Table 2.

Linkage disequilibrium (LD) between the specific Sr38 marker (VENTRIUP-LN2) and SNPs located on chromosome 2A in the TRP2015. Single marker analysis between the significant SNPs and stem rust resistance. Gene models underlying them based on the IWGSCv1.0 and TGAC v1.0 data bases.

SNP_ID	R 2	P-value	F-value	P.V.E	Target allele$	Allele effect	Gene model (IWGSC v1.0)	Gene model (TGCA v1.0)
S2A_2367215	1.00	0.001	13.24**	30.62%	C:A	−2.18	TraesCS2A01G004100.1	TRIAE_CS42_2AS_TGACv1 _114644_AA0368550.1
S2A_2708760	1.00	0.003	10.70**	25.07%	G:A	−2.22	TraesCS2A01G005500.1	TRIAE_CS42_2AS_TGACv1 _113850_AA0361440.1
S2A_2708784	0.71	0.001	12.22**	19.96%	G:A	−3.23
S2A_710988	0.91	0.002	10.26**	18.24%	A:G	−2.13	—
S2A_710997	0.91	0.002	10.26**	18.24%	C:T	−2.13	—
S2A_2336941	0.83	0.006	8.11**	13.50%	T:C	−2.25	TraesCS2A01G003700.1	TRIAE_CS42_2AS_TGACv1 _113891_AA0361970.1
S2A_2336947	0.83	0.006	8.11**	13.50%	G:C	−2.25
S2A_2336965	0.83	0.006	8.11**	13.50%	G:A	−2.25
S2A_2336977	0.83	0.006	8.11**	13.50%	T:C	−2.25
S2A_2800711	0.83	0.008	7.69**	12.88%	A:G	−2.13	—
S2A_2800562	0.82	0.003	10.43**	16.45%	G:A	−2.56	—
S2A_2800596	0.82	0.003	10.04**	16.45%	G:A	−2.56	—
S2A_2800603	0.82	0.003	10.04**	16.45%	C:G	−2.56	—
S2A_2998843	0.82	0.018	6.03*	12.30%	T:A	−1.69	—
S2A_3965047	0.75	0.008	7.52**	12.85%	T:C	−2.33	TraesCS2A01G010200.1	TRIAE_CS42_2AS_TGACv1_112938_AA0348130.2
S2A_3965054	0.75	0.008	7.52**	12.85%	C:T	−2.33
S2A_710998	0.74	0.016	6.29*	12.02%	C:G	−1.64	—

R² Linkage Disequilibrium.

P.V.E. phenotypic variation explained by markers.

*P-value < 0.05.

**P-value < 0.01.

^$left bold allele is associated with increasing stem rust resistance.