Table 3 Summary of Major-QTLs (M-QTLs) for plant vigour and canopy conductance related traits using different genetic map. Low density (241 SSR marker-Varshney et al. 2014); high density (1007 SSR + SNP marker- Jaganathan et al. 2015) and ultra-high density (1557 SNP markers- Kale et al. 2015) markers were used for identification of QTLs. The trait on only measured at 2015 indicates (+) and newly identified additional QTLs with high density markers were indicated by (*). Details of traits code were mentioned in Table 1
Marker used | Trait code | Linkage groups (LGs) | Total QTLs | No. of QTLs in the QTL hotspot | Consistent QTLs | Genetic Size (cM) | Logarithm of the odds ratio (LOD) | Phenotypic variation explained (PVE, %) |
|---|---|---|---|---|---|---|---|---|
Low density-SSR | VIG | 4 | 2 | 2 | + | 2.00 | 7.0-32 | 13-44 |
High density-SSR + SNPs | VIG | 4 | 2 | 2 | + | 0.4-2.7 | 36-39 | 47-51 |
Ultra-high density-SNPs | VIG | 4 | 1 | 1 | + | 0.14 | 36.7 | 53.00 |
Low density-SSR | 3DL | 4 | 5 | 5 | 2 | 1.0-6.0 | 5.0-12 | 10-23 |
High density-SSR + SNPs | 3DL | 4 | 5 | 5 | 3 | 0.4-3.6 | 6.0-13 | 11-20 |
Ultra-high density-SNPs | 3DL | 4&6 | 4 | 3 | 1 | 0.15-13 | 2.3-9.8 | 11-19 |
Low density-SSR | PL | 4 | 3 | 3 | 1 | 5.0-7.0 | 6.0-6.0 | 12-13 |
High density-SSR + SNPs | PL | 4 | 3 | 3 | 1 | 1.3-5.6 | 6.0-9.0 | 10-14 |
Ultra-high density-SNPs | PL | 4 | 1 | 1 | 1 | 0.05 | 5.6 | 11 |
Low density-SSR | SDW | 4 | 5 | 5 | 3 | 3.0-7.0 | 4.0-10 | 10-20 |
High density-SSR + SNPs | SDW | 4 | 6* | 6 | 3 | 0.9-2.8 | 5.0-11 | 11-18 |
Ultra-high density-SNPs | SDW | 4 | 1 | 1 | 1 | 0.15 | 9.3 | 18 |
Low density-SSR | LAI | 4 | 2 | 2 | 2 | 4.0-7.0 | 5.0-7.0 | 10-16 |
High density-SSR + SNPs | LAI | 4 | 1 | 1 | – | 0.8 | 6.0 | 10 |
Ultra-high density-SNPs | LAI | 4 | 1 | 1 | 1 | 0.15 | 5.7 | 11 |
Low density-SSR | PH | 4 | 6 | 6 | 2 | 2.0-8.0 | 6.0-23 | 10-32 |
High density-SSR + SNPs | PH | 4 | 6 | 6 | 2 | 0.8-2.9 | 8.0-29 | 14-37 |
Ultra-high density-SNPs | PH | 2,4&7 | 7* | 5 | 3 | 3.4-0.14-0.10 | 4.9-21.7 | 10-39 |
Low density-SSR | PHG | 4 | 5 | 5 | 2 | 3.0-4.0 | 5.0-13 | 11-25 |
High density-SSR + SNPs | PHG | 4 | 9* | 9 | 3 | 1.1-4.6 | 7.0-17 | |
Ultra-high density-SNPs | PHG | 4&7 | 4 | 3 | 1 | 0.14-0.07 | 4.8-13.6 | 10-23 |
Low density-SSR | eT | 4 | 1 | 1 | 1 | 8.0 | 5.0 | 11 |
High density-SSR + SNPs | eT | 4 | 1 | 1 | 1 | 0.21 | 4.0 | 12 |
Ultra-high density-SNPs | eT | – | – | – | – | – | – | – |
Low density-SSR | eTR | 4 | 2 | – | 1 | 7.0-10 | 6.0-8.0 | 10-11 |
High density-SSR + SNPs | eTR | 3&4 | 4* | 3 | 2 | 2.0-5.0 | 3.0-6.0 | 11-14 |
Ultra-high density-SNPs | eTR | 4 | 1 | – | 1 | 0.48 | 5.7 | 11 |
Low density-SSR | T | 4&8 | 2 | 1 | 1 | 6.0-8.0 | 5.0 | 12-14 |
High density-SSR + SNPs | T | 5&8 | 2 | – | – | 2.9-3.5 | 3.0-6.0 | 10-14 |
Ultra-high density-SNPs | T | – | – | – | – | – | – | – |
Low density-SSR | TR | 7 | 3 | – | 1 | 5.0-13 | 3.0-5.0 | 10-17 |
High density-SSR + SNPs | TR | – | – | – | – | – | – | – |
Ultra-high density-SNPs | TR | 3 | 1 | – | – | 0.08 | 5.1 | 10 |
Low density-SSR | R-3D/PLA | 4, 6 &7 | 10 | – | 5 | 1.0-15.0 | 6.0-13 | 10-15 |
High density-SSR + SNPs | R-3D/PLA | 1,4, 6&7 | 13* | 1 | 4 | 0.3-4.2 | 7.0-14 | 10-16 |
Ultra-high density-SNPs | R-3D/PLA | – | – | – | – | – | – |