Table 5.
QTLs for root growth angle (RGA) identified across Colosseo×Lloyd and Meridiano×Claudio RIL populations, the association panel (Unibo-DP), and projected wheat QTLs
| SRA QTL | Chr. | CIa | QTL-tag SNP | Co×Ldb | SNPc | Mr×Cld | SNPe | Association panelf | SNPg | Wheat QTLsh |
|---|---|---|---|---|---|---|---|---|---|---|
| (cM) | (ID) | (effect, R 2, isignif.i)i | (allele) | (effect, R 2, signif.) | (allele) | (effect, R 2, signif.) | (allele) | (reference) | ||
| QRga.ubo-1B | 1B | 61–62–68 | IWA7700 | NS – – |
C/T | NS – – |
T/T | +7.2 (4.2) ** | C/T | |
| QRga.ubo-2A.1 | 2A | 7–10–12 | IWB16988 | NS – –– |
T/T | NS – –– |
T/T | +7.7 (4.7) ** | C/T | |
| QRga.ubo-2A.2 | 2A | 97–99–102 | IWA1597 | NS | T/T | NS | T/T | +10.8 (3.9) ** | C/T | (Ta6) |
| QRga.ubo-2A.3 | 2A | 208–211–213 | IWB20424 | NS | A/A | NS | A/A | +9.5 (7.5) *** | A/G | (Ta3) |
| QRga.ubo-2B.1 | 2B | 37–43–45 | IWB4604 | –10.0 (11.7) *** | T/C | NS | T/C | NS | C/T | |
| QRga.ubo-2B.2 | 2B | 70–72–75 | IWB73449 | NS | A/A | NS | G/G | +8.2 (6.2) ** | A/G | |
| QRga.ubo-2B.3 | 2B | 68–77–87 | IWB39220 | +6.0 (6.2) ** | A/A | NS | G/G | NS | A/G | |
| QRga.ubo-2B.4 | 2B | 100–114–130 | IWB62718 | +5.0 (4.4) ** | G/A | NS | A/A | NS | A/G | (Ta6) |
| QRga.ubo-2B.5 | 2B | 175–176–183 | IWB13830 = IWB7663 | NS | A/G | +5.8 (6.7) *** | A/G | +4.70 (2.4) * | A/G | |
| QRga.ubo-3A | 3A | 171–173–176 | IWB70610 | NS | A/A | NS | A/A | –6.9 (5.5) ** | A/G | |
| QRga.ubo-3B | 3B | 181–188–196 | wPt-5947 | NS | 1/0 | –4.6 (4.2) ** | 1/0 | NS | – | |
| QRga.ubo-4A | 4A | 154–156–159 | wPt-0538 | NS | 1/1 | NS | 1/1 | –12.5 (4.2) ** | 1/0 | |
| QRga.ubo-4B.1 | 4B | 33–35–38 | IWB73831 | NS | T/C | NS | T/C | –6.7 (4.6) ** | C/T | |
| QRga.ubo-4B.2 | 4B | 44–47–49 | IWB69501 | NS | T/C | NS | C/C | –8.6 (3.8) ** | C/T | |
| QRga.ubo-4B.3 | 4B | 66–75–91 | IWB60481 | +4.2 (2.4) ** | C/T | NS | C/C | NS | C/T | |
| QRga.ubo-4B.4 | 4B | 82–82–86 | IWB12276 | NS | A/A | –8.2 (13.8) *** | A/G | NS | A/G | |
| QRga.ubo-5B.1 | 5B | 2–3–13 | IWB75279 | NS | 1/1 | –5.6 (6.1) *** | 0/1 | NS | 1/0 | |
| QRga.ubo-5B.2 | 5B | 47–49–52 | IWB24957 | NS | C/C | NS | C/C | +15.0 (4.6) ** | C/T | |
| QRga.ubo-6A.1 | 6A | 70–72–75 | IWB50963 | NS | A/G | NS | A/G | –11.9 (5.2) ** | A/G | |
| QRga.ubo-6A.2 | 6A | 119–122–123 | IWB71119 | +10.0 (17.8) *** | G/A | NS | G/A | –10.6 (8.8) *** | A/G | |
| QRga.ubo-6A.3 | 6A | 127–130–136 | IWB24237 | NS | T/T | –5.8 (7.0) ** | T/C | NS | C/T | |
| QRga.ubo-6B.1 | 6B | 20–22–25 | IWB62692 | NS | A/A | NS | A/A | +6.8 (4.8) ** | A/G | (Ta3) |
| QRga.ubo-6B.2 | 6B | 143–145–147 | IWB13062 | NS | G/G | NS | G/G | –7.0 (4.5) ** | A/G | (Ta3) |
| QRga.ubo-7A.1 | 7A | 4–10–21 | wPt-9207 | +6.0 (5.5) *** | 0/1 | NS | 1/1 | NS | 1/0 | (Ta4) |
| QRga.ubo-7A.2 | 7A | 128–130–133 | IWA2752 | NS | C/C | NS | C/C | +11.8 (7.1) *** | C/T | |
| QRga.ubo-7A.3 | 7A | 125–131–135 | IWB35428 | NS | T/T | +5.6 (6.5) ** | C/– | NS | C/T | |
| QRga.ubo-7A.4 | 7A | 145–147–150 | IWB56095 | NS | C/T | NS | –/C | –7.2 (5.3) ** | C/T | |
| QRga.ubo-7A.5 | 7A | 177–180–183 | IWB3169 | NS | C/C | NS | T/C | +10.4 (7.2) *** | C/T | |
| QRga.ubo-7B | 7B | 175–177–180 | IWB371 | NS | G/G | NS | G/G | +12.8 (5.1) ** | A/G |
a Refers to the tetraploid wheat consensus map (Maccaferri et al., 2015).
b Allelic effect reported as double-dose substitution of the Colosseo versus Lloyd allele. A positive sign indicates that the Colosseo allele increases the trait, and vice versa.
c SNP alleles in the RIL population: Colosseo allele (first)/Lloyd allele (second).
d SNP allelic effect (a) reported as double-dose substitution (2a) of the Meridiano versus Claudio allele. A positive sign indicates that the Meridiano allele increases the trait and vice versa; NS, non-significant.
e SNP alleles in the mapping population: Meridiano allele (first)/Claudio allele (second).
f SNP allelic effect (a) reported as double-dose (2a) substitution of the A or C allele (reported first) versus the G or T allele (reported second).
g SNP alleles in Unibo-DP. The allele with the highest frequency is reported as bold italic font.
h Literature references are listed in Supplementary Fig. S2.
i RGA is expressed as degress while R 2 is expressed as a percentage; QTL effect significance; RIL populations, **LOD 2–3; ***LOD>3; GWAS in Unibo-DP, **marker-wise P≤0.01; ***marker-wise P≤0.001; ****experiment-wise P≤0.05 (=marker-wise P≤0.0001).