Table 3. QTL with same effect direction between TeoNAM and BC₂S₃.

Trait	QTL	Chr	QTL peak (V4) (Mb)	Support interval (V4) (Mb)	QTL peak (cM)	Support interval (cM)	P-value	TIL01	TIL03	TIL11	TIL14	TIL25	8759a	Candidate gene
BARE	BARE4.3	4	55.9	39.0–124.3	61.5	58.2–66.8	4.72E–07	0.19	0.25	0.19	0.14b	0.09b	0.63	tga1
DTA	DTA1.1	1	4.5	2.8–5.6	9.0	3.4–13.2	1.26E–16	0.59	1.02	1.23	1.31	0.77	0.81	zagl1
DTA	DTA3.3	3	231.4	226.3–233.4	167.2	156.7–170.0	4.54E–08	0.64	1.05	0.68	0.13b	0.73	0.49
DTA	DTA5.1	5	6.9	6.7–7.2	30.7	29.2–31.5	2.62E–18	1.11	0.80	1.11	1.24	1.30	0.66	Zmm31
DTA	DTA7.2	7	180.4	180.1–180.8	140.7	139.3–141.8	2.92E–14	0.53	1.37	0.77	0.58	1.16	0.59	dlf1
DTA	DTA8.1	8	126.9	126.6–126.9	68.3	68.2–68.3	4.05E–54	1.64	2.00	2.63	1.72	1.59	1.54	ZCN8
DTA	DTA9.1	9	117.5	115.7–118.8	72.9	72.4–74.6	4.76E–33	0.65	3.16	1.24	0.74	1.39	0.79	ZmCCT9
DTA	DTA10.1	10	95.4	94.9–99.4	54.7	54.3–55.1	9.29E–121	3.47	3.22	2.46	4.87	4.54	3.61	ZmCCT10
EB	EB7.1	7	121.5	103.9–132.7	64.8	60.1–72.7	5.18E–14	0.02b	0.01b	0.06	0.05	0.01b	0.05
ED	ED1.3	1	277.1	265.1–283.1	134.7	127.6–141.3	6.45E–06	−1.02	−0.28b	−1.38	−0.25b	−0.64	−1.87	tb1
ED	ED2.4	2	217.2	211.9–223.4	123.3	116.8–133.5	1.22E–06	−0.46b	−0.79	−0.39b	−0.72	−0.85	−0.88	smk1
ED	ED3.2	3	218.4	214.8–219.8	140.1	133.8–142.3	1.34E–13	−1.18	−0.45	−0.72	−0.34b	−1.33	−0.89
ED	ED4.1	4	7.8	6.8–11.1	23.8	21.5–30.1	1.50E–11	−1.59	−0.48	−0.01b	−0.64	−0.25b	−0.74
ED	ED7.2	7	163.6	160.4–164.2	98.0	94.1–98.4	2.47E–19	−0.67	−0.94	−1.59	−1.30	−0.78	−0.81
EL	EL7.1	7	125.5	123.7–130.3	66.8	65.7–70.5	4.64E–17	−0.82	−0.34	−0.56	−0.21b	−0.81	−0.97
EL	EL8.1	8	156.5	150.4–157.6	82.5	78.1–83.4	2.84E–11	−0.19b	−0.48	−0.15b	−0.21b	−0.68	−0.66
EL	EL10.1	10	115.0	115.0–118.9	58.5	58.8–60.0	6.87E–40	−0.12b	−0.88	−0.85	−1.68	−1.17	−1.34	GIF1
GLCO	GLCO4.1	4	42.1	39.0–42.1	59.6	58.2–59.6	5.98E–24	0.01b	0.12	0.08b	0.31	0.37	0.27
GLUM	GLUM4.1	4	42.1	40.4–55.9	59.6	59.1–61.5	2.57E–168	0.74	0.77	0.73	0.93	1.06	0.8	tga1
KRN	KRN1.3	1	298.5	298.1–299.6	165.7	164.9–168.2	2.73E–16	−0.51	−0.58	−0.35	−0.09b	−0.26	−0.63	ids1
KRN	KRN4.3	4	243.5	241.6–244.8	145.6	137.4–152.1	8.27E–07	−0.22	−0.41	−0.18	−0.23	−0.23	−0.55
KRN	KRN5.1	5	2.4	2.3–2.9	12.7	11.7–15.0	8.72E–14	0.36	0.51	0.12b	0.40	0.24	0.3
KRN	KRN7.1	7	95.2	21.5–123.7	58.6	49.6–65.7	7.00E–11	−0.36	−0.18	−0.54	−0.06b	−0.42	−0.26	ra1
KRN	KRN8.2	8	171.3	169.6–173.4	106.8	100.8–113.0	6.70E–13	−0.49	−0.40	−0.38	−0.04b	−0.15b	−0.25
KW	KW1.2	1	234.3	222.8–252.5	110.3	106.5–116.4	6.01E–10	−0.01	−0.01	−0.01	−0.00b	−0.01	−0.01
KW	KW2.1	2	53.3	36.9–57.5	74.3	64.3–76.1	1.32E–11	−0.01	−0.00b	−0.01	−0.01	−0.00b	−0.01
KW	KW4.2	4	170.1	156.8–174.8	82.8	73.6–84.2	1.69E–08	−0.01	−0.01	−0.01	−0.00b	−0.00b	−0.01
KW	KW8.1	8	137.7	132.5–145.9	72.7	70.4–75.4	1.31E–12	−0.00b	−0.01	−0.01	−0.01	−0.01	−0.01
REPE	REPE1.1	1	47.0	46.5–51.8	64.9	64.4–68.3	2.71E–11	−0.10	−0.10	−0.06	−0.10	−0.10	−0.10	P1
SHN	SHN1.1	1	265.1	264.1–265.1	127.6	127.2–127.6	3.21E–16	0.08	0.09	0.18	0.17	0.11	0.07	ZmSh1-1
SHN	SHN6.1	6	162.5	162.2–163.6	98.2	97.4–101.1	3.49E–11	0.06	0.04b	0.17	0.03b	0.10	0.06
STAM	STAM1.2	1	270.5	269.8–270.5	130.2	129.5–130.2	1.23E–27	0.28	0.02b	0.12	0.07	0.09	0.11	tb1
TILN	TILN3.2	3	138.3	137.6–158.6	80.5	80.2–86.2	5.22E–24	0.00b	0.42	0.33	0.08b	0.20	0.14	ZAG2
TILN	TILN5.1	5	69.0	36.0–140.7	75.4	69.9–82.7	6.66E–10	0.18	0.24	0.14	0.14	0.16	0.10
TILN	TILN10.1	10	62.5	25.3–82.1	47.7	45.0–51.1	4.10E–13	0.15	0.24	0.06b	0.08b	0.28	0.12

BARE, barren ear base; DTA, days to anthesis; EB, ear branch number; ED, ear diameter; EL, ear length; GLCO, glume color; GLUM, glume score; KRN, kernel row number; KW, kernel weight; REPE, red pericarp; SHN, shattering; STAM, staminate spikelet; TILN, tiller number. Chr, chromosome; JLM, joint linkage mapping; TeoNAM, teosinte nested association mapping.

^aThe allele effect of 8759 relative to maize was estimated in BC₂S₃ by Shannon (2012).

^bIndicates that the additive allele effect of teosinte relative to maize estimated from JLM in TeoNAM is not significant.