Table 2. Mean SNP association r² and number of markers (N_m) inside and outside hypothesis-defined testing regions in the NCRPIS panel.

		Shank length		Cob length		Kernel row number
		r2:	Nm:	r2:	Nm:	r2:	Nm:
Hypothesis or background	Coding or noncoding	×10−4	N × 103	×10−4	N × 103	×10−4	N × 103
Domestication QTL
Hypothesis	Coding	9.27	21.5	9.18	27.2	9.20	17.8
Background	Coding	9.19	226.4	9.40	220.7	9.52	230.2
Difference	Coding	0.08		−0.22**		−0.32**
Hypothesis	Noncoding	9.09	15.4	9.16	19.6	9.43	13.6
Background	Noncoding	9.29	141.9	9.38	137.7	9.42	143.7
Difference	Noncoding	−0.20**		−0.22		0.01
Domestication sweep
Hypothesis	Coding	9.30	15.0	9.39	15.0	9.45	15.0
Background	Coding	9.20	232.9	9.37	232.9	9.50	232.9
Difference	Coding	0.10		0.02		−0.05
Hypothesis	Noncoding	9.52	10.4	9.31	10.4	9.52	10.4
Background	Noncoding	9.25	146.9	9.35	146.9	9.41	146.9
Difference	Noncoding	0.27**		−0.04**		0.11
Improvement sweep
Hypothesis	Coding	9.22	11.9	9.50	11.9	9.60	11.9
Background	Coding	9.20	236.0	9.37	236.0	9.49	236.0
Difference	Coding	0.02		0.13		0.11
Hypothesis	Noncoding	9.56	9.0	9.53	9.0	9.20	9.0
Background	Noncoding	9.25	148.4	9.34	148.4	9.43	148.4
Difference	Noncoding	0.31**		0.19		−0.23*

Significantly different at * P = 0.05 and ** P = 0.01, respectively.