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

作物学报 ›› 2023, Vol. 49 ›› Issue (5): 1170-1183.doi: 10.3724/SP.J.1006.2023.22024

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

水稻种质资源稻瘟病抗性全基因组关联分析

周海平¹(), 张帆², 陈凯³, 申聪聪³, 朱双兵³, 邱先进⁴^,^*(), 徐建龙²^,³^,⁵^,^*()

¹温州市农业科学研究院/浙南作物育种重点实验室, 浙江温州 325000
²中国农业科学院作物科学研究所, 北京 100081
³岭南现代农业科学与技术广东省实验室深圳分中心/中国农业科学院农业基因组研究所, 广东深圳 518210
⁴长江大学农学院, 湖北荆州 434025
⁵海南省崖州湾种子实验室, 海南三亚 572024

收稿日期:2022-04-24 接受日期:2022-09-05 出版日期:2023-05-12 网络出版日期:2022-09-15
通讯作者: *徐建龙, E-mail: xujianlong@caas.cn; 邱先进, E-mail: xjqiu216@yangtzeu.edu.cn
作者简介:E-mail: zhouhaiping7583@126.com
基金资助:
海南崖州湾种子实验室揭榜挂帅项目(B21HJ0216);温州市农业新品种选育协作组专项(2019ZX006)

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

ZHOU Hai-Ping¹(), ZHANG Fan², CHEN Kai³, SHEN Cong-Cong³, ZHU Shuang-Bing³, QIU Xian-Jin⁴^,^*(), XU Jian-Long²^,³^,⁵^,^*()

¹Wenzhou Academy of Agricultural Sciences/South-Zhejiang Crop Breeding Key Laboratory, Wenzhou 325000, Zhejiang
²Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
³Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, Guangdong, China
⁴College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China
⁵Hainan Yazhou Bay Seed Laboratory, Sanya 572024, Hainan, China

Received:2022-04-24 Accepted:2022-09-05 Published:2023-05-12 Published online:2022-09-15
Contact: *E-mail: xujianlong@caas.cn;E-mail: xjqiu216@yangtzeu.edu.cn
Supported by:
Hainan Yazhou Bay Seed Laboratory(B21HJ0216);Wenzhou Agricultural New Variety Breeding Collaborative Project(2019ZX006)

摘要/Abstract

摘要：

稻瘟病是一种对全球水稻生产威胁极大的真菌性病害, 鉴定抗稻瘟病基因并将其导入到现有感病品种改良品种的抗性是控制这种病害的有效途径。本研究利用5个稻瘟病菌株鉴定了212份籼稻和235份粳稻种质资源的苗瘟抗性, 分别筛选到8个和12个抗全部5个菌株的籼稻和粳稻种质材料。采用全基因组关联分析在籼粳混合群体、籼稻和粳稻种质资源中共定位到43个影响水稻苗瘟抗性的QTL, 抗GD00-193、GD08-T19、GD17-CQ16、HB1708和HLJ13-856菌株的QTL分别为9、4、14、14和2个。其中, 12个抗病QTL仅在籼稻亚群中检测到, 7个仅粳稻亚群中检测到, 1个为籼粳2个亚群共同检测到, 说明籼稻抗稻瘟病总体好于粳稻, 而且稻瘟病抗性存在明显的籼粳分化。同时影响水稻对2个及2个以上菌株的抗性或在2个及2个以上群体中同时被定位到的QTL共计11个, 利用候选区间关联分析和单倍型分析鉴定到23个抗病候选基因, 不同抗病候选基因在籼、粳群体中的分布频率不同。研究结果为水稻品种稻瘟病抗性分子改良提供种质资源和有利基因信息及不同抗病基因的育种利用策略。

关键词: 稻瘟病抗性, 种质资源, 全基因组关联分析, 数量性状位点, 有利等位基因

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

周海平, 张帆, 陈凯, 申聪聪, 朱双兵, 邱先进, 徐建龙. 水稻种质资源稻瘟病抗性全基因组关联分析[J]. 作物学报, 2023, 49(5): 1170-1183.

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.

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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]

水稻种质资源稻瘟病抗性全基因组关联分析

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

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