基于Meta-QTL和RNA-seq的整合分析挖掘水稻抗稻瘟病候选基因

doi:10.3724/SP.J.1006.2022.12031

Abstract

Abstract:

Magnaporthe oryzae seriously devastates rice production, and resistant cultivars can lose resistance within a few years due to the pathogenic variability of M. oryzae. Therefore, it is essential to explore continuously novel blast-resistance genes for breeding broad-spectrum resistance cultivars. In this study, firstly, 50 Meta-QTLs (including at least 2 original QTLs) were identified on 12 chromosomes by meta-analysis of blast-resistance 783 QTLs from 43 literatures. The average interval distance was 0.87 Mb in these Meta-QTLs, which contained a total of 4718 interval genes. Subsequently, based on integrated analysis of blast-resistance Meta-QTLs and RNA-seq, the result identified 2193 common genes which were not only located on blast-resistance Meta-QTLs, but also significantly differentially expressed in response to the M. oryzae. Among them, 22 cloned genes had been reported to be involved in defense responses to M. oryzae and other stresses. Furthermore, 99 resistance gene analogues (RGA) and 112 transcription factors (TF) were screened out from the above common genes, which were utilized to construct gene co-expression networks (GCEN). Based on the Top 20 of the connection degrees, hub genes were identified in the GCEN. Among them, OsJAMyb, bsr-d1, and OsWRKY76 had been reported to be against rice blast, and OsSPL9 was related to resistance to rice stripe virus. The left hub genes were considered as important potential resistance genes which need further functional verification to prepare for breeding broad-spectrum resistance rice cultivars.

Key words: rice (Oryza sativa L.), blast resistance, meta-analysis, RNA-seq, candidate gene

TIAN Tian, CHEN Li-Juan, HE Hua-Qin. Identification of rice blast resistance candidate genes based on integrating Meta-QTL and RNA-seq analysis[J].Acta Agronomica Sinica, 2022, 48(6): 1372-1388.

Figures/Tables 9

Table 1

Summary of QTLs information related to rice blast resistance"

作图群体 Population	群体类型 Population type	群体大小 Number of population	作图方法 Mapping method	QTL数目 Number of QTLs	参考文献 Reference
Moreberekan×Co39	RILs	281	IM	22	Wang et al., 1994^[28]
IR64×Azucena	DH	114	IM	13	Bagali et al., 2000^[4]
Nipponbare×Owarihatamochi	F₂	146	IM	4	Fukuoka et al., 2001^[29]
Zhong 156×Gumei 2	RILs	146	CIM	2	Fan et al., 2001^[30]
Kahei×Koshihikari	F₂	241	SMA	2	Miyamoto et al., 2001^[31]
Khao Dawk Mali 105×CT9993	RILs	141	SIM, CIM	6	Sirithunya et al., 2002^[32]
Lemont×Teqing	RILs	284	IM	11	Tabien et al., 2002^[33]
Norin 29×Chubu 32	F₂	149	IM	1	Zenbayashi et al., 2002^[34]
Lemont×Teqing	RILs	292	IM	14	Loan et al., 2003^[35]
Zhenshan 97×Minghui 63	RILs	241	CIM	12	Chen et al., 2003^[36]
IR64×Azucena	DH	105	CIM	9	Sallaud et al., 2003^[37]
Bala×Azucena	RILs	205	CIM	29	Talukder et al., 2004^[38]
Bala×Azucena	RILs	100	CIM	12	Talukder et al., 2005^[39]
ZYQ8×JX17	DH	127	SMA	77	Xu et al., 2004^[40]
Zhong 156×Gumei 2	RILs	304	MIM	21	Wu et al., 2005^[6]
URN12×Koshihikari	F₂	136	IM	2	Sato et al., 2006^[41]
作图群体 Population	群体类型 Population type	群体大小 Number of population	作图方法 Mapping method	QTL数目 Number of QTLs	参考文献 Reference
Llanos 5×Fanny	RILs	120	IM, CIM	37	Lopez et al., 2006^[42]
KDML105×JHN	RILs	587	SIM, sCIM	14	Noenplab et al., 2006^[43]
Bala×Azucena	Nd	No	CIM	83	Ballini et al., 2008^[44]
Suweon 365×Chucheong	RILs	190	CIM	54	Cho et al., 2008^[45]
Heikezijing×Suyunuo	RILs	166	CIM	44	Shi et al., 2010^[46]
IR64×Azucena	DH	111	CIM	4	Kongprakhon et al., 2010^[47]
Lemont×Jasmine 85	RILs	227	CIM	9	Jia et al., 2011^[48]
Way Rarem×Oryzica Llanos 5	BILs	123	IM	16	Lestari et al., 2011^[49]
TAM×KHZ	F_2:3	192	CIM	7	Sabouri et al., 2011^[50]
IR68835×KDML105	BILs	83	SMA	19	Korinsak et al., 2011^[51]
TY×CO39	RILs	363	CIM	22	Wang et al., 2012^[52]
MR219×IRGC105491	BILs	261	CIM	9	Rahim et al., 2012^[53]
MR219×IRGC105491	BILs	63	CIM	13
MWG×EW8	DH	96	CIM	3	Yang et al., 2012^[54]
Pongsu seribu 2×Mahsuri	F₃	296	IM, CIM	40	Ashkani et al., 2013a^[55]
Pongsu seribu 2×Mahsuri	F₃	188	SMA, IM, CIM	13	Ashkani et al., 2013b^[56]
Bodao×Suyunuo	RILs	155	CIM	13	Huan et al., 2014^[57]
IT×Koshihikari	F₃	124	CIM	1	Mizobuchi et al., 2014^[58]
R287×Ximaxian	BILs	299	CIM	29	Liu et al., 2015^[59]
GV×VN	F₂	114	SIM	2	Urso et al., 2016^[5]
landraces	Landraces	276	SMA	31	Wu et al., 2016^[60]
Heikezijing×Suyunuo	RILs	162	ICIM	2	Fang et al., 2016^[61]
Danteshwari×Dagaddeshi	RILs	122	CIM	14	Mandal et al., 2017^[62]
Nekken 2×Hokuriku 193	F₃	243	CIM	9	Nagaoka et al., 2017^[63]
Heikezijing×Suyunuo	RILs	162	ICIM	5	He et al., 2017^[64]
Cybonnet×Saber	RILs	243	ICIM	22	Chen et al., 2018^[65]
Bodao×Suyunuo	RILs	212	ICIM	2	Fang et al., 2019^[66]
Jin 23B×CR071	BILs	239	CIM	16	Jiang et al., 2020^[67]
Jin 23B×Qinggu'ai 3	BILs	237	CIM	13

Table 1

Fig. 1

Table 2

Meta-analysis of blast-resistant QTLs in rice"

Meta-QTL	染色体 Chr.	侧翼标记 Flanking markers		置信区间 95% CI (Mb)	图距 Map distance (Mb)	原始QTL Original QTLs	区间基因 Interval gene		已报道的抗稻瘟病基因 Published blast-resistance gene
Metaq1-2	1	UMC32-RM243		7.34-7.97	0.63	3	89		Pi27(t)^[68]
Metaq1-4	1	OSR3-C2340		34.03-34.47	0.44	3	51
Metaq2-1	2	C149-RM174		5.91-7.01	1.10	3	143
Metaq2-2	2	RG25-RZ401		21.77-24.047	2.28	4	295
Metaq2-3	2	RZ58-RM6		28.69-29.58	0.89	2	124
Metaq2-5	2	RM482-RZ213		35.27-35.37	0.10	2	20		Pi25(t)^[37], Pi-tq5^[69], Pi-b^[70]
Metaq3-1	3	RM1332-RG409		2.45-3.50	1.04	2	182
Metaq3-2	3	RM1338-RM232		8.39-9.76	1.37	2	210
Metaq3-3	3	RM15080-RM15111		15.40-15.69	0.30	2	41
Metaq3-4	3	RM411-RM487		21.43-22.02	0.59	4	52
Metaq3-5	3	RM5626-ud3001344		24.86-25.04	0.18	7	15
Metaq4-1	4	RM1359-G271		19.86-20.17	0.31	6	48
Metaq4-2	4	RM1136-CT206		25.04-25.36	0.32	5	16
Metaq4-4	4	G264-RG214		31.34-31.66	0.32	5	51	Pi39(t)^[71], Pi46(t)^[72]
Metaq4-5	4	RM124-RM280		34.74-34.99	0.25	2	34
Metaq5-1	5	RM122-RM2010		0.31-0.49	0.18	3	132
Metaq5-2	5	RM574-RM437		3.45-3.88	0.43	3	51
Metaq5-3	5	wd5001198-wd5001344		10.36-10.86	0.50	2	13
Metaq5-4	5	R2289-RM161		18.96-20.90	1.95	2	220
Metaq5-5	5	C43-RM3476		22.26-23.91	1.64	7	229
Metaq6-1	6	RZ2-C226A		3.36-3.54	0.17	3	24
Metaq6-2	6	RZ144-RZ667		6.72-6.93	0.21	6	30
Metaq6-3	6	RM19779-RM527		9.31-9.86	0.55	9	30	Pi40(t)^[73], Pi26^[6], Pi59(t)^[74]
Metaq6-6	6	RZ242-RG653		28.96-29.03	0.06	4	15	Pi-tq1^[69]
Metaq7-1	7	ud7000014-RG773		0.31-4.05	3.74	2	458
Metaq7-2	7	RM180-L538T7		5.74-7.74	2.00	5	158
Metaq7-3	7	RM5481-RM11		16.20-19.26	3.06	4	225
Metaq7-4	7	RM182-RZ626		21.51-23.11	1.60	4	208
Metaq7-5	7	R1789-C507		26.53-26.71	0.18	8	26
Metaq8-1	8	RM25-ud8000289		4.38-4.65	0.27	2	34
Metaq8-2	8	RM310-RM547		5.12-5.59	0.48	9	67	Pi42(t)^[75]
Metaq8-3	8	ud8000924-RM44		14.78-16.57	1.79	6	89
Metaq8-4	8	RM7049-ud8001357		20.81-21.03	0.21	9	24
Metaq9-1	9	R1687-C1454		8.35-9.63	1.28	4	62	Pi15^[76]
Metaq9-2	9	R1751-RM434		14.36-15.66	1.30	5	154
Metaq9-3	9	RM108-CT6		19.30-20.17	0.87	5	150
Metaq9-4	9	RM1553-RM24777		21.00-22.05	1.04	10	168
Metaq10-1	10	RM7217-R2174		4.64-5.50	0.86	5	53
Metaq10-2	10	G1125-RM8207		7.35-9.81	2.46	2	114
Meta-QTL	染色体 Chr.	侧翼标记 Flanking markers	置信区间 95% CI (Mb)		图距 Map distance (Mb)	原始QTL Original QTLs	区间基因 Interval gene	已报道的抗稻瘟病基因 Published blast-resistance gene
Metaq10-5	10	RG561-RM228	21.78-22.24		0.47	2	95
Metaq11-1	11	RM26198-RM552	4.42-4.84		0.42	7	36
Metaq11-4	11	RM6680-RM2596	18.62-19.97		1.35	5	110	Pi38^[77], Pi34^[78], Pi7(t)^[28],
Metaq11-5	11	RM27088-RM2191	23.77-24.66		0.89	4	73	Pi47^[79]
Metaq11-6	11	RM224-L190	27.67-28.24		0.56	9	49	Pik^[80], Pik-p^[81], Pi44(t)^[82], Pi-1(t)^[83], Pi1^[84], Pik-m^[85], Pi49^[86], Pi-hk1^[87], Pi43(t)^[75]
Metaq12-1	12	RZ816-RM491	2.43-3.58		1.16	6	143
Metaq12-2	12	G1391-ud12000339	5.81-6.14		0.33	4	14	Pi-tq6^[69], Pi6(t)^[88]
Metaq12-3	12	RM101-ud12000566	8.83-9.23		0.40	4	16
Metaq12-4	12	C625-ud12000700	11.06-11.32		0.26	13	23	Pi-42(t)^[75], Pi58(t)^[74]
Metaq12-5	12	RM27982-RM7102	12.63-13.21		0.58	3	27	Pi48^[79]
Metaq12-6	12	RM309-RM3326	21.45-21.74		0.29	9	27

Table 2

Fig. 2

Fig. 3

Fig. 4

Table 3

Table 4

Hub genes of connection degree Top 20 in the down-regulated gene coexpression network"

Meta-QTL	Degree值 Degree score	基因ID Gene ID	基因符号 Gene symbol	表达倍数 log₂(Fold Change)	功能注释 Function annotation
Metaq9-1	56	Os09g0326100	—	-6.34	Receptor-like protein kinase 5 precursor
Metaq7-1	56	Os07g0106000	—	-2.85	Ser/thr protein phosphatase family protein
Metaq12-1	56	Os12g0149700	—	-4.77	Protein kinase
Metaq7-2	55	Os07g0211400	OsKAPP	-1.54	Protein kinase-associated protein phosphatase
Metaq10-5	55	Os10g0561500	OsRLCK307	-1.89	Protein kinase family protein
Metaq7-1	55	Os07g0116900	—	-1.71	NB-ARC domain containing protein
Metaq5-4	55	Os05g0406800	—	-3.82	Receptor-like protein kinase precursor
Meta-QTL	Degree值 Degree score	基因ID Gene ID	基因符号 Gene symbol	表达倍数 log₂(Fold Change)	功能注释 Function annotation
Metaq4-5	55	Os04g0685900	OsRLCK174	-1.88	Receptor protein kinase TMK1 precursor
Metaq5-5	55	Os05g0478300	—	-5.79	Receptor-like protein kinase 2 precursor
Metaq7-1	55	Os07g0134200	OsRLCK222	-3.21	Receptor protein kinase CLAVATA1 precursor
Metaq5-5	55	Os05g0467000	OsCDPK16	-2.41	CAMK_CAMK_like.29-CAMK includes calcium/ calmodulin dependent protein kinases
Metaq5-5	55	Os05g0480400	—	-1.89	Inactive receptor kinase At2g26730 precursor
Metaq2-1	55	Os02g0215900	OsGIRL1	-3.52	Receptor kinase
Metaq7-3	55	Os07g0501800	—	-4.16	Leucine-rich repeat family protein
Metaq6-1	55	Os06g0170100	OsWAK63	-8.85	OsWAK63-OsWAK receptor-like protein kinase
Metaq7-1	55	Os07g0145400	OsGHR1	-10.94	Leucine-rich repeat family protein
Metaq7-5	55	Os07g0641200	OsCDPK30	-3.12	CAMK_CAMK_like.36-CAMK includes calcium/ calmodulin depedent protein kinases
Metaq5-5	55	Os05g0466900	—	-1.91	Protein kinase family protein
Metaq4-2	55	Os04g0506100	—	-2.90	Receptor-like protein kinase precursor
Metaq2-1	54	Os02g0212900	OsRLCK66	-2.77	Cysteine-rich receptor-like protein kinase 35 precursor

Table 4

Table 5

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Meta-QTL	Degree值 Degree score	基因ID Gene ID	基因符号 Gene symbol	表达倍数 log₂(Fold Change)	功能注释 Function annotation
Metaq2-3	73	Os02g0700300	OsDLN66	10.04	MYB family transcription factor
Metaq9-2	73	Os09g0417600	OsWRKY76	9.10	WRKY76
Metaq3-4	73	Os03g0437200	bsr-d1	8.88	ZOS3-12-C2H2 zinc finger protein
Metaq5-4	73	Os05g0418800	NAC87	8.23	No apical meristem protein
Metaq5-1	73	Os05g0121600	RSR1	8.14	AP2 domain containing protein
Meta-QTL	Degree值 Degree score	基因ID Gene ID	基因符号 Gene symbol	表达倍数 log₂(Fold Change)	功能注释 Function annotation
Metaq11-6	73	Os11g0686250	OsWRKY41	8.11	WRKY63
Metaq11-6	73	Os11g0684000	OsJAMyb	7.54	MYB family transcription factor
Metaq8-1	73	Os08g0179400	OsbHLH070	7.49	Expressed protein
Metaq2-2	73	Os02g0603600	OsbHLH110	5.58	Helix-loop-helix DNA-binding domain containing protein
Metaq5-4	73	Os05g0421600	OsNAC52	5.27	No apical meristem protein
Metaq11-6	73	Os11g0685700	OsWRKY61	4.67	WRKY61
Metaq2-2	73	Os02g0606200	OsBBX4	4.62	B-box zinc finger family protein
Metaq7-1	73	Os07g0111400	OsWRKY29	4.57	WRKY29
Metaq2-1	73	Os02g0221100	OsbHLH029	4.29	Helix-loop-helix DNA-binding domain containing protein
Metaq7-1	73	Os07g0119300	—	4.09	MYB family transcription factor
Metaq2-2	73	Os02g0610500	OsCOL4	3.56	CCT/B-box zinc finger protein
Metaq1-2	73	Os01g0236700	OsNLP3	3.46	NIN
Metaq7-4	73	Os07g0568300	OsTZF6	2.68	Zinc finger family protein
Metaq7-3	73	Os07g0484700	—	2.07	MYB family transcription factor
Metaq5-4	73	Os05g0408200	OsSPL9	1.94	OsSPL9-SBP-box gene family member

Meta-QTL	基因ID Gene IDs	已公布的基因 Published genes	表达倍数 log₂(Fold Change)	差异表达 Differential exprssion		抵御胁迫 Resistance to stress
Metaq3-1	Os03g0160100	OsEDR1	2.29	上调Up-regulation		Blast^[101]; Xoo^[95]
Metaq3-2	Os03g0277000	OsGDI3	2.19	上调Up-regulation		Disease resistance^[102,103]
Metaq3-3	Os03g0390200	OsSAPK1	3.01	上调Up-regulation		Xoo^[104]
Metaq3-4	Os03g0437200	Bsr-d1	8.88	上调Up-regulation		Blast^[97]
Metaq5-1	Os05g0110900	OsRLCK176	1.90	上调Up-regulation		Xoo^[105]; Chitin^[106]
Metaq5-4	Os05g0408200	OsSPL9	1.94	上调Up-regulation		RDV^[100]
Metaq7-1	Os07g0129200	OsPR1a	6.48		上调Up-regulation	Pathogen infection^[107]
Metaq7-2	Os07g0217600	CYP71Z2	14.17		上调Up-regulation	Xoo^[108]
Metaq7-3	Os07g0471300	OsAGO18	3.43		上调Up-regulation	Virus^[109]
Metaq7-3	Os07g0492000	OsNDPK1	2.42		上调Up-regulation	Bacterial pathogens^[110]
Metaq7-3	Os07g0500300	OsGAP	3.55		上调Up-regulation	ABA^[111]
Metaq7-4	Os07g0545800	CIGR1	1.56		上调Up-regulation	Blast and gibberellin^[112]
Metaq7-4	Os07g0569100	OsREM4.1	2.22		上调Up-regulation	ABA^[113]
Metaq9-2	Os09g0417600	OsWRKY76	9.10		上调Up-regulation	Blast^[99]
Metaq9-2	Os09g0417800	OsWRKY62	9.46		上调Up-regulation	Xoo^[114]
Metaq10-5	Os10g0564500	OsSAPK3	4.85		上调Up-regulation	Xoo^[104]
Metaq11-1	Os11g0195500	OsPAD4	2.02		上调Up-regulation	Xoo^[115]
Metaq11-6	Os11g0684000	OsJAMyb	7.54		上调Up-regulation	Blast^[98]
Metaq5-1	Os05g0111300	OsMT2b	-4.24		下调Down-regulation	ROS^[116]
Metaq7-1	Os07g0152000	OsTCP21	-1.92		下调Down-regulation	RRSV^[117]
Metaq9-3	Os09g0513000	OsBIANK1	-2.12		下调Down-regulation	Blast^[118]
Metaq9-4	Os09g0544800	OsRacGEF1	-3.50		下调Down-regulation	Blast^[25]

Identification of rice blast resistance candidate genes based on integrating Meta-QTL and RNA-seq analysis

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