Table 4.

Candidate genes for each significantly SNP associated with TL, SD, and KR and its respective encoding product

Chr a	Trait	SNP physical position (bp)	Gene ID	Encoding
2	TL	168,004,182	GRMZM2G504910	Tetratricopeptide repeat (TPR)
3	TL	7,081,859	GRMZM2G104081b	hex1 (hexokinase1)
4	TL	190,444,179	GRMZM2G013128b	Double Clp-N motif-containing P-loop nucleoside triphosphate hydrolases superfamily protein
4	TL	190,679,094	GRMZM2G033820	Phospholipase A2
7	TL	154,739,818	GRMZM2G077008bc	Histidine kinase, hybrid-type, ethylene sensor
		154,741,622
7	TL	155,702,328	GRMZM2G861541	Expressed protein
10	TL	133,337,924	GRMZM2G057084	Calcium/calmodulin-dependent protein kinase
		133,337,925
		133,337,950
1	SD	208,315,891	GRMZM2G101422	Expressed protein
1	SD	293,163,491	GRMZM2G060702b	Actin depolymerizing factor 4
2	SD	59,729,532	GRMZM2G389097	Leucine-rich receptor-like protein kinase family
5	SD	176,870,721	GRMZM2G325683c	Expressed protein
3	KR	187,742,562	GRMZM2G438551	cystatin1
3	KR	204,458,505	GRMZM2G111666	basic Helix-Loop-Helix (bHLH) transcription f.
3	KR	204,586,960	GRMZM2G091494c	Starch branching enzyme interacting protein-1
3	KR	222,733,400	GRMZM2G055578c	Glycine-rich protein
			GRMZM2G055629	Plant thionin family protein precursor/Defensin
4	KR	227,101,950	GRMZM2G116314	Ubiquitin thiolesterase
		227,101,985
5	KR	93,580,059	GRMZM2G037308c	Phytosulfokine receptor
6	KR	88,149,024	GRMZM5G876960	Polyamine oxidase (propa-1,3-diamine-forming)
		88,149,036
7	KR	15,072,370	GRMZM2G316256	Catalase//L-ascorbate peroxidase
7	KR	19,347,596	GRMZM2G042627	Kinase associated protein phosphatase

^a Chr, chromosome; TL, tunnel length; SD, stem damage; and KR, kernel resistance.

^b Gene containing the significant SNP within an exonic region.

^c Gene containing the significant SNP within an intronic region.