Table 1.
Quantitative trait loci (QTL) linked markers used as fixed effects in the least-squares (LS) model for the 45th international bread wheat screening nursery (IBWSN)
| Dataset | Marker | Marker synonyma | Chromosome | Genetic position in cM (Popseq map) | Physical position in bps (Popseq map) | Expected genes | Average p value |
Average R 2 | Frequencyb |
|---|---|---|---|---|---|---|---|---|---|
| Leaf rust | |||||||||
| Seedling 2010 | GBS_24751 | gbsHWWAMP38350 | 2BS | 0 | 3,863,480 | Lr16 | 2.15E−10 | 0.18 | 0.8 |
| GBS_37247 | WCSS1_contig470290_1DS-434 | 1DS | 2.7 | 1,241,625 | Lr42 | 2.57E−09 | 0.15 | 0.5 | |
| Seedling 2012 | GBS_37247 | WCSS1_contig470290_1DS-434 | 1DS | 2.7 | 1,241,625 | Lr42 | 4.33E−14 | 0.24 | 1 |
| GBS_38357 | – | – | – | – | – | 2.04E−10 | 0.17 | 0.8 | |
| El Batan 2010 | GBS_8842 | WCSS1_contig3334901_3AS-4592 | 3AS | 9.4 | 3,823,808 | – | 5.24E−07 | 0.12 | 1 |
| GBS_30281 | WCSS1_contig7120458_4AL-2167 | 4AL | 121.9 | 210,542,445 | – | 2.13E−07 | 0.12 | 0.9 | |
| El Batan 2012 | GBS_12317 | – | – | – | – | 3.42E−06 | 0.09 | 0.5 | |
| GBS_30281 | WCSS1_contig7120458_4AL-2167 | 4AL | 121.9 | 210,542,445 | – | 6.67E−06 | 0.08 | 0.5 | |
| El Batan 2013 | GBS_1926 | – | – | – | – | – | 5.60E−08 | 0.12 | 0.9 |
| GBS_30281 | WCSS1_contig7120458_4AL-2167 | 4AL | 121.9 | 210,542,445 | – | 6.21E−08 | 0.12 | 0.9 | |
| GBS_5135 | – | – | – | – | – | 2.69E−07 | 0.11 | 0.5 | |
| Stem rust | |||||||||
| Njoro 2010 | GBS_22856 | WCSS1_contig10511286_3B-5360 | 3B | – | 90,941,978 | Sr2 | 3.89E−10 | 0.16 | 1 |
| GBS_36529 | WCSS1_contig10759567_3B-1965 | 3B | 76.4 | 370,963,380 | Sr12 | 9.17E−09 | 0.14 | 0.5 | |
| GBS_2454 | WCSS1_contig2284473_5BS-12,686 | 5BS | 4.2 | 4,471,954 | – | 3.19E−09 | 0.14 | 0.5 | |
| Njoro 2011 | GBS_22856 | WCSS1_contig10511286_3B-5360 | 3B | – | 90,941,978 | Sr2 | 1.04E−08 | 0.18 | 1 |
| GBS_13047 | gbsHWWAMP18106 | 3B | 0 | 312,463 | Sr2 | 8.10E−08 | 0.17 | 0.9 | |
| GBS_23598 | – | – | – | – | 1.20E−07 | 0.15 | 0.7 | ||
| Stripe rust | |||||||||
| Quito 2011 | GBS_6432 | WCSS1_contig5219749_2AS-4945 | 2AS | 8.8 | 6,792,755 | Yr17 | 2.91E−10 | 0.16 | 1 |
| Toluca 2012 | 2.41E−13 | 0.21 | 1 | ||||||
| Toluca 2013 | GBS_702 | WCSS1_contig5304580_2AS-10,182 | 2AS | 0 | 944,474 | 0.0E+00 | 0.29 | 1 | |
| GBS_6432 | WCSS1_contig5219749_2AS-4945 | 2AS | 8.8 | 6,792,755 | 0.0E+00 | 0.32 | 0.9 | ||
aMarkers prefixed by gbsHWWAMP are from the hard winter wheat association mapping panel available in T3 database and markers prefixed by WCSS1_contig are from the CSS GBS 2014 physical map, where ‘WCSS1’ stands for wheat chromosome survey sequence
bThe frequency of the marker in the ten cross-validation folds