Table 3.

Favorable alleles and effects of 47 SNP loci significantly (P < 4.99 × 10⁻⁵) associated with kernel number per spike in the germplasm set.

SNP name	Chr.	Position (cM)	Favorable allele	Freq. (%)	Allele effect
					14JZ	14YZ	15JZ	15YZ	16XX	Average
wsnp_Ex_c41953_48657850	1A	106.27	TT	19.70		0.61
BS00010868_51	1B	9.68	CC	34.85					1.42
Kukri_rep_c101799_95	1B	64.46	AA	37.44		1.54
GENE-1086_1111	2A	25.97	AA	8.33			1.11
BS00022896_51	2A	109.52	TT	64.82					2.78	1.16
Tdurum_contig92425_1612	2A	151.57	AA	36.89			1.45
BS00014345_51	2B	88.86	CC	65.53						1.19
BS00037278_51	2B	96.14	AA	50.00	1.10
wsnp_JD_c12346_12606967	2B	130.62	AA	36.89				0.45
D_contig13956_175	2D	63.47	GG	35.96					0.52
D_contig35123_619	2D	66.03	GG	67.42				1.14
D_F5XZDLF02JSEI4_223	2D	66.03	GG	66.29			1.15
BobWhite_c10539_201	2D	77.80	AA	70.45	1.39	1.50	1.15	1.19	2.92	1.20
wsnp_Ex_c12223_19533198	2D	82.82	GG	46.32					0.86
wsnp_JD_c43971_30568640	3A	109.95	CC	66.67		1.33
Ra_c3994_598	3A	109.95	TT	37.00					1.54
Excalibur_c73633_120	3B	65.55	GG	92.82	2.04	2.11				2.02
BS00066466_51	3B	71.34	TT	36.96				1.65
Kukri_c35105_294	3B	73.94	TT	65.91	1.40
Kukri_c18420_705	3D	148.48	TT	67.42		1.13
tplb0051b16_1324	4A	48.98	GG	36.59					1.47
BS00075746_51	4B	61.84	CC	69.55						2.90
Tdurum_contig54854_547	4B	65.59	GG	66.67			1.10
Excalibur_c29933_351	5A	13.42	TT	36.32					1.54
RAC875_c84991_116	5A	15.58	CC	36.89		1.45
BS00064412_51	5A	15.61	CC	67.42					1.20
Tdurum_contig10759_260	5A	84.13	AA	36.95			0.61
Tdurum_contig13025_774	5B	40.57	AA	36.89	0.45
D_contig24916_701	5D	70.11	GG	36.89				1.45
D_contig65543_191	5D	73.99	AA	35.32		0.60
Kukri_rep_c102792_163	5D	83.51	CC	66.67	1.26
BobWhite_c3750_335	5D	136.83	AA	36.89						0.45
Tdurum_contig11413_700	6A	63.70	AA	36.89	1.45
Ra_c12362_422	6A	79.08	AA	36.76		0.51
Tdurum_contig63539_178	6A	82.38	CC	36.89					1.40
BS00063906_51	6B	59.92	GG	50.00	1.88				1.96	1.72
Tdurum_contig29027_92	6D	68.00	GG	67.05			1.15
D_GDEEGVY01CQJ66_272	7A	127.75	CC	36.89		1.45
wsnp_BF474379A_Ta_2_2	7A	135.81	CC	36.89				1.45
GENE-4456_153	7B	72.74	TT	41.29	2.80	2.24	3.25	2.51	3.68	2.67
IACX5767	7B	150.60	GG	11.41			1.50
BS00003630_51	7B	150.60	TT	61.45	1.50
D_GDS7LZN02H6ID8_55	7D	91.57	GG	67.80				1.20
CAP7_c1383_548	7D	101.06	AA	61.36		1.11
Kukri_c35508_426	7D	102.12	TT	36.89				1.45
D_GA8KES401AVKPJ_56	7D	106.28	CC	66.29					1.12
D_contig10938_340	7D	135.55	CC	64.77		1.19