. 2022 Mar 4;62(3):965–981. doi: 10.1002/csc2.20692

TABLE 3.

Summary of the quantitative trait loci (QTL) identified by genome wide association studies (GWAS) for Hagberg falling number (HFN), protein content (PRT), test weight (TW), and grain yield (YLD)

Trait	QTL	Chr	Peak SNP	cM	bp	−log₁₀ P	Marker R² ^a	Effect ^b	Allele Freq
HFN	HFN_1B.1	1B	Jagger_c5878_119	0	1,254,498	3.10	0.079	28.42	0.58
HFN	HFN_3A.1 ^c	3A	RAC875_c99055_69	283.735979	728,322,627	4.08	0.114	−30.65	0.47
HFN	HFN_3B.1	3B	BS00099738_51	227.3745367	759,168,681	3.04	0.077	−31.32	0.73
HFN	HFN_6A.1 ^c	6A	Kukri_c29110_360	88.77758706	Un	3.83	0.103	−31.56	0.61
HFN	HFN_6A.2 ^c	6A	BS00082104_51	192.8384162	581,841,966	3.69	0.098	32.95	0.38
HFN	HFN_7B.1 ^c	7B	RAC875_c525_202	261.6310052	750,082,927	4.78	0.134	−44.19	0.19
PRT	PRT_1A.1	1A	BS00086680_51	71.0976257	281,657,026	3.26	0.087	0.39	0.52
PRT	PRT_1A.2	1A	Excalibur_c13489_867	96.6018344	452,020,371	3.03	0.079	−0.36	0.38
PRT	PRT_1A.3	1A	RAC875_c5882_307	231.6429733	589,054,742	3.01	0.079	−0.33	0.34
PRT	PRT_2A.1	2A	RAC875_rep_c69619_78	207.5522799	734,352,032	3.15	0.083	−0.33	0.56
PRT	PRT_2B.1	2B	BS00046165_51	260.7730538	697,510,384	3.04	0.080	0.44	0.19
PRT	PRT_3A.1 ^c	3A	wsnp_Ku_c30545_40369365	107.2210875	363,458,708	3.34	0.090	−0.35	0.52
PRT	PRT_3B.1 ^c	3B	wsnp_Ex_c20652_29734133	112.6476302	292,024,034	3.39	0.091	−0.44	0.79
PRT	PRT_3B.2	3B	RAC875_c58159_989	155.9566423	564,248,743	3.10	0.081	−0.46	0.83
PRT	PRT_3B.3 ^c	3B	GENE_1618_780	279.0622821	820,894,420	3.02	0.079	−0.33	0.52
PRT	PRT_6B.1 ^c	6B	BS00009795_51	12.20934913	4,876,473	3.36	0.090	‐0.35	0.44
TW	TW_1B.1 ^c	1B	RAC875_rep_c95069_54	81.49097047	336,647,904	3.12	0.080	−1.24	0.21
TW	TW_3B.1 ^c	3B	GENE_1771_541	57.06175117	32,458,901	3.60	0.095	1.20	0.36
TW	TW_3B.2 ^c	3B	RAC875_c58159_989	155.9566423	571,753,368	3.20	0.083	−1.43	0.86
TW	TW_3B.3 ^c	3B	Excalibur_c33274_498	207.7302565	738,752,902	3.21	0.083	2.04	0.05
TW	TW_3B.	3B	BS00073480_51	269.7509427	812,721,677	3.41	0.089	−1.91	0.91
YLD	YLD_1A.1 ^c	1A	RAC875_rep_c105092_114	72.6102779	304,040,711	4.03	0.109	0.62	0.50
YLD	YLD_1A.2 ^c	1A	wsnp_CAP8_c4785_2322876	166.3032581	544,054,745	3.28	0.085	0.56	0.79
YLD	YLD_2A.1 ^c	2A	RAC875_c48625_182	22.63785838	18,636,671	4.30	0.118	0.57	0.53
YLD	YLD_2A.2 ^c	2A	RAC875_c16993_839	245.2533379	774,815,015	4.57	0.127	−0.73	0.38
YLD	YLD_2B.1	2B	BS00002660_51	38.40853424	16,025,160	3.09	0.079	0.50	0.57
YLD	YLD_2B.2 ^c	2B	BS00091099_51	221.2304675	578,601,402	3.97	0.107	−0.55	0.54
YLD	YLD_2B.3 ^c	2B	BS00046165_51	260.7730538	697,510,384	3.45	0.090	−0.70	0.19
YLD	YLD_2B.4 ^c	2B	Kukri_c34553_188	319.3174469	766,234,466	5.56	0.161	−1.00	0.17
YLD	YLD_2D.1 ^c	2D	wsnp_Ex_c1668_3169623	35.64284331	Un	3.94	0.106	0.59	0.70
YLD	YLD_3A.1	3A	wsnp_Ex_c8884_14841846	179.8202073	625,239,797	3.13	0.08027	−0.51	0.73
YLD	YLD_5B.1 ^c	5B	CAP8_rep_c5825_165	3.286161131	15,054,913	3.27	0.0847	0.5	0.4
YLD	YLD_6A.1 ^c	6A	BS00082812_51	0.502519793	639,383	4.22	0.11534	0.73	0.78
YLD	YLD_6A.2 ^c	6A	wsnp_Ku_c3354_6228393	132.9525631	430,933,984	3.43	0.09203	−0.71	0.24
YLD	YLD_6B.1 ^c	6B	Kukri_c21405_2131	15.73078008	166,814	3.8	0.10161	−0.73	0.19

Note. The most significant marker at each QTL is listed. Genetic (Gardner et al., 2016) and physical (IWGSC, ²⁰¹⁸) map positions for peak single nucleotide polymorphisms (SNPs) at each QTL are indicated. Where SNPs were anchored to physical map regions currently not allocated to a chromosome designation in the wheat reference genome assembly, the bp position is recorded as unknown (Un). SNP effect at each QTL were determined via two methods (defined below).

^{^a}

SNP effects determined via the outputs of the software TASSELL.

^{^b}

SNP effects determined via modeling the effects considering just those QTL identified for a specific trait.

^{^c}

GWAS hits identified using both kinship and kinship+PCA to correct for population structure. The remaining hits were identified using kinship correction only.