Assessment of Rice Sheath Blight Resistance Including Associations with Plant Architecture, as Revealed by Genome-Wide Association Studies

Li, Danting; Zhang, Fantao; Pinson, Shannon R. M.; Edwards, Jeremy D.; Jackson, Aaron K.; Xia, Xiuzhong; Eizenga, Georgia C.

doi:10.1186/s12284-022-00574-4

Rice

Table 3 QTL associated with sheath blight (ShB) tolerance in the Rice Diversity Panel 1 (RDP1), arranged in chromosomal order to indicate when a QTL region associated with more than one trait

From: Assessment of Rice Sheath Blight Resistance Including Associations with Plant Architecture, as Revealed by Genome-Wide Association Studies

QTL	Chr	Start of QTL region (bp)	End of QTL region (bp)	QTL size (bp)	Peak SNP (bp)^a	-log₁₀(p)	Trait^b	Study location, year^c	Panel^d	Refer-ence allele^e	Reference allele effect^e	Candidate gene(s)
QTL	Chr	Start of QTL region (bp)	End of QTL region (bp)	QTL size (bp)	Peak SNP (bp)^a	-log₁₀(p)	Trait^b	Study location, year^c	Panel^d	Refer-ence allele^e	Reference allele effect^e	MSU ID^f	Gene symbol(s)^g or name(s)	Citation
qShB1	1	3650475	6013771	2363296	3852467	5.35	ShB-field	AR17	AUS	C	− 1.03	LOC_Os01g08710	OsWRKY102	Pooja et al. (2015)
qShB2	2	23195252	24805469	1610217	24095212	5.58	ShB-DI	NC-gh	INDAUS	C	0.51	LOC_Os02g39330	CHITINASE 6	Nakazaki et al. (2006)
qShB3-1	3	7054964	9262436	2207472	7210477	5.83	ShB-field	AR17	TRJ	T	− 0.92	LOC_Os03g13210	POXN	Gupta et al. (2012)
↓												LOC_Os03g13820	OsRLCK105	Vij et al. (2008)
↓												LOC_Os03g14000	OsACBP5	Liao et al. (2020), Panthapulakkal Narayanan et al. (2019)
qShB3-2	3	14819510	22780248	7960738	15552510	5.58	ShB-DI	AR-gh	JAP	T	0.77	LOC_Os03g27120	OsMC1	Wang and Zhang (2014), Huang et al. (2015)
↓					17960988	9.57	ShB-DI	AR-gh	TRJ	A	− 0.94	LOC_Os03g27170	OsMC3	Wang and Zhang (2014), Huang et al. (2015)
↓					19749554	6.12	ShB-field	AR16	TEJ	C	0.86	LOC_Os03g27190	OsMC8	Wang and Zhang (2014), Huang et al. (2015)
↓												LOC_Os03g27210	OsMC2	Wang and Zhang (2014), Huang et al. (2015)
↓												LOC_Os03g28940	TIFY10A	Shimizu et al. (2013)
↓												LOC_Os03g32314	OsAOC	Yoeun et al. (2018), Yu et al. (2020)
↓												LOC_Os03g33012	OsWRKY33	Shi et al. (2020)
qShB3-3	3	31569875	35543780	3973905	32191693	5.20	ShB-field	ARall	INDAUS	C	1.16	LOC_Os03g56820	FAH2	Nagano et al. (2016)
↓					34808860	5.41	ShB-field	ARall	AUS	A	− 0.71	LOC_Os03g60710	OsRLCK118	Li et al. (2017)
qShB4-1	4	4302304	7036317	2734013	4352304	5.21	ShB-field	ARall	AUS	G	− 0.72	LOC_Os04g10060	OsKS4	Park et al. (2012)
qShB4-2	4	13238768	16035378	2796610	13889641	5.75	ShB-field	NC18	395	T	0.46	LOC_Os04g24220	OsWAK32	Yuan et al. (2018)
↓												LOC_Os04g24510	OsWAK36	Yuan et al. (2018), Zhang et al. (2005)
↓												LOC_Os04g27860	OsRPS27	Saha et al. (2017)
qShB4-3	4	29559997	31797355	1961020	31471017	6.23	ShB-field	AR17	TRJ	G	− 0.94	LOC_Os04g51460	OsXET9	Dong et al. (2011)
qShB6-1	6	6804694	8440362	1635668	8112438	6.37	ShB-field	ARall	JAP	T	− 0.48	LOC_Os06g14540	GH9B3	Huang et al. (2019)
qShB6-2	6	21393533	24656415	3262882	23884567	5.67	ShB-DI	AR-gh	TRJ	C	− 0.67	LOC_Os06g40790	OsMLO7	Nguyen et al. (2016)
↓												LOC_Os06g41010	OsSAP1	de Freitas et al. (2019)
qShB7	7	22723331	25791908	3068577	25286267	5.54	ShB-field	ARall	TRJ	G	− 0.83	LOC_Os07g42370	TIFY10B	Ye et al. (2009)
qShB8-1	8	17404835	19452954	2048119	19393988	6.02	ShB-DI	NC-gh	AUS	A	0.96	LOC_Os08g29660	OsWRKY69	Berri et al. (2009), Choi et al. (2017)
qShB8-2	8	26787346	28440581	1653235	28417969	7.41	ShB-DI	NC-gh	AUS	A	− 0.81	LOC_Os08g42580	OsCERK1	Carotenuto et al. (2017)
↓												LOC_Os08g42700	PIBH8	Wang et al. (2001)
↓												LOC_Os08g44400	OsGRX20	Ning et al. (2018)
↓												LOC_Os08g44480	OsRPS25	Saha et al. (2017)
qShB9	9	21000812	22806305	1805493	21159446	5.96	ShB-DI	NC-gh	INDAUS	C	− 0.42	LOC_Os09g37006	OsAlba7	Verma et al. (2018)
↓												LOC_Os09g37270	OsRacGEF2	Akamatsu et al. (2015)
↓												LOC_Os09g39910	OsABC9	Oh et al. (2021)
qShB10	10	6072028	10023439	3951411	7584959	6.28	ShB-field	AR17	TRJ	C	− 0.92	LOC_Os10g11500	PR1-101	Mitsuhara et al. (2008)
↓												LOC_Os10g11980	OsAT1	Mori et al. (2007)
↓												LOC_Os10g13550	IREN	Ootsubo et al. (2016)
qShB11-1	11	8996571	12711977	3715406	10435614	5.36	ShB-DI	AR-gh	JAP	C	− 0.85	LOC_Os11g17380	OsRLCK321	Vij et al. (2008)
qShB11-2	11	16919914	19065774	2145860	17974233	5.39	ShB-DI	NC-gh	IND	C	1.03	LOC_Os11g31190	SWEET14	Blanvillain-Baufume et al. (2017)
qShB12	12	16108674	17979174	1870500	17674629	6.40	ShB-DI	AR-gh	AUS	G	− 0.95	LOC_Os12g29220	SWEET13	Liu et al. (2011)
↓												LOC_Os12g29430	OsWAK125	Dixit et al. (2015), Zhang et al. (2005)
↓												LOC_Os12g32820	OsABC12	Oh et al. (2021)

^aO. sativa SNPs are identified by their physical location based on the Os-Nipponbare-Reference-IRGSP-1.0 assembly (Kawahara et al. 2013)
^bSheath blight severity was rated (0 = resistant, 9 = severe) using both field (ShB-field) and microchamber (ShB-DI) studies. The field studies in Arkansas had two replications each year and the field study in China and the microchamber studies each had three replications
^cAR16 and AR17 indicates GWA-mapping used trait BLUPs calculated across two replications evaluated in Arkansas, USA in 2016 and 2017, respectively, while ARall indicates BLUPs calculated across both years, and NC18 indicates BLUP data were from the single-year study with three replications conducted in Nanning, China in 2018
^dPanels are defined as the complete Rice Diversity Panel 1 (395) and subpopulation groups, tropical japonica (TRJ), temperate japonica (TEJ), aus (AUS) and indica (IND). The two O. sativa subspecies Indica (INDAUS) comprised of IND and AUS and Japonica (JAP) comprised of TEJ and TRJ. QTL were often identified in GWA-mapping of more than one population (e.g., in INDAUS and AUS); the table presents the results based on the least-complex population in which the QTL was found significant
^eReference allele based on the Os-Nipponbare-Reference-IRGSP-1.0 assembly (Kawahara et al. 2013). A negative allele effect at a ShB locus reflects reduced disease severity, or increased tolerance
^fMSU ID is the Rice Genome Annotation Project locus identified for the candidate gene (Kawahara et al. 2013)
^gGene nomenclature followed the standardized nomenclature for rice genes used in Oryzabase (Yamazaki et al. 2010)

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