,050	4.05E-07	4.30
	qHB176-1	6	10,425,293	8.48E-08	4.22	6	10,451,191	1.60E-06	12.64					Piz-t/Pi2/Pi9/Pi50/Pi-gm ^[23]
	qHB176-2	6	22,699,279	1.41E-07	8.36
	qHB177									7	4,833,062	1.18E-08	10.94	qDI₁₄-7 ^[31]
	qHB178-1	8	6,463,393	2.81E-11	10.82	8	6,463,393	4.42E-11	32.11
	qHB178-2	8	20,852,827	2.77E-06	1.81									GF14c ^[39]
	qHB1710									10	5,633,234	2.00E-07	8.35
	qHB1711	11	20,645,223	1.72E-07	10.16
HLJ13-856	qHL132					2	35,127,933	1.26E-07	18.93					Pib ^[29]
	qHL1311	11	7,037,500	1.42E-06	2.02									Pia/RGA4/Os11gRGA4 /RGA5/Os11gRGA5 ^[32,33]

Identification of rice blast resistance in xian and geng germplasms by genome- wide association study

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