Table 3.
List of the heading date (HD) and plant height (PTHT) quantitative trait loci (QTL) identified in the Krasnodarskij 3352 × Carolino 164 recombinant inbred line (RIL) and (WIR 911 × Carolino164) × Carolino164 backcross inbred line (BIL) mapping populations.
| QTLa | Chr. | QTL region (cM) | QTL interval (Mb) | Marker nearest LOD peak | Peak position (cM) | LOD value | Additive effectb | PVEc |
|---|---|---|---|---|---|---|---|---|
| Krasnodarskij 3352 × Carolino 164 RIL population | ||||||||
| qHD2-1 | 2 | 34.3–35.3 | 5.72–5.84 | 2_5837031 | 35.0 | 5.7 | −1.64 | 7.5 |
| qHD2-2 | 2 | 41.3–41.8 | 7.15–7.24 | 2_7238793 | 41.5 | 10.6 | 2.31 | 14.8 |
| qHD3 | 3 | 142.3–142.8 | 31.02–31.19 | 3_31190989 | 142.5 | 5.3 | −1.54 | 6.5 |
| qHD7 | 7 | 47.3–48.3 | 9.26–10.11 | 7_10111835 | 48.0 | 16.6 | −3.27 | 28.3 |
| qPTHT1 | 1 | 149.8–150.8 | 38.05–38.28 | 1_38239037 | 150.0 | 10.4 | −4.82 | 5.7 |
| qPTHT3 | 3 | 2.36–3.14 | 0.73–0.85 | 3_851612 | 3.0 | 6.9 | −3.84 | 3.4 |
| qPTHT4-1 | 4 | 80.3–82.3 | 28.01–28.10 | 4_28098691 | 80.5 | 12.3 | −5.88 | 7.9 |
| qPTHT4-2 | 4 | 82.3–83.8 | 28.01–28.69 | 4_28685882 | 83.5 | 7.8 | 4.68 | 4.8 |
| qPTHT5-1 | 5 | 4.26–5.43 | 0.77–0.81 | 5_805425 | 5.0 | 6.5 | −3.67 | 3.3 |
| qPTHT5-2 | 5 | 16.3–17.8 | 2.27–2.29 | 5_2291156 | 16.5 | 15.2 | 6.29 | 9.6 |
| qPTHT5-3 | 5 | 87.3–88.3 | 25.44–25.54 | 5_25502053 | 87.5 | 12.1 | −5.32 | 7.0 |
| qPTHT7 | 7 | 43.8–46.3 | 8.32–8.81 | 7_8806939 | 44.5 | 19.6 | −7.69 | 14.1 |
| qPTHT9-1 | 9 | 11.3–11.8 | 8.51–8.52 | 9_8515797 | 11.5 | 23.1 | −8.98 | 18.6 |
| qPTHT9-2 | 9 | 16.3–17.3 | 9.33–9.78 | 9_9778764 | 17.5 | 10.0 | 4.91 | 5.4 |
| (WIR 911 × Carolino164) × Carolino164 BIL population | ||||||||
| qHD3-1 | 3 | 0.0–0.3 | 0.73–0.85 | 3_730996 | 0.0 | 14.9 | −4.56 | 27.8 |
| qHD3-2 | 3 | 16.3–19.3 | 5.09–5.54 | 3_5534861 | 17.0 | 3.3 | −1.82 | 4.5 |
| qHD3-3 | 3 | 100.3–101.3 | 31.76–31.89 | 3_31893660 | 101.0 | 3.2 | −1.95 | 4.5 |
| qHD6 | 6 | 18.3–20.3 | 9.32–9.69 | 6_9314865 | 19.0 | 15.3 | 6.17 | 28.8 |
| qPTHT4 | 4 | 45.3–46.3 | 22.23–22.44 | 4_22231867 | 46.0 | 3.5 | −4.40 | 12.2 |
| qPTHT11 | 11 | 64.3–65.3 | 24.73–24.93 | 11_24728131 | 65.5 | 3.0d | −6.79 | 10.8 |
The RIL population had 134 progeny genotyped with 2,794 SNP markers and the BIL population had 92 progeny genotyped with 2,590 SNP markers.
Quantitative trait loci (QTL) are declared based on the Inclusive Composite Interval Mapping (ICIM) approach using the IciMapping software (Meng et al., 2015) and 0.5-step, 0.005-pin ICIM_Add settings unless otherwise noted.
A positive additive effect indicates that the Krasnodarskij 3352 or WIR 911 allele increases the phenotype for that trait; a negative additive effect indicates that the Carolino164 allele increases the trait.
PVE is the percentage of total phenotypic variation explained by an individual QTL, as estimated by R2 values from ICIM analysis.
LOD score is close to the 90% confidence value of 3.01 (based on 1,000 permutations for the PTHT trait).