Genome-wide association study (GWAS) reveals the genetic architecture of four husk traits in maize

BMC Genomics

Table 2 SNPs, chromosomal position and candidate genes significantly associated with three husk traits identified by GWAS using MLM method

Trait	SNP	Chr	Position (bp)	Allele^a	R²(%)^b	MAF^c	P-value	Gene	Gene interval (bp)	Annotation	Pathway^d
HN	chr4.S_205554186	4	205554186	A/C	2.6	0.06	9.40E-06	GRMZM2G016447	205553899-205557585	Unknown	n.d
HN	SYN10582	5	17966191	G/A	0.2	0.19	6.43E-06	GRMZM2G097364	17965846-17977924	Unknown	n.d
HN	chr5.S_203403202	5	203403202	C/A	1.9	0.31	6.41E-06	GRMZM2G542272	203402576-203403244	Unknown	n.d
HN	chr9.S_123419252	9	123419252	C/G	4.1	0.18	2.57E-06	GRMZM2G124239	123411699-123426029	Vacuolar protein sorting-associated protein 52	Cellular trafficking
HN	chr10.S_143066093	10	143066093	C/G	3.7	0.08	1.00E-05	GRMZM2G396846	143066059-143068062	Global transcription factor group E7	Transcriptional regulation
Total^e					11.2
HW	chr5.S_215787314	5	215787314	T/C	4.9	0.18	4.51E-06	GRMZM2G056598	215781414-215787413	Chromatin remodeling 4	Transcriptional regulation
Total^e					4.9
HT	chr5.S_11925326	5	11925326	C/T	8.2	0.06	1.06E-06	GRMZM2G157166	11925082-11925880	Oxysterol binding protein-related protein 1A	Metabolism
HT	chr6.S_106444300	6	106444300	C/T	7.2	0.06	3.37E-06	GRMZM2G404081	106425279-106427173	GDSL/SGNH-like acyl-esterase family	Metabolism
HT	chr8.S_145474885	8	145474885	T/C	11.5	0.09	2.08E-06	GRMZM2G029077	145474389-145483146	Adaptin family	Cellular trafficking
Total^e					21.4

^aMajor/minor allele, underlined bases are the favorable alleles
^bPercentage of phenotypic variation explained by the additive effect of the single significant SNP
^c Minor allele of frequency
^d n.d means not denoted
^e Total percentage of phenotypic variation explained by all significant SNPs

ISSN: 1471-2164