Genome-wide association analysis and QTL mapping reveal the genetic control of cadmium accumulation in maize leaf

BMC Genomics

Table 3 Significant associations and corresponding QTLs detected by genome-wide association study and QTL mapping of leaf Cd concentration at seeding and maturing stage in maize

No.	Possible causative SNP	Allele^a	MAF	Position (bp)	-log₁₀(P)	R² (%)	Candidate gene	Function description	Distance to Gene^b
1	PZE-102118224	A/G	0.397	158,453,594	7.29	15.25	GRMZM2G455491	Cadmium/zinc-transporting ATPase	64.18 kb
1	PZE-102118224	A/G	0.397	158,453,594	7.29	15.25	GRMZM2G175576	Cadmium/zinc-transporting ATPase	42.64
2	SYN395	A/G	0.376	158,609,741	9.54	20.1	GRMZM2G175576	Cadmium/zinc-transporting ATPase	202.75 kb
3	SYN30994	A/C	0.387	160,798,026	7.99	16.74	GRMZM2G171370	ZIP transcription factor	158.95 kb
4	SYN30995	A/C	0.378	160,798,113	8.89	18.67			158.86 kb
5	SYN30993	A/C	0.352	160,957,319	9.48	23.03			Intron
6	SYN25051	A/G	0.308	161,275,547	12.7	27.12	GRMZM2G124103	Vacuolar ATPase G subunit	72.26 kb
7	SYN33611	A/G	0.386	164,889,910	9.28	19.52	GRMZM2G085939	Calmodulin-binding heat-shock protein	85.30 kb
8	PZE-102120786	A/C	0.329	164,893,346	10.9	23.1	GRMZM2G085939	Calmodulin-binding heat-shock protein	81.87 kb
9	PZE-102120896	A/G	0.416	165,068,962	6.77	14.16	GRMZM2G386138	Cupin domain containing protein	Intron
10	SYN33167	A/G	0.366	165,105,090	8.42	17.66	GRMZM2G047727	Ubiquitin fusion protein	Intron
11	PZE-102120959	A/G	0.414	165,259,741	6.49	13.56	GRMZM2G085153	Nucleic acid binding protein	2.67 kb
12	PZE-102120961	A/C	0.426	165,259,881	7.43	15.54	GRMZM2G085153	Nucleic acid binding protein	2.53 kb

^a The letter under the line is the nucleotide minor frequency
^b Genes identified within 300 kb of SNPs detected by the distant of LD decay are indicated

ISSN: 1471-2164