Table 3.

SNPs highly significant associated with seed coat deficiency (SCD) detected by single-marker analysis (SMA) in Pop1 (V11-0883 × V12-1626) within two stable QTL regions

QTLa	Marker ID	Position (cM)	LODb
			2016	2017	2018	AVE
qSCD15	Gm15_5312718	22.1	–	–	6.7*	5.9*
	Gm15_6272006	24.8	–	–	6.7*	6.0*
qSCD20	Gm20_34626867	44.1	–	13.1*	–	12.1*
	Gm20_34942502	44.5	–	13.8*	–	12.8*
	Gm20_34881595	44.7	–	13.9*	–	13.2*
	Gm20_35625615	47.9	7.3*	11.7*	–	11.8*
	Gm20_36002148	51.3	6.3*	13.3*	6.7*	12.9*
	Gm20_36095037	52.0	6.4*	13.5*	6.7*	13.1*
	Gm20_36153048	52.8	6.3*	13.3*	6.4*	13.1*
	Gm20_36651429	55.4	–	13.3*	6.4*	12.9*
	Gm20_36710448	55.8	6.4*	11.8*	–	11.9*

^aQTL: the QTL detected by CIM and/or IM, see in Table 2

^bLOD: logarithm of odds

*SNPs significantly associated with seed coat deficiency at p < 0.0001