Table 4. Markers significantly associated with seedling resistance in the WBDC to P. graminis f. sp. tritici pathotypes TTKSK, QCCJB, HKHJC, MCCFC, and P. graminis f. sp. secalis culture 92-MN-90.
| Marker | MAFa | Alleles | TTKSK | QCCJB | MCCFC | HKHJC | 92-MN-90 | R2b | POPSEQ Distance (cM)c | LDd | Gene Namee | Gene Functionf | Resistance Sourceg |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| S1H_15633898 | 0.06 | G/A | – | – | +Ki | – | – | 0.09 | 27.06 | 0.24 | SP2–SP6 | ||
| S1H_71499376 | 0.05 | G/A | –* | +K* | +KG* | –* | –* | 0.14–0.24 | 46.4 | 0.20 | SP6 | ||
| S1H_74214978 | 0.07 | A/G | – | – | – | – | +K | 0.11 | 46.47 | 0.29 | SP6 | ||
| S1H_135744206 | 0.05 | C/T | +K* | +K* | +K* | –* | –* | 0.15–0.25 | 47.8 | 0.00 | SP6 | ||
| S1H_189554644h | 0.05 | T/C | – | – | +K | – | – | 0.08 | 47.93 | 0.00 | SP2 | ||
| S1H_329009785 | 0.05 | C/G | – | – | – | – | +K | 0.17 | 48.19 | 0.01 | SP6 | ||
| S1H_482689791 | 0.05 | T/A | – | – | +K | – | – | 0.12 | 71.05 | 0.06 | SP6 | ||
| S1H_493058484 | 0.14 | G/T | +K* | –* | –* | –* | +K* | 0.09–0.11 | 80.27 | 0.01 | SP6 | ||
| S1H_503256550 | 0.10 | G/A | – | – | – | +K | – | 0.12 | 86.28 | SP2 | |||
| S2H_6224512 | 0.08 | C/T | – | – | +K | – | – | 0.06 | 5.31 | 0.12 | SP2 | ||
| S2H_118241413 | 0.07 | T/C | – | – | +K | – | – | 0.09 | 54.94 | 0.06 | SP2 | ||
| S2H_624272241 | 0.05 | T/C | – | – | +K | – | – | 0.04 | 67.68 | 0.00 | SP1 | ||
| S2H_698149422 | 0.14 | C/T | – | – | – | – | +KG | 0.14 | 105.54 | 0.00 | SP6 | ||
| S2H_704316447 | 0.14 | C/T | +K | – | – | – | – | 0.07 | 107.38 | HORVU2Hr1G104640 | U-box domain-containing protein | SP1 | |
| S3H_2871173 | 0.07 | C/T | +K* | –* | +K* | –* | –* | 0.17–0.22 | 2.03 | 0.05 | SP6 | ||
| S3H_28096251 | 0.12 | G/T | – | – | – | – | +K | 0.09 | 33.91 | 0.03 | SP2–SP6 | ||
| S3H_59710586 | 0.08 | T/C | – | – | +K | – | – | 0.18 | 45.86 | 0.31 | SP2–SP6 | ||
| S3H_130142435 | 0.05 | A/T | +K* | –* | +KG* | –* | –* | 0.16–0.27 | 48.72 | 0.28 | SP2–SP3 | ||
| S3H_161744326 | 0.11 | G/C | – | – | – | – | +K | 0.16 | 49.7 | 0.02 | SP2–SP4–SP6 | ||
| S3H_443833059 | 0.08 | G/A | – | – | – | – | +K | 0.07 | 51.91 | 0.10 | SP2 | ||
| S3H_521836324 | 0.06 | C/T | – | – | +K | – | – | 0.13 | 59.45 | 0.02 | SP2 | ||
| S3H_655238400 | 0.05 | G/T | – | – | – | +K | – | 0.05 | 127.31 | SP2 | |||
| S4H_84342294 | 0.05 | G/A | –* | –* | +K* | –* | +K* | 0.16–0.19 | 51.04 | 0.60 | SP6 | ||
| S4H_96878120 | 0.05 | C/T | +K | – | – | – | – | 0.14 | 51.32 | 0.53 | SP6 | ||
| S4H_100361862 | 0.08 | T/G | – | +K | – | – | – | 0.15 | 51.32 | 0.37 | SP2–SP6 | ||
| S4H_152479331 | 0.06 | T/C | – | – | – | – | +K | 0.17 | 51.38 | 0.46 | SP6 | ||
| S4H_166776967 | 0.06 | G/C | – | – | – | – | +K | 0.15 | 51.47 | 0.70 | SP6 | ||
| S4H_189407280 | 0.08 | C/T | +K* | +K* | +K* | –* | –* | 0.15–0.19 | 51.42 | 0.80 | SP2–SP6 | ||
| S4H_426125219 | 0.05 | G/A | +K* | –* | +K* | –* | +K* | 0.11–0.18 | 51.48 | SP2–SP6 | |||
| S5H_4727167 | 0.05 | C/T | +K | – | – | – | – | 0.13 | 7.42 | 0.07 | SP2–SP6 | ||
| S5H_299790192 | 0.05 | G/C | – | – | +K | – | – | 0.10 | 44.22 | 0.01 | SP6 | ||
| S5H_464225644 | 0.05 | C/T | +K* | –* | +K* | –* | –* | 0.06 | 50.01 | 0.02 | SP6 | ||
| S5H_596737839 | 0.06 | C/T | +K* | +K* | +K* | –* | +K* | 0.10–0.15 | 123.89 | 0.06 | HORVU5Hr1G094700–HORVU5Hr1G094710 | Disease resistance-responsive (dirigent-like protein) family protein | SP2–SP6–SP7 |
| S5H_630137153 | 0.07 | G/A | +KG* | +KG* | +KG* | –* | +KG* | 0.17–0.23 | 143.5 | SP6 | |||
| S6H_14901366 | 0.07 | A/T | –* | +K* | +K* | –* | +KG* | 0.12–0.16 | 15.62 | 0.00 | SP3–SP6 | ||
| S6H_150096979 | 0.07 | C/T | – | – | +K | – | – | 0.06 | 53.58 | 0.15 | SP3 | ||
| S6H_267991768h | 0.05 | G/A | – | – | +KG | – | – | 0.06 | 55.06 | 0.00 | SP3 | ||
| S6H_415545279 | 0.06 | C/T | –* | +KG* | +KG* | –* | +KG* | 0.14–0.18 | 60.02 | 0.05 | SP6 | ||
| S6H_553884761 | 0.06 | G/C | – | – | +K | – | – | 0.08 | 93.89 | 0.03 | SP3 | ||
| S6H_575766386h | 0.06 | G/A | +KG* | –* | –* | –* | +K* | 0.11–0.12 | 117.87 | HORVU6Hr1G091540 | Protein kinase superfamily protein | SP6 | |
| S7H_14599947 | 0.05 | C/T | +KG* | +KG* | +KG* | –* | +KG* | 0.14–0.20 | 11.62 | 0.00 | SP6 | ||
| S7H_88235964 | 0.05 | G/A | – | – | +K | – | +K | 0.05–0.06 | 62.12 | 0.00 | SP2 | ||
| S7H_112969908 | 0.05 | C/G | – | – | +KG | – | – | 0.12–0.16 | 66.36 | 0.00 | HORVU7Hr1G041160 | Membrane attack complex component/perforin (MACPF) domain | SP6 |
| S7H_156723880 | 0.46 | G/A | +K | – | – | – | – | 0.07 | 68.12 | 0.02 | HORVU7Hr1G047080 | MATE efflux family protein | SP6 |
| S7H_526203164 | 0.05 | G/C | +KG | – | – | – | – | 0.12–0.16 | 77.4 | SP6 |
MAF, Minor allele frequency for SNP marker.
R2, Proportion of phenotypic variance range explained by SNP marker.
POPSEQ map distance in cM.
Linkage disequilibrium (LD) estimated as r2 between sequentially listed marker pairs within a chromosome (next marker in the list). Marker pairs having LD with r2 ≥ 0.2 are in boldface.
Gene name is according to barley genome annotation (http://webblast.ipk-gatersleben.de/barley_ibsc/downloads/).
Gene function is listed for cases where the SNP marker is part of a gene implicated in disease resistance.
Subpopulation source(s) for resistance alleles.
Possible coincident QTL identified previously in the WBDC for QCCJC, MCCFC, and 92-MN-90 (Steffenson et al. 2007), where S1H_189554644 was coincident with QTL bpb-9717_58.7_MCCFC; S6H_267991768 was coincident with QTL bpb-4783_77.4_MCCFC; and S6H_575766386 was coincident with QTL bpb-2304/bpb-0403/bpb-7146_137_92-MN-90.
+, SNP markers found to be significantly associated with P. graminis resistance using the K model (K), G model (G), or using both of the K and G models (KG). Significant association of multiple P. graminis cultures with the same markers is indicated by an asterisk (*).