Current Status of Conventional and Molecular Interventions for Blast Resistance in Rice

doi:10.1016/j.rsci.2017.08.001

Abstract

Abstract:

Pyricularia oryzae anamorph of Magnaporthe oryzae is one of the most notorious fungal pathogens causing severe economic loss in rice production worldwide. Various methods, viz. cultural, biological and molecular approaches, are utilized to counteract this pathogen. Moreover, some tolerant or resistant rice varieties have been developed with the help of breeding programmes. Isolation and molecular characterization of different blast resistance genes now open the gate for new possibilities to elucidate the actual allelic variants of these genes via various molecular breeding and transgenic approaches. However, the behavioral pattern of this fungus breakups the resistance barriers in the resistant or tolerant rice varieties. This host-pathogen barrier will be possibly countered in future research by comparative genomics data from available genome sequence data of rice and M. oryzae for durable resistance. Present review emphasized fascinating recent updates, new molecular breeding approaches, transgenic and genomics approaches (i.e. miRNA and genome editing) for the management of blast disease in rice. The updated information will be helpful for the durable, resistance breeding programme in rice against blast pathogen.

Key words: backcross breeding, gene pyramiding, allele mining, transgenic technology, rice, blast resistance, CRISPR/Cas9, molecular breeding, bioinformatics approach

Srivastava Deepti, Shamim Md, Kumar Mahesh, Mishra Anurag, Pandey Pramila, Kumar Deepak, Yadav Prashant, Harrish Siddiqui Mohammed, Narayan Singh Kapildeo. Current Status of Conventional and Molecular Interventions for Blast Resistance in Rice[J]. Rice Science, 2017, 24(6): 299-321.

Figures/Tables 8

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Fungicide	Nature	Mode of action	Active ingredient per hm²	Reference
Probenazole	Systemic	Activates plant defence response	1000-2400 mL	Filippi and Prabhu, 1997
Tricyclazole	Systemic	Melanin biosynthesis inhibitor-R (polyhydroxyl-naphthalene reductase)	225-300 mL	Anwar and Bhat, 2005
Azoxystrobin	Systemic	QOI complex 3 inhibitor	170 mL	Neelakanth et al, 2017
Isoprothiolane	Systemic	Phospholipid biosynthesis (methyltransferase) and/or choline biosynthesis inhibitor	300 mL	Sachin and Rana, 2011
Propiconazole	Systemic	Sterol biosynthesis (14-demethylase) inhibitor	125 mL	Prasanna Kumar and Veerabhadraswamy, 2014
Benomyl	Systemic	Benomyl binds to microtubules, interfering with cell functions, such as meiosis and intracellular transportation	120 mg	Kapoor and Singh, 1982
Edifenphos	Systemic	Inhibitor of the biosynthesis of phosphatidylcholine	250-300 mg	Anon, 1992; Filippi and Prabhu, 1997
Iprobenfos	Systemic	Inhibitor of the biosynthesis of phosphatidylcholine	300-500 mL	Gohel and Chauhan, 2015
Pyroquilon	Systemic	Inhibitor of melanin biosynthesis inhibitors (MBIs)	500 mL	Tsuda et al, 1998
Diclocymet	Systemic	Inhibitor of melanin biosynthesis inhibitors (MBIs)	300 mL	Kurahash, 2001
Carpropamid	Root-systemic	Inhibits the enzyme scytalone dehydratase essential for the synthesis of the melanin biosynthesis and also induce resistance in plants	139 mL	Motoyama et al, 1999
Fenoxanil	Systemic	Inhibitor of melanin biosynthesis inhibitors (MBIs)	120-150 mg	Nishimura and Hino, 2002
Metominostrobin	Systemic	Inhibits respiratory electron transfer	100 mg	-
Zineb	Contact	When being applied, it is converted to an isothiocyanate, and inactivates the sulphahydral groups enzymes of fungi	1500 mg	-
Hexaconazole	Systemic	Inhibits ergosterol biosynthesis (steroid dimethylation inhibitor)	50 mL	Prasanna Kumar et al, 2011
Carbendszim 12% + Mancozeb 63%	Contact and systemic	Carbendazim works by inhibiting spindle formation at the mitosis stage and mancozeb affects the nervous system	750 mg	Venkata Rao and Muralidharan, 1983
Eprobenfos	Systemic	Eprobenfos block the synthesis of phospholipid and alters the membrane structure of fungus by increasing the permeability with consequent loss of vital cellular component	240 mL	-
Kresoxim methyl	Contact and systemic (local)	Acts by binding to Qo site, blocking electron transfer and respiration of the fungi	250 mg	Prasanna Kumar et al, 2011
Tebuconazole	Systemic	Dimethylase inhibitor: interferes in process of building the structure of fungal cell wall	187.5 mL	Ghazanfar et al, 2009

Fungicide	Nature	Mode of action	Active ingredient per hm²	Reference
Probenazole	Systemic	Activates plant defence response	1000-2400 mL	Filippi and Prabhu, 1997
Tricyclazole	Systemic	Melanin biosynthesis inhibitor-R (polyhydroxyl-naphthalene reductase)	225-300 mL	Anwar and Bhat, 2005
Azoxystrobin	Systemic	QOI complex 3 inhibitor	170 mL	Neelakanth et al, 2017
Isoprothiolane	Systemic	Phospholipid biosynthesis (methyltransferase) and/or choline biosynthesis inhibitor	300 mL	Sachin and Rana, 2011
Propiconazole	Systemic	Sterol biosynthesis (14-demethylase) inhibitor	125 mL	Prasanna Kumar and Veerabhadraswamy, 2014
Benomyl	Systemic	Benomyl binds to microtubules, interfering with cell functions, such as meiosis and intracellular transportation	120 mg	Kapoor and Singh, 1982
Edifenphos	Systemic	Inhibitor of the biosynthesis of phosphatidylcholine	250-300 mg	Anon, 1992; Filippi and Prabhu, 1997
Iprobenfos	Systemic	Inhibitor of the biosynthesis of phosphatidylcholine	300-500 mL	Gohel and Chauhan, 2015
Pyroquilon	Systemic	Inhibitor of melanin biosynthesis inhibitors (MBIs)	500 mL	Tsuda et al, 1998
Diclocymet	Systemic	Inhibitor of melanin biosynthesis inhibitors (MBIs)	300 mL	Kurahash, 2001
Carpropamid	Root-systemic	Inhibits the enzyme scytalone dehydratase essential for the synthesis of the melanin biosynthesis and also induce resistance in plants	139 mL	Motoyama et al, 1999
Fenoxanil	Systemic	Inhibitor of melanin biosynthesis inhibitors (MBIs)	120-150 mg	Nishimura and Hino, 2002
Metominostrobin	Systemic	Inhibits respiratory electron transfer	100 mg	-
Zineb	Contact	When being applied, it is converted to an isothiocyanate, and inactivates the sulphahydral groups enzymes of fungi	1500 mg	-
Hexaconazole	Systemic	Inhibits ergosterol biosynthesis (steroid dimethylation inhibitor)	50 mL	Prasanna Kumar et al, 2011
Carbendszim 12% + Mancozeb 63%	Contact and systemic	Carbendazim works by inhibiting spindle formation at the mitosis stage and mancozeb affects the nervous system	750 mg	Venkata Rao and Muralidharan, 1983
Eprobenfos	Systemic	Eprobenfos block the synthesis of phospholipid and alters the membrane structure of fungus by increasing the permeability with consequent loss of vital cellular component	240 mL	-
Kresoxim methyl	Contact and systemic (local)	Acts by binding to Qo site, blocking electron transfer and respiration of the fungi	250 mg	Prasanna Kumar et al, 2011
Tebuconazole	Systemic	Dimethylase inhibitor: interferes in process of building the structure of fungal cell wall	187.5 mL	Ghazanfar et al, 2009

Chr	Gene		Tightly linked marker				Map position (cM)			Donor rice			Resistance type			Reference
Chr	Gene		Type			Name	Map position (cM)			Donor rice			Resistance type			Reference
1	Pit		SNP			t311, t256, t8042	16.1			Tjahaja			Complete			Hayashi et al, 2006
	Pi27(t)		SSR			RM151, RN259	28.4-38.8			Q14			Complete			Sallaud et al, 2006
	Pitp(t)		SSR			RM246	114.1			Tetep			Partial			Barman et al, 2004
	Pi35(t)		SSR			RM1216, RM1003	132.0-136.6			Hokkai 188			Partial			Nguyen et al, 2006
	Pi37		SSR			RM302, RM212, FPSM1, FPSM2, FPSM4	136.1			St.No.1			Complete			Lin et al, 2007
			STS			S15628, FSTS1, FSTS2, FSTS3, FSTS4
	Pi64		SSR			RM11715, RM11787	-			Yangmaogu			Complete			Ma et al, 2015
	Pish		RFLP			-	148.7-154.8			Shin 2			Complete			Zhu et al, 2004
2	Pid1(t)		SSR			RM262	87.5-89.9			Digu			Complete			Chen et al, 2004
	Pig(t)		SSR			RM166, RM208	142.0-154.1			Guangchangzhan			Complete			Shi et al, 2012
	Pitq5		RFLP			RG520, RZ446B, RZ446A, RG654, RG256	150.5-157.9			Teqing			Complete			Zhou et al, 2004
	Piy1(t)		SSR			RM3248, RM20	153.2-154.1			Yanxian 1			-			Fukuta et al, 2004
	Piy2(t)		SSR			RM3248, RM20	153.2-154.1			Yanxian 1			-			Fukuta et al, 2004
	Pib		SNP			b213, b28, b2, b3989, Pibdom	154.1			Tohoku, IL9, Koshiihikari			Complete			Hayashi et al, 2006
	Pi14(t)		Isozyme			Amp-1	32.6			Maowang			Complete			Tabien et al, 2000
	Pi16(t)		Isozyme			Amp-1	34.3			AUS373, Maowamg			Complete			Pan et al, 1996
	Pi-Da(t)		SSR			RM5529, RM211	12.6			Dacca 6			-			Lei et al, 2005; Shi et al, 2012
3	Pi66(t)		SSR			RM487, RM16, RM55, RM168				AS201			Partial			Liang et al, 2016
4	Pi21		STS			P702D03-#79	58.6			Owarihatamochi			Partial			Pan et al, 1998
	Pikur1		Isozyme			-	86.0			Kuroka			-			Fukuoka et al, 2007
	Pi39(t)		SSR			RM3843, RM5473	107.4-108.2			Chubu 111 (Haonaihuan)			-			Shinoda et al, 1971
	Pi(t)		-			-	12.2			P167(1)			-			Causse et al, 1994
	Pi5(t)		RFLP			RG788, RG498	12.0			RIL29 (Morobere kan)			Complete			Wang et al, 1994
5	Pi26(t)		RFLP			RG313	22.5-24.7			Azucena			-			Ahn et al, 1996; Nguyen et al, 2006
	Pi23(t)		-			-	59.3-99.5			Sweon 3655			-			Terashima et al, 2008
	Pi10		InDel			OPF62700	88.5-102.8			Tongil			Complete			Wu et al, 2005
6	Pi22(t)		RFLP			-	38.7-41.9			Sweon 365			-			Terashima et al, 2008
	Pi26		RFLP			K17, K2123	22.5-63.2			Gumei 2			Complete			Ahn et al, 1996
	Pi27(t)		RFLP			Est-2	51.9			IR64			-			Nguyen et al, 2006
	Pi40(t)		SSR			RM3330, RM527	54.1-61.6			IR65482-4-136-2-2			-
			CAPS			S2539
	Piz-5		STS			BS2-Pi9, NBS4-Pi9	58.7			Tadukan			Complete			Deng et al, 2006
	Piz		InDel			z4794	58.7			Zenith			Complete			Hayashi et al, 2006
			SNP			z60510, z5765, z56592, z565962										Wang et al, 2012
	Piz-t		InDel			z4794	58.7			Torde 1			Complete			Deng et al, 2006
	Pi9		-			-	58.7			75-1-127 (101141)			Complete			Qu et al, 2006; Koide et al, 2013
	Pi25(t)		RFLP			A7-RG456	63.2-64.6			Gumei 2			-			Ahn et al, 1996
	Pid2		CAPS			CAPS1, CAPS8	65.8			Digu			Complete			Chen et al, 2006
	Pigm(t)		CAPS			C26348	65.8			Gumei 4			-			Naqvi and Chattoo, 1996
	Pitq1		RFLP			RZ682, C236, RG653, RZ508	103.0-124.4			Teqing			Complete			Zhou et al, 2004
	Pi8		Isozyme			Amp-3, pgi-2, Amp-3	98.0			Kasalath			Complete			Tabien et al, 2000
	Pi13(t)		Isozyme			Amp-3	74.6-78.2			Mawong			Complete			Pan et al, 1996
	Pi13		RFLP			R2123, R538	68.1			Kasalath			-			Fjellstrom et al, 2006; Hayasaka et al, 1995
	Pi2(t)		RFLP			RG64	2.8			Cultivar 5173			Complete			Yu et al, 1991; Zhou et al, 2006
	Pi2-2		SSR			AP5659-3, RM19817	58.7			Jefferson						Ballini et al, 2008
	Pi50(t)		InDel			GDAP51, GDAP16	46.8						-			Jiang et al, 2012
	Pi40(t)		SSR, CAPS			RM3330, RM527 S2539	54.1-61.6			CO39, IR50			-			Jeung et al, 2007
	Pi59(t)		SSR			RM19835				Haoru × US-2			-			Zhou et al, 2006
7	Pi17(t)		-			-	94.0-104.0			Kasalath			Complete			Zhu et al, 2004
8	Pi36		SSR			RM5647	21.6-25.2			Q61			-			Zhu et al, 1993
			CAPS			CRG2, CRG3, CRG4
	Pi33		SSR			RM72, RM44	45.4			IR64, Bala			Complete			Pan et al, 1995
Chr		Gene		Tightly linked marker				Map position (cM)			Donor rice			Resistance type			Reference
Chr		Gene		Type	Name			Map position (cM)			Donor rice			Resistance type			Reference
8		Pizh/Pi11(t)		RFLP	RZ617			53.2-84.8			Zhaiyeqing			Complete			Berruyer et al, 2003
		Pi29(t)		RFLP	RZ617, RGA-IR86			69.0			IR64			-			Nguyen et al, 2006
		PiGD-1(t)		RFLP	-			11.3			Sanhuangzan 2						He et al, 2012
		Pi55(t)		SSR, STS	H2, H66			100.6			Yuejingsimiao 2, Sanhuangzan 2						Liu et al, 2005; He et al, 2012
9		Pii2(t)		-	-						Ishikari Shiroke			-			Pan et al, 2003
		Pi5(t)		CAPS	94A20r, 76B14f, 40N23r			31.3-33.0			RIL125, RIL249, RIL260 (Moroberekan)			Complete			Mackill and Bonman, 1992
				SNP	JJ817												Kinoshita and Kiyosawa, 1997
		Pi3(t)		-	-			31.3-33.0			Pai-Kan-Tao			Complete			Liu et al, 2004
		Pi15		RAPD	BAPi15486, BAPi15782, BAPil5844			31.3-34.9			GA25			Complete
		Pi56(t)		SSR	RM24022			31.3			SHZ-2, BC-10 × TXZ-13			Complete			Jeon et al, 2003
		Pihk2		SSR InDel	RM24048, RM24065, RM7390, RM3912, RM24019 ID3, ILP-7, ID-5, ID-9, ILP-19						Heikezijing			Complete			He at al, 2017
10		Pi28(t)		RFLP	RZ500			114.7			Azucena			-			Nguyen et al, 2006
		PiGD-2(t)		RFLP	R16			3.9			Sanhuangzhan 2			-			He et al, 2012
11		Pia		CAPS	Yca72			36			Aichi Asahi			Complete			Zenbayashi et al, 2002
		PiCO39(t)		CAPS	RGA8, RZ141, RGACO39			49.1			CO39			Complete			Kwon et al, 2008
		Pilm2		RFLP	L457B, G2132b, RZ536, RG1109			56.2-117.9			Lemont			Complete			Zhou et al, 2004
		Pi30(t)		RFLP	OpZ11-f, RGA-IR14			59.4-60.4			IR64			-			Nguyen et al, 2006
		Pi7(t)		-	-			71.4-84.3			RIL29 (Moroberekan)			Complete			Miyamoto et al, 2001
		Pi34		RFLP	C1172, E2021			79.1-91.4			Chubu 32			Partial			Yunoki et al, 1970
		Pi38		SSR	RM206, RM21			79.1-88.7			Tadukan			-			Goto, 1970
		Pif		-	-			-			St No.1			Partial			Gowda et al, 2006
		Pb1		-	-			85.7-91.4			Modan			Partial			Fuentes et al, 2008
		Pi44(t)		AFLP	AF348, AF349			91.4-117.9			RIL29 (Moroberekan)			Complete			Chen et al, 1999; Chauhan et al, 2002
		Pikh/Pi54		SSR	RM206, RM144, RM224, RM1233			101.9			Tetep, Taipei 309			Complete			Fjellstrom et al, 2006; Hayasaka et al, 1995; Wu et al, 2013
		Pi1		SNP	CRG11-7, K28			112.1-117.9			C101LAC (Lac23)						Prasad et al, 2009
		Pi7(t)		RFLP	RG103A, RG16			71.4-84.3			RIL29 (Moroberekan)			Complete			Wang et al, 1994
		Pikm		InDel SSR	k6861, k2167 RM254, RM144			115.1-117.0			Tsuyake			Complete			Sun et al, 2013; Li et al, 2007
				SNP	k641, k6441, k473, k7237
		Pi18(t)		RFLP	RZ536			117.9			Suweon 365			Complete			Li et al, 2007; Ahn et al, 2000
		Pik		InDel	k6816, k2167			119.9-120.3			Kusabue			Complete			Hayashi et al, 2006
		Pik-p		SNP	k641, k39575, k403, k3957			119.9-120.3			HR22			Complete			Hayashi et al, 2006
		Pik-s		SSR	RM144, RM224, RM1233			115.1-117.3			Shin 2			Complete			Fjellstrom et al, 2006
		Pik-g		-	-			-			GA20			Complete			Tabien et al, 2000
		Pise1		-	-			-			Sensho			-			Izawall and Iwasakizl, 2000
		Pi-hk1		SSR	RM27248, RM27318			-			Heikezijing			Complete			Liu et al, 2012
		Pikur2		-	-			-			Kuroka			-			Goto, 1970
		Pi-1(t)		SSR	RM12331, RM224			112.1-117.9			ILs C10LAC and C101A5			-			Sharma et al, 2005
		Pi47		SSR	RM206, RM224						XZ3150 × CO39			Complete			Ahn et al, 2000
		Pi49		STS	K10, K134			1.01-1.89			CO39						Chen et al, 1999
		Pi60(t)		InDel	K1-4, E12						93-11			Complete			Huang et al, 2006
		Pi-jnw1		SSR InDel	RM27150, RM27381 W26, W28, BS33, BS39, BS71						Jiangnanwan			Complete			Wang et al, 2016
		Pi65(t)		SNP InDel	SNP-2, SNP-8 InDel-1			-			Guangyu 129			Complete			Zheng et al, 2016
12		Pi24		RGA	RGA3			10.3			Zhong 156			Complete			Zhuang et al, 2002; Hua et al, 2012
		Pi62(t)		RFLP	RG869			12.2-26.0			Yashiromochi			-			Kumar et al, 2010
		Pitq6		RFLP	RG341a, RG869, L102, G1468a, RZ397, RZ257			29.2-47.5			Teqing			Complete			Zhu et al, 2000
Chr		Gene		Tightly linked marker					Map position (cM)			Donor rice			Resistance type			Reference
Chr		Gene		Type	Name				Map position (cM)			Donor rice			Resistance type			Reference
12		Pi6(t)		RFLP	RG869				32.6-63.2			Apura			Complete			Yu et al, 1991
		Pi12(t)		-	-				42.8-53.0			Hongjiaozhan			Complete			-
		Pi31(t)		RFLP	O10-800				44.3			IR64			-			Nguyen et al, 2006
		Pi32(t)		RFLP	AF6				47.5			IR64			-			Nguyen et al, 2006
		Ipi(t)		RFLP	RG241X				47.6-58.3			BS125 × WL02			-			Causse et al, 1994
		IPi3(t)		RFLP	RG241X				47.6-58.3			BS125 × WL02			-			Causse et al, 1994
		Pi157		-	-				49.5-62.2			Moroberecan			-			-
		Pita		SNP RAPD	ta642, ta801, ta3, ta577, ta5, pita440, pita1042, pita403 SP4B9, SP9F3				50.4			Taducan Yashiro-mochi, Tsuyuake			Complete			Hayashi et al, 1998
		Pi39(t)		CAPS	39M6, 39M7				50.4			Q15						Bryan et al, 2000
		Pi20(t)		SSR	RM1337, RM5364, RM7102				51.5-51.8			IR24			Complete			Liu et al, 2007
		PiGD-3(t)		SSR	RM179				55.8			Sanhuangzhan 2			-			Liu et al, 2007
		Pi42(t)		STS SSR	STS5 RRS44, RRS51, RRS60, RRS63, RRS6							DHR9						Kumar et al, 2010
		Pi4(t)		RFLP	RG869, RZ397				47.5			Apura						Nguyen et al, 2006
		Pita-2		SNP	ta642, ta801, ta3, ta577				50.4			Shimokita			Complete			Hyashi et al, 1998
		Pi19(t)		-	-							Aichi Asahi			Complete			Inukai and Nelson, 1994
		Pi21(t)		RFLP	-				43.4-59.6			Suweon 365						Terashima et al, 2008
		Pi58(t)		SSR	RM27954, RM27933, RM3103							Haoru × US-2						Zhou et al, 2004
		Pi48		SSR	RM5364, RM7102							XZ3150 × CO39			Complete			Ahn et al, 2000
		Pi61(t)		InDel	M2, S29							93-11			Complete			Huang et al, 2011

Chr	Gene		Tightly linked marker				Map position (cM)			Donor rice			Resistance type			Reference
Chr	Gene		Type			Name	Map position (cM)			Donor rice			Resistance type			Reference
1	Pit		SNP			t311, t256, t8042	16.1			Tjahaja			Complete			Hayashi et al, 2006
	Pi27(t)		SSR			RM151, RN259	28.4-38.8			Q14			Complete			Sallaud et al, 2006
	Pitp(t)		SSR			RM246	114.1			Tetep			Partial			Barman et al, 2004
	Pi35(t)		SSR			RM1216, RM1003	132.0-136.6			Hokkai 188			Partial			Nguyen et al, 2006
	Pi37		SSR			RM302, RM212, FPSM1, FPSM2, FPSM4	136.1			St.No.1			Complete			Lin et al, 2007
			STS			S15628, FSTS1, FSTS2, FSTS3, FSTS4
	Pi64		SSR			RM11715, RM11787	-			Yangmaogu			Complete			Ma et al, 2015
	Pish		RFLP			-	148.7-154.8			Shin 2			Complete			Zhu et al, 2004
2	Pid1(t)		SSR			RM262	87.5-89.9			Digu			Complete			Chen et al, 2004
	Pig(t)		SSR			RM166, RM208	142.0-154.1			Guangchangzhan			Complete			Shi et al, 2012
	Pitq5		RFLP			RG520, RZ446B, RZ446A, RG654, RG256	150.5-157.9			Teqing			Complete			Zhou et al, 2004
	Piy1(t)		SSR			RM3248, RM20	153.2-154.1			Yanxian 1			-			Fukuta et al, 2004
	Piy2(t)		SSR			RM3248, RM20	153.2-154.1			Yanxian 1			-			Fukuta et al, 2004
	Pib		SNP			b213, b28, b2, b3989, Pibdom	154.1			Tohoku, IL9, Koshiihikari			Complete			Hayashi et al, 2006
	Pi14(t)		Isozyme			Amp-1	32.6			Maowang			Complete			Tabien et al, 2000
	Pi16(t)		Isozyme			Amp-1	34.3			AUS373, Maowamg			Complete			Pan et al, 1996
	Pi-Da(t)		SSR			RM5529, RM211	12.6			Dacca 6			-			Lei et al, 2005; Shi et al, 2012
3	Pi66(t)		SSR			RM487, RM16, RM55, RM168				AS201			Partial			Liang et al, 2016
4	Pi21		STS			P702D03-#79	58.6			Owarihatamochi			Partial			Pan et al, 1998
	Pikur1		Isozyme			-	86.0			Kuroka			-			Fukuoka et al, 2007
	Pi39(t)		SSR			RM3843, RM5473	107.4-108.2			Chubu 111 (Haonaihuan)			-			Shinoda et al, 1971
	Pi(t)		-			-	12.2			P167(1)			-			Causse et al, 1994
	Pi5(t)		RFLP			RG788, RG498	12.0			RIL29 (Morobere kan)			Complete			Wang et al, 1994
5	Pi26(t)		RFLP			RG313	22.5-24.7			Azucena			-			Ahn et al, 1996; Nguyen et al, 2006
	Pi23(t)		-			-	59.3-99.5			Sweon 3655			-			Terashima et al, 2008
	Pi10		InDel			OPF62700	88.5-102.8			Tongil			Complete			Wu et al, 2005
6	Pi22(t)		RFLP			-	38.7-41.9			Sweon 365			-			Terashima et al, 2008
	Pi26		RFLP			K17, K2123	22.5-63.2			Gumei 2			Complete			Ahn et al, 1996
	Pi27(t)		RFLP			Est-2	51.9			IR64			-			Nguyen et al, 2006
	Pi40(t)		SSR			RM3330, RM527	54.1-61.6			IR65482-4-136-2-2			-
			CAPS			S2539
	Piz-5		STS			BS2-Pi9, NBS4-Pi9	58.7			Tadukan			Complete			Deng et al, 2006
	Piz		InDel			z4794	58.7			Zenith			Complete			Hayashi et al, 2006
			SNP			z60510, z5765, z56592, z565962										Wang et al, 2012
	Piz-t		InDel			z4794	58.7			Torde 1			Complete			Deng et al, 2006
	Pi9		-			-	58.7			75-1-127 (101141)			Complete			Qu et al, 2006; Koide et al, 2013
	Pi25(t)		RFLP			A7-RG456	63.2-64.6			Gumei 2			-			Ahn et al, 1996
	Pid2		CAPS			CAPS1, CAPS8	65.8			Digu			Complete			Chen et al, 2006
	Pigm(t)		CAPS			C26348	65.8			Gumei 4			-			Naqvi and Chattoo, 1996
	Pitq1		RFLP			RZ682, C236, RG653, RZ508	103.0-124.4			Teqing			Complete			Zhou et al, 2004
	Pi8		Isozyme			Amp-3, pgi-2, Amp-3	98.0			Kasalath			Complete			Tabien et al, 2000
	Pi13(t)		Isozyme			Amp-3	74.6-78.2			Mawong			Complete			Pan et al, 1996
	Pi13		RFLP			R2123, R538	68.1			Kasalath			-			Fjellstrom et al, 2006; Hayasaka et al, 1995
	Pi2(t)		RFLP			RG64	2.8			Cultivar 5173			Complete			Yu et al, 1991; Zhou et al, 2006
	Pi2-2		SSR			AP5659-3, RM19817	58.7			Jefferson						Ballini et al, 2008
	Pi50(t)		InDel			GDAP51, GDAP16	46.8						-			Jiang et al, 2012
	Pi40(t)		SSR, CAPS			RM3330, RM527 S2539	54.1-61.6			CO39, IR50			-			Jeung et al, 2007
	Pi59(t)		SSR			RM19835				Haoru × US-2			-			Zhou et al, 2006
7	Pi17(t)		-			-	94.0-104.0			Kasalath			Complete			Zhu et al, 2004
8	Pi36		SSR			RM5647	21.6-25.2			Q61			-			Zhu et al, 1993
			CAPS			CRG2, CRG3, CRG4
	Pi33		SSR			RM72, RM44	45.4			IR64, Bala			Complete			Pan et al, 1995
Chr		Gene		Tightly linked marker				Map position (cM)			Donor rice			Resistance type			Reference
Chr		Gene		Type	Name			Map position (cM)			Donor rice			Resistance type			Reference
8		Pizh/Pi11(t)		RFLP	RZ617			53.2-84.8			Zhaiyeqing			Complete			Berruyer et al, 2003
		Pi29(t)		RFLP	RZ617, RGA-IR86			69.0			IR64			-			Nguyen et al, 2006
		PiGD-1(t)		RFLP	-			11.3			Sanhuangzan 2						He et al, 2012
		Pi55(t)		SSR, STS	H2, H66			100.6			Yuejingsimiao 2, Sanhuangzan 2						Liu et al, 2005; He et al, 2012
9		Pii2(t)		-	-						Ishikari Shiroke			-			Pan et al, 2003
		Pi5(t)		CAPS	94A20r, 76B14f, 40N23r			31.3-33.0			RIL125, RIL249, RIL260 (Moroberekan)			Complete			Mackill and Bonman, 1992
				SNP	JJ817												Kinoshita and Kiyosawa, 1997
		Pi3(t)		-	-			31.3-33.0			Pai-Kan-Tao			Complete			Liu et al, 2004
		Pi15		RAPD	BAPi15486, BAPi15782, BAPil5844			31.3-34.9			GA25			Complete
		Pi56(t)		SSR	RM24022			31.3			SHZ-2, BC-10 × TXZ-13			Complete			Jeon et al, 2003
		Pihk2		SSR InDel	RM24048, RM24065, RM7390, RM3912, RM24019 ID3, ILP-7, ID-5, ID-9, ILP-19						Heikezijing			Complete			He at al, 2017
10		Pi28(t)		RFLP	RZ500			114.7			Azucena			-			Nguyen et al, 2006
		PiGD-2(t)		RFLP	R16			3.9			Sanhuangzhan 2			-			He et al, 2012
11		Pia		CAPS	Yca72			36			Aichi Asahi			Complete			Zenbayashi et al, 2002
		PiCO39(t)		CAPS	RGA8, RZ141, RGACO39			49.1			CO39			Complete			Kwon et al, 2008
		Pilm2		RFLP	L457B, G2132b, RZ536, RG1109			56.2-117.9			Lemont			Complete			Zhou et al, 2004
		Pi30(t)		RFLP	OpZ11-f, RGA-IR14			59.4-60.4			IR64			-			Nguyen et al, 2006
		Pi7(t)		-	-			71.4-84.3			RIL29 (Moroberekan)			Complete			Miyamoto et al, 2001
		Pi34		RFLP	C1172, E2021			79.1-91.4			Chubu 32			Partial			Yunoki et al, 1970
		Pi38		SSR	RM206, RM21			79.1-88.7			Tadukan			-			Goto, 1970
		Pif		-	-			-			St No.1			Partial			Gowda et al, 2006
		Pb1		-	-			85.7-91.4			Modan			Partial			Fuentes et al, 2008
		Pi44(t)		AFLP	AF348, AF349			91.4-117.9			RIL29 (Moroberekan)			Complete			Chen et al, 1999; Chauhan et al, 2002
		Pikh/Pi54		SSR	RM206, RM144, RM224, RM1233			101.9			Tetep, Taipei 309			Complete			Fjellstrom et al, 2006; Hayasaka et al, 1995; Wu et al, 2013
		Pi1		SNP	CRG11-7, K28			112.1-117.9			C101LAC (Lac23)						Prasad et al, 2009
		Pi7(t)		RFLP	RG103A, RG16			71.4-84.3			RIL29 (Moroberekan)			Complete			Wang et al, 1994
		Pikm		InDel SSR	k6861, k2167 RM254, RM144			115.1-117.0			Tsuyake			Complete			Sun et al, 2013; Li et al, 2007
				SNP	k641, k6441, k473, k7237
		Pi18(t)		RFLP	RZ536			117.9			Suweon 365			Complete			Li et al, 2007; Ahn et al, 2000
		Pik		InDel	k6816, k2167			119.9-120.3			Kusabue			Complete			Hayashi et al, 2006
		Pik-p		SNP	k641, k39575, k403, k3957			119.9-120.3			HR22			Complete			Hayashi et al, 2006
		Pik-s		SSR	RM144, RM224, RM1233			115.1-117.3			Shin 2			Complete			Fjellstrom et al, 2006
		Pik-g		-	-			-			GA20			Complete			Tabien et al, 2000
		Pise1		-	-			-			Sensho			-			Izawall and Iwasakizl, 2000
		Pi-hk1		SSR	RM27248, RM27318			-			Heikezijing			Complete			Liu et al, 2012
		Pikur2		-	-			-			Kuroka			-			Goto, 1970
		Pi-1(t)		SSR	RM12331, RM224			112.1-117.9			ILs C10LAC and C101A5			-			Sharma et al, 2005
		Pi47		SSR	RM206, RM224						XZ3150 × CO39			Complete			Ahn et al, 2000
		Pi49		STS	K10, K134			1.01-1.89			CO39						Chen et al, 1999
		Pi60(t)		InDel	K1-4, E12						93-11			Complete			Huang et al, 2006
		Pi-jnw1		SSR InDel	RM27150, RM27381 W26, W28, BS33, BS39, BS71						Jiangnanwan			Complete			Wang et al, 2016
		Pi65(t)		SNP InDel	SNP-2, SNP-8 InDel-1			-			Guangyu 129			Complete			Zheng et al, 2016
12		Pi24		RGA	RGA3			10.3			Zhong 156			Complete			Zhuang et al, 2002; Hua et al, 2012
		Pi62(t)		RFLP	RG869			12.2-26.0			Yashiromochi			-			Kumar et al, 2010
		Pitq6		RFLP	RG341a, RG869, L102, G1468a, RZ397, RZ257			29.2-47.5			Teqing			Complete			Zhu et al, 2000
Chr		Gene		Tightly linked marker					Map position (cM)			Donor rice			Resistance type			Reference
Chr		Gene		Type	Name				Map position (cM)			Donor rice			Resistance type			Reference
12		Pi6(t)		RFLP	RG869				32.6-63.2			Apura			Complete			Yu et al, 1991
		Pi12(t)		-	-				42.8-53.0			Hongjiaozhan			Complete			-
		Pi31(t)		RFLP	O10-800				44.3			IR64			-			Nguyen et al, 2006
		Pi32(t)		RFLP	AF6				47.5			IR64			-			Nguyen et al, 2006
		Ipi(t)		RFLP	RG241X				47.6-58.3			BS125 × WL02			-			Causse et al, 1994
		IPi3(t)		RFLP	RG241X				47.6-58.3			BS125 × WL02			-			Causse et al, 1994
		Pi157		-	-				49.5-62.2			Moroberecan			-			-
		Pita		SNP RAPD	ta642, ta801, ta3, ta577, ta5, pita440, pita1042, pita403 SP4B9, SP9F3				50.4			Taducan Yashiro-mochi, Tsuyuake			Complete			Hayashi et al, 1998
		Pi39(t)		CAPS	39M6, 39M7				50.4			Q15						Bryan et al, 2000
		Pi20(t)		SSR	RM1337, RM5364, RM7102				51.5-51.8			IR24			Complete			Liu et al, 2007
		PiGD-3(t)		SSR	RM179				55.8			Sanhuangzhan 2			-			Liu et al, 2007
		Pi42(t)		STS SSR	STS5 RRS44, RRS51, RRS60, RRS63, RRS6							DHR9						Kumar et al, 2010
		Pi4(t)		RFLP	RG869, RZ397				47.5			Apura						Nguyen et al, 2006
		Pita-2		SNP	ta642, ta801, ta3, ta577				50.4			Shimokita			Complete			Hyashi et al, 1998
		Pi19(t)		-	-							Aichi Asahi			Complete			Inukai and Nelson, 1994
		Pi21(t)		RFLP	-				43.4-59.6			Suweon 365						Terashima et al, 2008
		Pi58(t)		SSR	RM27954, RM27933, RM3103							Haoru × US-2						Zhou et al, 2004
		Pi48		SSR	RM5364, RM7102							XZ3150 × CO39			Complete			Ahn et al, 2000
		Pi61(t)		InDel	M2, S29							93-11			Complete			Huang et al, 2011

Trait	Gene/QTL	Marker type	Technique	Application	Reference
Blast resistance	Pi1, Piz-5, Pita	RFLP	MAS	Pyramiding of three near isogenic lines (C101LAC, C101A51 and C101PKT) for blast resistance into a single cultivar CO39, each carrying the major genes Pi1, Piz-5 and Pita, respectively	Hittalmani et al, 2000
Blast resistance	Pi1	SSR, ISSR	MABB	Applied for backcross breeding of variety	Liu et al, 2002
Bacterial blight resistance and blast resistance	Xa21, Piz	SSR	MAS	Pyramiding of target traits	Narayanan et al, 2002
Blast resistance	Pid1, Pib, Pita, Pi2	SSR	MAS	Pid1, Pib and Pita genes were introduced into G46B, while Pi2 was introduced into Zhenshan 97B	Chen et al, 2004
Blast resistance	Piz	SSR	MAS	Successfully used for selection of blast resistance in a wide array of rice germplasm	Fjellstrom et al, 2006
Blast resistance and bacterial blight resistance and sheath blight resistance	Xa13, Xa21, Pi54, qSBR11	SSR	MAS	Transfer genes conferring the resistances toward three different diseases in rice	Singh V K et al, 2012
Blast resistance	Pita	Gene specific	MAS	Existence of Pita gene in 141 rice germplasms was determined, but the results were more articulated when Pita gene was introduced through advanced breeding lines	Wang et al, 2007
Blast resistance	Pi1, Pi2, Pi33	SSR	MABB	Introgressed into Jin23B	Chen et al, 2008
Blast resistance and bacterial blight	Pi1, Pi2, Xa23	SSR	MABB	Sucessfully applied for breeding variety Rongfeng B	Fu et al, 2012
Blast resistance	Piz-5, Pi54	SSR	MABB	Transfer blast resistance genes from donor lines (C101A51 and Tetep) into PRR78 to develop Pusa 1602 (PRR78 + Piz-5) and Pusa 1603(PRR78 + Pi54), respectively	Singh et al, 2013
Blast resistance	Pi9	Gene specific	MABB	Applied to introgress the cultivar Luhui 17	Wen and Gao, 2011
Blast resistance	Pi1, Piz	SSR	MABB	Pyramiding of Pi1 and Piz-5 genes into introduced PRR78	Gouda et al, 2013
Blast resistance	Pi39	InDel	MABB	Introgressed into Chinese cultivar Q15	Hua et al, 2015
Blast resistance and bacterial blight	Pi2, Xa21, Xa33	SSR	MABB	Introgressed into RPHR-1005	Kumar et al, 2016
Blast resistance	Pi40	SSR	MABB	Introgressed into elite cultivars Turkish, Osmancik-97 and Halilbey	Beser et al, 2016
Blast resistance	Pi1, Pi2	SSR	MABB	Introgressed into Intan variety and BPT5204	Hegde and Prashanthi, 2016
Blast resistance	Pi46, Pita	SSR	MABB	Introgressed into Hang hui 179 (HH179)	Xiao et al, 2016
Blast resistance	Pi2, Pi9	SNP	MABB	Introgressed into R179	Luo et al, 2016
Blast resistance	Pizt, Pi2, Pigm, Pi40, Pi9, Piz	SSR	MAS	Introgressed into Yangdao 6	Wu et al, 2016
Blast resistance	Pi1, Pi2, Pi33	SSR	MAS	Introgressed into Russian rice varieties	Usatov et al, 2016
Blast resistance	Pi9, Pizt, Pi54	SNP	MABB	Introgressed into japonica rice 07GY31	Xiao et al, 2016
Blast resistance	Pi-b, Pik-h	SSR	MAS	Introgressed into MR219	Tanweer et al, 2015