Table 3.

Genome-wide significant associations for coleoptiles phenotype under anaerobic germination (AG) using MLM

Traits	SNP^a	Chr.	Peak position^b	P value	—log10 (P)	Allleles	MAF	Known loci
CD-AN2d	S1_ 39674301	1	39674301	1.48E-10	9.83	A/C	0.2	Hsu and Tung 2015; qCD-1(ES) (Yang et al. 2019a, 2019b)
	S2_ 21568963	2	21568963	3.14E-09	8.5	C/T	0.2
	S2_ 35360509	2	35376690	7.98E-11	10.1	A/G	0.2
	S5_ 7135836	5	7135836	2.32E-11	10.63	C/T	0.1
	S5_ 22190175	5	22190175	2.69E-11	10.57	G/A	0.2
	S6_ 20797781	6	20797781	8.49E-12	11.07	G/A	0.1	Hsu and Tung 2015
	S8_ 13123867	8	13123867	2.65E-11	10.58	G/T	0.1
	S8_ 11595732	8	11595732	5.64E-10	9.25	A/T	0.1
CD-AN3d	S5_ 27918754	5	27918754	1.69E-09	8.77	A/G	0.4	Hsu and Tung 2015
CD-AN4d	S1_ 32866906	1	32866906	1.24E-09	8.91	G/A	0.2
	S3_ 27854371	3	27854371	5.11E-16	15.29	A/G	0.3
	S3_ 2828271	3	2828271	4.16E-11	10.38	A/G	0.2
	S3_ 28290634	3	28290634	3.02E-10	9.52	G/A	0.1
	S3_ 32459722	3	32459722	1.20E-09	8.92	C/T	0.5
	S3_ 7243651	3	7243651	4.89E-09	8.31	C/A	0.2
	S3_ 15571447	3	15571447	2.23E-08	7.65	G/T	0.3
	S5_ 27918754	5	27918754	1.72E-11	10.76	A/G	0.4	Hsu and Tung 2015
	S5_ 18621890	5	18621890	9.76E-11	10.01	A/C	0.1
	S5_ 21585755	5	21585755	1.21E-08	7.92	T/A	0.2
	S7_ 18722403	7	18722403	3.45E-09	8.46	T/C	0.2	qAG 7.2 (Septiningsih et al. 2013; Hsu and Tung 2015)
	S8_ 22721012	8	22721012	1.31E-09	8.88	A/G	0.2
	S8_ 9946213	8	9946213	2.51E-08	7.6	T/A	0.2	Hsu and Tung 2015
	S11_ 19165397	11	19165397	4.62E-09	8.34	C/A	0.3	qAG 11(Jiang et al. 2006; Angaji et al. 2009; Zhang et al. 2017)
CL-AN3d	S3_ 24689629	3	24689629	4.71E-08	7.33	T/C	0.4
CL-AN4d	S1_ 25099585	1	25099585	1.73E-08	7.76	G/A	0.2
CL-AN4d	S3_ 24689629	3	24689629	1.83E-08	7.74	T/C	0.4

Note: MAF minor allele frequency

^aThe SNP positions were based on the annotation data on Reference genome IRGSP-1.0 (RAP-DB, http://rapdb.dna.affrc.go.jp/)

^bPosition of the SNP showing the most significant association for AG