Genome-wide association mapping revealed a diverse genetic basis of seed dormancy across subpopulations in rice (Oryza sativa L.)

Table 2 Genome-wide significant association signals of GP in the freshly harvested seeds using LMM method

Pop	Signals	Lead SNP^b	Chr	Position	P -Value	Contr %	Known gene	Dis (kb)	QTL	Reference
Whole	FHS1.1^ca	sf0131727984	1	31727984	5.3E-10	1.6	GA2ox3	66
	FHS1.2	sf0132299347	1	32299347	1.8E-08	18.9	GH3–2	−75
	FHS4.1	sf0415712552	4	15712552	2.7E-08	6.7
	FHS5.1	sf0523711156	5	23711156	4.9E-09	8.7	EUI1	−35	qDGR5b	[33]
	FHS7.0^c	sf0723792996	7	23792996	5.1E-08	18.3	Sdr4	3
	FHS11^a	sf1114334640	11	14334640	3.3E-08	1.4
Aus	FHS1.1^ca	sf0131727984	1	31727984	8.2E-09	6.0	GA2ox3	66
	FHS2.1	sf0217781998	2	17781998	1.9E-07	71.1
Indica	FHS1.3	sf0116084564	1	16084564	7.4E-08	0.3
	FHS7.0^c	sf0723792996	7	23792996	1.2E-08	44.9	Sdr4	3
Japonica	FHS1.4	sf0121684641	1	21684641	1.1E-07	1.7	OsEF3	−43
	FHS2.2	sf0217958009	2	17958009	6.8E-08	5.0
	FHS4.2	sf0416131386	4	16131386	7.2E-09	10.7
	FHS4.3	sf0421133500	4	21133500	2.5E-09	4.7
	FHS5.2^a	sf0510583389	5	10583389	8.4E-08	3.8
	FHS8.1	sf0822226957	8	22226957	2.2E-08	36.8	OsbohE	−9
	FHS8.2	sf0825914157	8	25914157	1E-10	4.1	OsISA	−16
	FHS10	sf1008134438	10	8134438	6.7E-08	2.5

FHS signals for germination percentage in freshly harvested seeds, followed by the chromosome and the signal number in the chromosome. Lead SNPs ID, the first two digits after sf indicate the chromosome number followed by the position on chromosome. Contr., contribution to the phenotype variance. Dis, the distance from known gene locus to the lead SNP with the negative sign representing upstream
^acommonly detected signals in FHS and ARS
^bfor more information see Additional file 6
^cCommonly detected signals between subpopulations

ISSN: 2730-6844