Table 3.

Significant SNPs and candidate genes identified as associated with stress tolerance indices of four drought tolerance-related traits based on GWAS of 125 wheat genotypes at the seedling stage

Trait	Marker	Chr	Allele	Marker position	log(p)	Gene ID	SNP-Gene distance (bp)	R2%	Gene function	Gene length & or. (bp)
PH_STI	Kukri_c40909_784	3A	T/C	423958992	4.45	TraesCS3A02G226500	Within gene	12.66	Auxilin-related protein 1	15337+
	Excalibur_c63730_660	3B	T/C	416279752	4.49	TraesCS3B02G258600	Within gene	12.79	Polygalacturonase	4667+
	Tdurum_contig28384_102	3B	A/G	416283216	4.45	TraesCS3B02G258700	Within gene	12.66	Peptide deformylase	4797−
	Kukri_rep_c75974_432	3B	A/C	416799894	4.45	TraesCS3B02G259100	5942	12.66	Receptor-like kinase	5116−
	RAC875_c17404_1160	3D	A/G	305863726	4.13	TraesCS3D02G224500	Within gene	11.69	Auxilin-related protein 1	16040+
	wsnp_Ex_c683_1341113	4D	A/G	54447007	4.77	TraesCS4D02G080400	27391	13.61	B3 domain-containing protein	2171+
	BS00003185_51	6A	A/G	596165675	4.02	TraesCS6A02G372300	Within gene	11.35	Methyltransferase-like protein	3186+
RL_STI	GENE-4268_101	6A	A/C	585192104	4.75	TraesCS6A02G353500	Within gene	13.55	Kinase	7573+
	IACX473	6A	A/C	585192973	4.75	TraesCS6A02G353500	Within gene	13.55	Kinase	7573+
	BS00075300_51	7B	T/C	713379927	4.61	TraesCS7B02G452000	74089	13.13	Pm3-like disease resistance protein	5229−
	BS00075299_51	7B	T/C	713379957	4.7	TraesCS7B02G452000	74059	13.37	Pm3-like disease resistance protein	5229−
RDW_STI	Excalibur_c35183_406	7A	T/C	8694709	4.56	TraesCS7A02G021400	Within gene	14.76	NBS-LRR-like resistance protein	4838−
	BS00075300_51	7B	T/C	713379927	4.69	TraesCS7B02G452000	74089	15.21	Pm3-like disease resistance protein	5229−
	BS00075299_51	7B	T/C	713379957	4.4	TraesCS7B02G452000	74059	14.23	Pm3-like disease resistance protein	5229−
SDW_STI	RAC875_c24163_501	1A	T/C	32546271	4.92	TraesCS1A02G051100	Within gene	13.6	F-box/LRR-repeat protein	2641+
	Kukri_c40909_784	3A	T/C	423958992	4.63	TraesCS3A02G226500	Within gene	12.77	Auxilin-related protein 1	15337+
	Kukri_rep_c70097_286	3B	T/G	415930394	4.11	TraesCS3B02G258000	Within gene	11.27	Auxilin-related protein 1	12142−
	Excalibur_c63730_660	3B	T/C	416279752	3.95	TraesCS3B02G258600	Within gene	10.79	Polygalacturonase	4667+
	Tdurum_contig28384_102	3B	A/G	416283216	4.63	TraesCS3B02G258700	Within gene	12.77	Peptide deformylase	4797−
	Kukri_rep_c75974_432	3B	A/C	416799894	4.63	TraesCS3B02G259100	5942	12.77	Receptor-like kinase	5116−
	RFL_Contig2538_204	3B	T/C	455681347	4.24	TraesCS3B02G284600	Within gene	11.63	Regulator of Vps4 activity in the MVB pathway protein	5372−
	Excalibur_c8871_1890	3D	T/C	301442744	4.31	TraesCS3D02G220900	Within gene	11.85	Elongation factor	5712−

“PH” is plant height; “RL” root length; “RDW” root dry weight; “SDW” shoot dry weight; “STI” stress tolerance index; “Chr.” chromosome; “bp” base pair. “R²” is the phenotypic variation explained by each marker. “Or.” is the gene’s orientation that represents on which strand the genes are located. The (+) represents the forward strand, whereas the (−) represents the complementary strand