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 4 QTL associated with tiller number (TN) or panicle number (PN) in the Rice Diversity Panel 1 (RDP1), arranged in chromosomal order to better indicate that 14 of the 15 QTL regions were associated with both TN and PN

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^b	Panel^c	Refer-ence allele^d	Reference allele effect^d	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^b	Panel^c	Refer-ence allele^d	Reference allele effect^d	RAP ID^e	Gene symbol(s)^f or name (s)	Citation
qTN1-1	1	18814513	23871743	5057230	18864513	5.4	TN	AR-gh	AUS	C	1.51	LOC_Os01g33240	OsABCG33	Bird et al. (2007), Yasuno et al. (2009), Zhao et al. (2019)
qPN1-1		17980650	20789712	2809062	18692039	7.1	PN	AR-gh	AUS	G	1.43	LOC_Os01g34970	OsABCB2
↓												LOC_Os01g35030	OsABCB3
qTN1-2	1	38561275	41357900	2796655	41275767	6.4	TN	AR-gh	AUS	C	1.83	LOC_Os01g69830	OsSPL2^g	Dai et al. (2018)
qPN1-2		41677001	41952874	275873	41727001	5.0	PN	AR-gh	AUS	A	− 2.62	LOC_Os01g71310	OsCKX4^g	Wang et al. (2019)
↓					41902874	5.4	PN	AR-gh	JAP	T	0.92	LOC_Os01g72330	OsRR4	Panda et al. (2018)
qTN2-1	2	663286	3898253	3234967	902313 3096122	5.1 6.9	TN	AR-gh	AUSTEJ	A C	− 3.06 –1.18	LOC_Os02g05840	OsVIL2^g	Yoon et al. (2019)
qPN2-1		3046122	3208370	162248	3096122	5.9	PN	AR-gh	TEJ	C	− 1.18	LOC_Os02g04680	OsSPL3^g	Liu et al. (2015)
qTN2-2	2	23111877	23211877	100000	23161877	5.4	TN	AR-gh	TEJ	C	− 2.15	LOC_Os02g38130	OsNAC50	A NAM, IRGSP-1.0, Kawahara et al. (2013)
qPN2-2		22525572	26480368	3954796	24663719	5.6	PN	AR-gh	TEJ	A	0.77	LOC_Os02g39920	OsBIP135	Fang et al. (2020)
↓												LOC_Os02g41450	OsNAC51	a NAM, IRGSP-1.0, Kawahara et al. (2013)
qTN4-1	4	12678105	15595957	2917852	13078293	7.3	TN	AR-gh	IND	G	− 1.66	LOC_Os04g23440	OsMADS25^g	Zhang et al. (2018)
↓					14591830	5.8	TN	AR-gh	JAP	G	− 6.88	LOC_Os04g23910	OsMADS82^g	Sui et al. (2016)
qTN4-2	4	21832919	28493892	6660973	21882919	7.2	TN	AR-gh	AUS	C	− 1.79	LOC_Os04g36070;	OsRR1^g	Wang et al. (2019)
↓					28443892	5.6	TN	AR-gh	INDAUS	CG	− 1.85	LOC_Os04g39489	OsAPP13^g	Wang et al. (2020)
qPN4	4	20986816	26514418	5527602	24460118	7.5	PN	AR-gh	INDAUS	A	− 1.12	LOC_Os04g46470	OsCCD7/HTD1^g	Zou et al. (2006)
↓					26425281	8.4	PN	AR-gh	AUS	G	− 1.61	LOC_Os04g46580	OsSPL7^g	Dai et al. (2018)
qTN6	6	27119407	27486520	367113	27058472	5.7	TN	AR-gh	AUS	T	− 2.64	LOC_Os06g44970	OsPin2^g	Chen et al. (2012)
qPN6		27204808	27800000	595192	27254808	5.3	PN	AR-gh	AUS	A	− 1.02	LOC_Os06g45310	OsSPL11	Preston and Hileman (2013), Liu et al. (2015)
qTN8-1	8	8359495	9777576	1418081	9513920	5.7	TN	AR-gh	IND	A	− 1.91	LOC_Os08g15840	OsXBO S35	Tavakol et al. (2015), Zhang et al. (2019a, b)
qPN8-1		9586995	11777086	2190091	9636995	6.1	PN	AR-gh	IND	T	− 1.33
qTN8-2	8	24971609	25071609	100000	25021609	5.5	TN	AR-gh	IND	C	2.10	LOC_Os08g39890	OsSPL14/ipa1^g	Liu et al. (2019)
qPN8-2		25864572	27370635	1506063	27320051	5.7	PN	AR-gh	IND	C	0.94	LOC_Os08g41720	OsPIN5b^g	Lu et al. (2015)
↓												LOC_Os08g42690	OsXBOS252	Tavakol et al. (2015), Zhang et al. (2019a, b)
qTN10	10	19312710	22648248	3335538	19373373	6.3	TN	AR-gh	AUS	C	2.81	LOC_Os10g35930	OsPLIM2c	Na et al. (2014)
qPN10		19536678	19636678	100000	19586678	5.9	PN	AR-gh	AUS	A	1.24	LOC_Os10g36703	OsSAUR56	Auxin-responsive, IRGSP-1.0, Kawahara et al. (2013)
↓												LOC_Os10g36710	CAMK gene	Ikeda et al. (2011)
qTN11-1	11	3999917	4144702	145880	4094702	5.5	TN	AR-gh	TRJ	A	0.79	LOC_Os11g06900	amidase family protein	IAA synthesis, Mano et al. (2010)
qPN11-1		3366987	4145797	777715	3416987	7.0	PN	AR-gh	TRJ	C	− 1.29	LOC_Os11g06820	OsAUX5	IRGSP-1.0, Kawahara et al. (2013)
↓												LOC_Os11g07700	OsNAC126	a NAM, IRGSP-1.0, Kawahara et al. (2013)
qTN11-2	11	12957650	17775288	4817638	14153306	5.9	TN	AR-gh	IND	C	1.65	LOC_Os11g25990	OsIAGLU^g	Choi et al. (2012)
↓					17698549	5.4	TN	AR-gh	TRJ	A	0.89	LOC_Os11g29840	OsLazy1	an auxin transporter gene per IRGSP-1.0, Kawahara et al. (2013)
qPN11-2		13707162	18455763	4748601	17429259	5.1	PN	AR-gh	IND	G	− 1.62	LOC_Os11g30370	OsSPL1 9	Liu et al. (2015), Dai et al. (2018)
↓					18405421	5.2	PN	AR-gh	AUS	T	− 2.10
qTN12-1	12	2585066	5102002	1603575	2635066	6.5	TN	AR-gh	AUS	G	1.68	LOC_Os12g05590	OsRCN3^g	Nakagawa et al. (2002)
qPN12-1		2654229	4029671	1375442	2714516	5.3	PN	AR-gh	AUS	A	1.16	LOC_Os12g05990	OsNAC134	NAM, IRGSP-1.0, Kawahara et al. (2013)
↓												LOC_Os12g07480	OsTCP28	branching factor, IRGSP-1.0, Kawahara et al. (2013)
qTN12-2	12	10383053	11837888	4823940	11787888	5.8	TN	AR-gh	IND	C	2.20	LOC_Os12g13720	OsABCG49	three other ABC transporters affect TN per Bird et al. (2007), Yasuno et al. (2009), Zhao et al. (2019)
qPN12-2		10394663	12121979	5158266	9285514	5.7	PN	AR-gh	AUS	C	1.48	LOC_Os12g17310	OsBIP134	Fang et al. (2020)
↓					12071590	5.7	PN	AR-gh	IND	C	1.33	LOC_Os12g21710	OsZ-ISO^g	Liu et al. (2020)
qTN12-3	12	14477811	17557077	3079266	15793337	5.6	TN	AR-gh	AUS	G	− 1.63	LOC_Os12g27994	OsDEC1	per Itoh et al. (2012), alters auxin/CK
qPN12-3		14110118	17563794	3453676	16483239	6.2	PN	AR-gh	AUS	T	− 1.29	LOC_Os12g28270	OsAH	Rampey et al. (2004)
↓												LOC_Os12g29330	OsNAC139	a No Apical Meristem protein per IRGSP-1.0, Kawahara et al. (2013)

Tillers were counted in three replications of young plants 5- to 6-weeks old grown in the greenhouse, planted with repeated checks in an augmented design so that greenhouse location effect could be removed from RDP1 accession data. Panicle number was counted in the same replication 2 and 3 plants grown to maturity
^aO. sativa SNPs are identified by their physical location based on the Os-Nipponbare-Reference-IRGSP-1.0 assembly (Kawahara et al. 2013)
^bTiller number (TN) was counted in three replications of 5- to 6-wk-old greenhouse grown plants; panicle number (PN) was evaluated using the same replications 2 and 3 plants grown to maturity. Best linear unbiased estimates (BLUEs) were calculated per replication, and across replications
^cPanels 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, except where inclusion of both INDAUS and AUS peaks validated the size of the overlapping qTN4-2 and qPN4
^dReference allele based on the Os-Nipponbare-Reference-IRGSP-1.0 assembly (Kawahara et al., 2013). A negative allele effect at a TN or PN locus reflects a reduction in the tiller number or panicle number associated with the reference allele
^eRAP ID is the Rice Annotation Project identification locus identified for the candidate gene
^fGene nomenclature followed the standardized nomenclature for rice genes used in Oryzabase (Yamazaki et al. 2010)
^gIndicates a candidate gene that has been reported to have direct effect on tiller number per the cited study. All other candidate genes are less direct, e.g. are a member of a gene family in which a different member has been shown by the cited study to have a direct effect on TN, or a gene documented to have a direct effect on a hormone known to affect TN

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