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 3 QTLs common across traits for the three panels. A – full panel; B – indica subpanel; C – japonica subpanel (P-values of the QTLs detected as significant at P < 5e-04)

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

QTLs	Chr	Position	Nb ass.	RWC_T0	RWC_T1	RWC_T2	RWC_T3	RWC_T4	RWC_S1	RWC_S2	RWC_S3	RWC_S4	Score1	Score2	Score3	Score4	Recovery	RCGR
A. Full panel
q1	1	23,006,901	1			3.2E-04
q1	1	23,083,234	2												4.9E-05		2.5E-04
q2	1	24,510,022	1												1.7E-04
		24,533,617	1												6.1E-05
		24,563,013	1												6.1E-05
q4	5	15,011,955	1													1.9E-05
		15,023,372	1													5.4E-05
		15,034,791	1													3.8E-04
		15,064,145	1													5.1E-05
		15,064,148	1													5.1E-05
		15,089,160	1													2.8E-04
		15,092,328	1													2.8E-04
		15,152,887	1													2.9E-04
		15,555,144	1													2.9E-04
		15,756,028	1													2.8E-04
		15,801,387	1													4.4E-04
q5	6	17,849,604	1															4.9E-05
q6	7	17,904,510	1									5.7E-05
		17,904,513	2					4.7E-04				5.7E-05
		17,947,305	2					1.9E-04				2.5E-05
		17,947,308	2					1.9E-04				2.5E-05
q7	7	19,695,647	1								1.5E-05
q8	7	20,730,455	1										5.4E-05
q8	7	20,791,018	1			2.6E-04
q9	8	298,529	2			3.4E-04				3.2E-04
q9	8	415,144	6			1.9E-05	2.1E-04			1.5E-04				1.8E-04	7.5E-05			6.5E-05
q10	8	4,048,851	1				1.8E-04
q10	8	4,053,013	1				7.2E-05
q12	11	2438,402	1			4.1E-04
		2,440,016	2			1.5E-04				4.9E-04
		2,441,445	1			4.1E-04
		2,444,894	2			1.0E-04				4.8E-04
		2,444,897	1			2.8E-04
		2,445,085	1			2.5E-04
		2,446,180	1			2.5E-04
q13	11	6,647,262	3		5.1E-06				2.0E-05				4.9E-04
q13*	11	6,662,124	3		2.5E-04								3.7E-04	3.1E-04
		6,691,388	3		2.6E-04				2.8E-04				4.2E-04
		6,691,391	3		4.4E-04				4.6E-04				3.5E-04
		6,706,811	4		1.2E-04		4.6E-04		2.2E-04								8.5E-05
		6,887,831	3		1.2E-04				1.3E-04				3.9E-04
q14	11	6,934,618	2		4.1E-06				6.0E-06
q15	11	7,603,100	2		2.2E-04				7.2E-05
q16	11	15,692,357	1						4.0E-04
		15,692,360	1						4.0E-04
		15,712,256	1						4.0E-04
		15,796,210	2		4.9E-04				8.2E-05
q17	11	19,980,023	1													1.9E-05
q17	11	20,322,700	1													1.9E-05
B. Indica subpanel
q1	1	22,974,974	1												1.4E-05
		23,006,901	2												2.4E-05		4.0E-04
		23,083,234	2												2.4E-05		4.0E-04
		23,151,112	2												2.4E-05		4.0E-04
		23,168,543	1												6.6E-05
		23,351,413	2			4.9E-04				3.6E-04
q4	5	15,011,955	1													1.6E-04
		15,023,372	1													3.1E-04
		15,064,145	1													3.8E-04
		15,064,148	1													3.8E-04
q6	7	17,904,510	2					2.3E-04				1.3E-04
		17,904,513	2					2.3E-04				1.3E-04
		17,912,789	1									2.8E-04
		17,947,305	2					8.3E-05				6.4E-05
		17,947,308	2					8.3E-05				6.4E-05
q9	8	298,529	1			3.1E-04
q9	8	415,144	6			1.3E-05	5.6E-06			1.9E-04					4.6E-06	3.5E-04	5.6E-05
q11	10	10,281,766	1													1.8E-05
q12	11	2438,402	1			1.8E-04
		2,440,016	3			6.8E-05	1.4E-04			2.5E-04
		2,441,445	1			1.8E-04
		2,444,894	4			5.9E-05	1.1E-04			3.0E-04					9.8E-05
		2,444,897	2			1.6E-04									2.1E-04
		2,445,085	3			1.6E-04	2.2E-04								9.0E-05
		2,446,177	2							3.1E-04					2.5E-04
		2,446,180	3			1.6E-04	2.2E-04								9.0E-05
q13	11	6,647,262	3		4.6E-05		4.2E-04		1.3E-04
q14	11	6,934,618	2		6.0E-05				6.3E-05
q15	11	7,603,100	1						3.5E-04
q16	11	15,796,210	1						3.8E-04
q17	11	19,980,023	1													8.2E-05
q17	11	20,322,700	1													8.2E-05
C. Japonica subpanel
q2	1	24,502,190	1										8.3E-05
		24,510,022	1										8.3E-05
		24,533,617	1										8.3E-05
		24,563,013	1										8.3E-05
q3	2	35,019,983	1	1.9E-04
q3	2	35,082,166	1	5.5E-05

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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