Table 4.
Twelve loci significantly (P < 0.005) associated with field resistance at the adult-plant stages in at least two environments and best linear unbiased predictions (BLUPs) data.
| QTL |
Tag-SNPa |
R2h of BLUP |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Name | GWAS stepb | Chromc | CI (cM)d | Index | Allelee | RAFf | Associated SNPg | IT | SEV | Environments with significant marker-trait associations |
| QYrEDWL.par-1AS | 2 | 1AS | 13.55–18.05 | IWB20818 | C/T | 0.13 | NA | 0.049 | 0.053 | MTV15-IT, MTV15-SEV, SPM15-SEV, BLUPs-IT, BLUPs-SEV |
| QYrEDWL-1AL | 1 | 1AL | 109.85–114.35 | IWB31208 | A/G | 0.18 | NA | 0.032 | 0.040 | SPM14-SEV, WHT14-SEV, BLUPs-IT, BLUPs-SEV |
| QYrEDWL-1B.1 | 1 | 1B | 56.35–60.85 | IWB29292 | G/T | 0.16 | IWB61058, IWB27767, IWA5278, IWA6674, IWB60913 | 0.036 | 0.032 | WHT14-IT, MTV15-IT, MTV14-SEV, BLUPs-IT, BLUPs-SEV |
| QYrEDWL-1BL.2 | 1 | 1BL | 103.75–108.25 | IWA3341 | A/C | 0.64 | IWB64037 | 0.037 | 0.035 | SPM14-IT, WHT14-IT, SPM15-IT, SPM14-SEV, BLUPs-IT, BLUPs-SEV |
| QYrEDWL.par-2BS | 2 | 2BS | 3.65–8.15 | IWB52168 | C/T | 0.13 | NA | 0.061 | 0.049 | WHT14-IT, CLF15-IT, SPM14-SEV, SMP15-SEV, CLF15-SEV, BLUPs-IT |
| QYrEDWL-2BS | 1 | 2BS | 14.45–18.95 | IWB59815 | G/T | 0.51 | NA | 0.026 | 0.042 | SPM15-SEV, CLF15-SEV, BLUPs-SEV |
| QYrEDWL.par-3BL | 2 | 3BL | 185.35–189.85 | IWB33031 | A/C | 0.70 | NA | 0.066 | 0.102 | SPM14-IT, MTV14-SEV, SPM14-SEV, CLF15-SEV, BLUPs-IT, BLUPs-SEV |
| QYrEDWL-4AL | 1 | 4AL | 166.35–170.85 | IWB2634 | C/T | 0.25 | NA | 0.032 | 0.023 | SPM15-IT, WHT14-SEV, SPM15-SEV, BLUPs-IT |
| QYrEDWL.par-4B.1 | 2 | 4B | 37.55–42.05 | IWB47531 | A/G | 0.79 | NA | 0.076 | 0.092 | MTV14-IT, SPM14-IT, SPM14-SEV, SPM15-SEV, BLUPs-IT, BLUPs-SEV |
| QYrEDWL.par-4BL.2 | 2 | 4BL | 89.45–93.95 | IWB74594 | C/T | 0.15 | NA | 0.046 | 0.050 | MTV15-IT, MTV15-SEV, CLF15-SEV, BLUPs-IT, BLUPs-SEV |
| QYrEDWL-5AL.1 | 1 | 5AL | 102.25–107.15 | IWB33606 | A/G | 0.20 | IWB65854, IWB75097, IWB50640 | 0.015 | 0.034 | CLF15-IT, SPM15-SEV, CLF15-SEV, BLUPs-SEV |
| QYrEDWL-5AL.2 | 1 | 5AL | 124.05–128.55 | IWB72387 | A/G | 0.67 | NA | 0.023 | 0.038 | WHT14-IT, MTV15-IT, MTV14-SEV, WHT14-SEV, SPM15-SEV, BLUPs-SEV |
aTag-SNP is the SNP with the strongest association in the defined QTL region. bSignificant SNPs (P < 0.005) identified in the first step of GWAS performing on 182 accessions and the second step of GWAS performing on 127 accessions with BLUP-IT > 3. cChromosome of the identified locus is based on the tetraploid wheat consensus map generated by Maccaferri et al. (2015a). dConfidence interval of Yr gene derived from a genetic distance of ±2.25 cM from the tag-SNPs; confidence interval based on the tetraploid wheat consensus map (Maccaferri et al., 2015a). eChromosome of the identified locus is based on the tetraploid wheat consensus map generated by Maccaferri et al. (2015a). Resistance allele of the tag-SNP is highlighted in bold and underlined. fResistance allele frequency of the tag-SNP. gSignificant SNPs that fall into a genetic distance of 2.25 cM from the tag-SNPs. NA means not applicable. hPhenotypic variances (R2) of infection type (IT) and disease severity (SEV) explained by the quantitative trait locus (QTL) calculated in MLM with Q and K model.