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.
From: Molecular marker dissection of stem rust resistance in Nebraska bread wheat germplasm
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 | — |
