Table 2.

Significant marker-trait associations (MTAs) identified by genome-wide association studies (GWAS) using the FarmCPU model for FHB disease index (DIS) and Fusarium-damaged kernels (FDK) in the hard winter wheat panel of 257 breeding lines.

Trait	SNP	Chr	Posa	MAFb	SNP effect	p value	FDR-adj p value	Another modelc
DIS	S2A_722857568	2A	722,857,568	0.17	3.70	2.72E-05	0.046	1,2,3,6
	S2B_725552556	2B	725,552,556	0.18	3.98	2.94E-05	0.046
	S3B_773516625	3B	773,516,625	0.14	−5.47	2.29E-07	0.001	1,2,3,6,7
	S4B_40315424	4B	40,315,424	0.16	−7.00	5.46E-14	0.000	1,2,3,4,5,6,7
	S4B_647586119	4B	647,586,119	0.26	3.51	2.37E-06	0.007	1,4,5
	S7A_48708273	7A	48,708,273	0.07	−4.74	1.96E-05	0.047	7
FDK	S3B_768314878	3B	768,314,878	0.40	3.61	8.23E-08	0.000	1,2,3,4
	S5A_619020400	5A	619,020,400	0.13	4.63	7.83E-07	0.000	1,2,7
	S6B_320696398	6B	320,696,398	0.12	4.05	7.41E-06	0.012
	S6B_718194425	6B	718,194,425	0.23	3.64	5.98E-07	0.001	1,2,3,4,5,6,7
	S6D_110313864	6D	110,313,864	0.06	−7.50	4.09E-08	0.000
	S7A_713432647	7A	713,432,647	0.12	−4.44	1.13E-05	0.015
	S7A_738859192	7A	738,859,192	0.34	2.87	3.51E-07	0.001
	S7B_707550430	7B	707,550,430	0.30	−2.86	3.7E-05	0.043	1,2,6

The MTAs were declared significant based on a false discovery rate (FDR) corrected p value threshold of 0.05.

^aThe physical position is based on IWGSC RefSeq v2.0 (IWGSC, 2018).

^bMAF refers to minimum allele frequency for the corresponding MTA.

^cThis column enlists ML-GWAS model(s), which identified the corresponding MTA in addition to FarmCPU. The MTAs was referred to as ‘reliable’ if identified by at least two ML-GWAS models. Various ML-GWAS models are: 1, mrMLM; 2, FastmrMLM; 3, FastmrEMMA, 4, pLARmEB; 5, pKWmEB; 6, ISIS EM-BLASSO; and 7, BLINK.