Mining candidate gene for rice aluminum tolerance through genome wide association study and transcriptomic analysis

Table 2 Top highest genome-wide significant association signals of RRE using MLM

Trait	Chr.	Position (IRGSP-1.0)	Reference allele	Alternative allele	Alternative allele frequency	-log₁₀(P)	Candidate/known gene^a
RRE	1	10,953,291	C	T	0.87	5.58	LOC_Os01g19360.1
	2	14,694,840	A	G	0.85	5.04
	3	34,440,793	A	T	0.88	5.45	LOC_Os03g60610.1
	6	7,814,182	A	G	0.73	5.24
	6	7,814,184	C	T	0.74	5.24
	6	7,814,207	C	T	0.75	5.06
	6	16,451,901	T	C	0.86	5.02	LOC_Os06g28860.1
	8	18,696,483	T	C	0.67	5.11
	8	2,885,626	A	G	0.63	5.10	LOC_Os08g05440.1
	8	2,885,642	A	T	0.61	5.04
	9	19,838,960	G	A	0.88	5.99
	10	10,133,350	T	C	0.58	5.30	LOC_Os10g20180.1
	10	8,299,577	T	C	0.71	5.03

Note: ^aGene ID of MSU rice genome annotation project (http://rice.plantbiology.msu.edu/)

ISSN: 1471-2229