Genome-wide Association Study of a Panel of Vietnamese Rice Landraces Reveals New QTLs for Tolerance to Water Deficit During the Vegetative Phase

Hoang, Giang Thi; Van Dinh, Lam; Nguyen, Thom Thi; Ta, Nhung Kim; Gathignol, Floran; Mai, Chung Duc; Jouannic, Stefan; Tran, Khanh Dang; Khuat, Trung Huu; Do, Vinh Nang; Lebrun, Michel; Courtois, Brigitte; Gantet, Pascal

doi:10.1186/s12284-018-0258-6

Rice

Table 4 List of candidate genes located within the identified QTLs

From: Genome-wide Association Study of a Panel of Vietnamese Rice Landraces Reveals New QTLs for Tolerance to Water Deficit During the Vegetative Phase

QTL name	Chr	QTL position	Traits	No of signif.SNPs	Gene ID	Gene annotation	References
q1	1	22974974–23324354	RWC_T2, RWC_S2, Score3, Recovery	6	LOC_Os01g40860	OsALDH2–1, aldehyde dehydrogenase
q1	1	22974974–23324354	RWC_T2, RWC_S2, Score3, Recovery	6	LOC_Os01g40870	OsALDH2–2, aldehyde dehydrogenase	Ma et al., 2016
q2	1	24234676-24848754	Score1	4	LOC_Os01g42850	OsATG7, postmeiotic anther development	Kurusu et al., 2015
q3	2	35019983-35135670	RWC_T0	2	LOC_Os02g57250	OsIAA10, auxin-responsive Aux 2FIAA gene
q4	5	14993554-15948192	Score4	11	LOC_Os05g25770	OsWRKY45, transcription factor	Tao et al., 2011
q4	5	14993554-15948192	Score4	11	LOC_Os05g25850	OsMSOD1, superoxide dismutase	de Deus et al., 2015; Song et al., 2014
q5	6	17773531-17849604	RCGR	1
q6	7	17904510-18115227	RWC_T4, RWC_S4	5	LOC_Os07g30590	OsLTPG20, LTPL55 - protease inhibitor seed storage LTP family protein precursor	Edstam et al., 2013
q7	7	19592999-19695647	RWC_S3	1
q8	7	20593830-20792416	RWC_T2, Score1	2
q9	8	298529-415144	RWC_T2, RWC_T3, RWC_S2, Score2, Score3, Score4, Recovery	2
q10	8	3775479-4300868	RWC_T3	2	LOC_Os08g07440	AP2/EREBP68, transcription factor
q10	8	3775479-4300868	RWC_T3	2	LOC_Os08g07060	OsCRR6, photosynthetic capacity	Yamori et al., 2011
q11	10	10281766	Score4	1
q12	11	2438402-2567319	RWC_T2, RWC_T3, RWC_S2, Score3	8	LOC_Os11g05470	OsRCN1, PEBP family protein, negative response to cold, salinity, and heat stress	Tripathi et al., 2012
					LOC_Os11g05480	OsbZIP79, transcription factor HBP-1b, dehydration and salt stress response	Nijhawan et al., 2008
					LOC_Os11g05640	OsbZIP80, transcription factor, dehydration stress response	Nijhawan et al., 2008
q13	11	6642371-6895086	RWC_T1, RWC_T3, RWC_S1, Score1, Score2, Recovery	6		NBS-LRR proteins, disease resistance	Magbanuaet al., 2014; Onaga, 2014; Hou et al., 2015
q14	11	6934618-7049977	RWC_T1, RWC_S1	1	LOC_Os11g12530	Protein kinase, drought stress response	Chandran et al., 2016
q15	11	7603100	RWC_T1, RWC_S1	1	LOC_Os11g13840	OsERF19, AP2 domain containing protein
q16	11	15672814-16164499	RWC_T1, RWC_S1	4	LOC_Os11g27329	OsSCP61, peptidase S10
q17	11	19956781-20322700	ScorT4	2

RWC_T0 relative water content before drought treatment, RWC_T1 to RWC_T4 relative water content after 1 to 4 weeks of drought stress, RWC_S1 to RWC_S4 slope of relative water content after 1 to 4 weeks of drought stress, Score1 to Score4 drought sensitivity score after 1 to 4 weeks of drought stress; Recovery recovery ability, RCGR relative crop growth rate

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