Table 2.

Significant SNPs and candidate genes identified as associated with stress susceptibility 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_SSI	Ku_c972_560	2A	A/G	42392191	4.54	TraesCS2A02G089200	74	19.35	Histone-lysine N-methyltransferase ASHH2	2001−
	TA003045-1227	2A	A/G	115120841	4.22	TraesCS2A02G162700	Within gene	17.88	Serine/arginine rich splicing factor, putative	2310−
	Kukri_c44997_377	2A	T/C	115140823	4.22	TraesCS2A02G162900	Within gene	17.88	Copper-translocating P-type ATPase family protein, expressed	2461−
	wsnp_Ex_rep_c69124_68035904	2A	A/G	115421998	4.22	TraesCS2A02G163000	Within gene	17.88	Calmodulin-binding transcription activator	8584+
	Kukri_c7169_105	2A	A/G	138183614	4.22	TraesCS2A02G179783	Within gene	17.87	NA	3699−
	TA001792-1026	2A	A/G	141166706	4.78	TraesCS2A02G181800	Within gene	20.5	S phase cyclin A-associated protein in the endoplasmic reticulum	13583+
	TA001351-1193	2A	T/C	151258885	4.22	TraesCS2A02G188200	Within gene	17.88	α-1,6-mannosyl-glycoprotein 2-β-N-acetylglucosaminyltransferase	11695+
	GENE-1181_262	2A	A/G	151263814	4.22	TraesCS2A02G188200	Within gene	17.88	α-1,6-mannosyl-glycoprotein 2-β-N-acetylglucosaminyltransferase	11695+
	Excalibur_c27210_183	2A	T/G	152010707	4.22	TraesCS2A02G188400	Within gene	17.88	Zinc finger protein-like protein	3815+
	BobWhite_c32226_104	2B	T/C	180822839	4.22	TraesCS2B02G201800	Within gene	17.89	Pentatricopeptide repeat-containing protein, putative	3426−
	GENE-2601_393	2D	T/C	122703750	4.22	TraesCS2D02G179100	Within gene	17.88	Methyltransferase-like protein	3311−
	Kukri_rep_c89183_282	3A	T/C	8686047	4.27	TraesCS3A02G009600	Within gene	18.11	U-box domain-containing protein	4780+
	Excalibur_rep_c104498_168	3B	A/G	16444577	4.35	TraesCS3B02G034400	Within gene	18.45	WD repeat-containing protein 1	5163+
	Excalibur_c7753_51	4A	A/G	707041300	4.27	TraesCS4A02G437200	Within gene	18.08	Protein ENHANCED DISEASE RESISTANCE 2-like	7934−
	GENE-4701_272	7B	A/G	626112422	4.03	TraesCS7B02G363700	Within gene	13.82	3-hydroxyisobutyrate dehydrogenase	3244−
RL_SSI	BS00086777_51	4A	A/G	739067906	5.14	TraesCS4A02G485400	Within gene	15.67	Acid invertase 1	3823+
	Tdurum_contig65998_182	6B	A/G	717967277	4.10	TraesCS6B02G469000	Within gene	12.36	PRLI-interacting factor A	2255−
RDW_SSI	IACX5803	1A	A/C	563180048	4.01	TraesCS1A02G397500	Within gene	12.94	Ubiquitin	730−
	Excalibur_c49496_705	1B	T/C	652453983	4.01	TraesCS1B02G426200	Within gene	12.94	RING/U-box superfamily protein	4769+
	IAAV565	1B	T/C	652457867	4.95	TraesCS1B02G426300	Within gene	16.13	Ras-related protein	1690−
	wsnp_JD_c5316_6447231	1D	A/G	2077073	4.74	TraesCS1D02G003900	Within gene	18.12	Peroxisomal membrane protein PEX14	3921−
	tplb0046b02_1751	2A	T/C	734887845	4.2	TraesCS2A02G508200	Within gene	13.6	Sulfate transporter	6002+
	BS00065327_51	2B	T/G	731481895	4.39	TraesCS2B02G535600	Within gene	14.24	3-ketoacyl-CoA synthase	1690−
	wsnp_RFL_Contig1892_1042675	2D	T/C	601600198	4.2	TraesCS2D02G508800	Within gene	13.6	Sulfate transporter	5947+
	Kukri_c22953_855	7D	A/G	18000929	4.05	TraesCS7D02G035000	496	13.1	NBS-LRR disease resistance protein	2647−
SDW_SSI	BobWhite_c35311_122	1B	T/C	286044097	4.16	TraesCS1B02G163800	7845	13.89	Photosystem I P700 chlorophyll a apoprotein A1	1652+
	Excalibur_c10198_691	3A	A/C	64324895	4.54	TraesCS3A02G099900	9136	15.44	Cytochrome P450, family 88, subfamily A, polypeptide 3	465−
	wsnp_BE426418A_Ta_2_1	3A	T/C	725738598	5.99	TraesCS3A02G502300	Within gene	25.42	NAD(P)H:plastoquinone dehydrogenase complex subunit O	1626+
	tplb0037i09_749	4D	A/G	51309211	4.38	TraesCS4D02G077100	5424	14.81	OBF binding protein 1	661−
	CAP7_c6648_230	5A	A/G	353989255	4.69	TraesCS5A02G165400	Within gene	16.08	Ribulose bisphosphate carboxylase small chain	1371+
	BobWhite_c9670_25	6A	T/C	492805334	4.54	TraesCS6A02G267300	Within gene	15.44	Phosphoribulokinase	2360+

“PH” is plant height; “RL” root length; “RDW” root dry weight; “SDW” shoot dry weight; “SSI” stress susceptibility 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