Genome-wide association study of important agronomic traits within a core collection of rice (Oryza sativa L.)

BMC Plant Biology

Table 3 Top highest genome-wide significant association signals of agronomic traits using EMMAX

Trait	Chr.	Position (IRGSP 1.0)	Reference allele	Alternative allele	Alternative allele frequency	-log₁₀(P)	R² (%)^a	Candidate/known gene^b
Grain width	1	11,789,024	C	A	0.77	6.29	9.41
Heading days	2	3,970,385	G	A	0.05	6.20	11.54
	3	32,824,935	T	A	0.05	6.21	8.57	CK1 [29]
	3	32,824,941	C	G	0.05	6.08	10.75	CK1 [29]
	4	463,322	G	A	0.95	7.86	12.86
	4	463,371	G	A	0.94	7.41	10.97
	8	15,918,110	G	A	0.05	6.21	7.42
	8	15,918,112	C	T	0.05	6.10	4.38
	9	18,628,054	T	C	0.13	6.04	6.87
Seed set rate	4	31,539,937	A	G	0.18	7.35	9.45	LOC_Os04g52940.1
	7	7,918,286	G	A	0.07	6.16	5.21
	7	8,178,284	A	G	0.12	6.47	3.15
	7	8,299,577	G	A	0.07	6.33	14.26
	7	8,390,152	C	T	0.07	6.08	5.27
	7	8,390,155	C	T	0.07	6.09	8.25
	7	8,447,659	T	C	0.09	6.45	9.64	LOC_Os07g14800.1

Note: ^aR² represents the genetic variants explained by the significant SNPs. ^bGene ID of MSU rice genome annotation project (http://rice.plantbiology.msu.edu/)

ISSN: 1471-2229