Table 5.
Quantitative trait loci (QTL) associated with various traits measured across different environments including hydroponics, glasshouse and two field experiments (Merredin2017 and Merredin2018) under (A) saline and (B) control conditions QTL highlighted in blue and yellow represent major loci on CaLG04 controlling inherent growth-related traits and salinity specific traits, respectively.
| (A) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Environment | Trait | QTL | Chromosome | Left marker | dist(cM) | Right marker | dist(cM) | Size | Prob | % Var | LOD |
| Hydroponics | Seedling biomass | salsBqtl.1 | CaLG04 | SNP14_C14_12_74(C) | 71.61 | SNP15_C14_13_06 | 72.17 | −0.1984 | 0 | 48.5 | 23.6345 |
| Hydroponics | Seedling biomass | salsBqtl.2 | CaLG01 | SNP27 | 39.67 | SNP23 | 50.16 | 0.1269 | 0 | 16.5 | 7.7398 |
| Merredin2017 | Chloride | salClqtl.1 | CaLG05 | DArT616 | 78.37 | DArT610(C) | 83.02 | −0.0573 | 0 | 55.5 | 4.9976 |
| Hydroponics | Chloride | salClqtl.2 | CaLG04 | SNP14_C14_12_74(C) | 71.61 | SNP15_C14_13_06 | 72.17 | −2.828 | 0.0001 | 32.2 | 14.728 |
| Merredin2017 | Number of filled pods | salFPqtl.1 | CaLG04 | SNP201 | 27.87 | SNP2_ Ca4_75 | 29.89 | 2.1991 | 0 | 21.3 | 6.9352 |
| Merredin2018 | Number of filled pods | salFPqtl.2 | CaLG04 | DArT417 | 88.95 | SNP203 | 90.37 | 1.5338 | 0 | 15.1 | 5.1737 |
| Merredin2018 | Necrosis | salNecrosisqtl.1 | CaLG05 | DArT595 | 97.52 | DArT553 | 111.41 | −0.2285 | 1.00E−04 | 20.5 | 3.2408 |
| Merredin2017 | Necrosis | salNecrosisqtl.2 | CaLG04 | SNP148(C) | 18.22 | SNP201 | 27.87 | −0.3491 | 0 | 39.1 | 12.6845 |
| Merredin2018 | Necrosis | salNecrosisqtl.3 | CaLG04 | SNP14_C14_12_74(C) | 71.61 | SNP15_C14_13_06 | 72.17 | 0.2697 | 0 | 34 | 5.4586 |
| Hydroponics | Necrosis | salNecrosisqtl.4 | CaLG03 | DArT273(C) | 68.63 | DArT255(C) | 88.75 | −0.6299 | 0 | 41.9 | 12.8835 |
| Merredin2017 | Seed number | salSNqtl.1 | CaLG04 | SNP201 | 27.87 | SNP2_ Ca4_75 | 29.89 | 3.6812 | 0 | 28.5 | 9.0112 |
| Merredin2017 | Seed number | salSNqtl.2 | CaLG04 | DArT417 | 88.95 | SNP203 | 90.37 | 2.7537 | 0 | 23.2 | 7.5854 |
| Merredin2017 | Seed number | salSNqtl.3 | CaLG01 | DArT71 | 0 | DArT1751 | 10.48 | −1.9377 | 0 | 9.9 | 3.3289 |
| Merredin2017 | 100–seed weight | salSWqtl.1 | CaLG05 | DArT595 | 97.52 | DArT553 | 111.41 | 1.3526 | 0 | 21.8 | 20.5363 |
| Glasshouse | 100–seed weight | salSWqtl.2 | CaLG04 | SNP14_C14_12_74(C) | 71.61 | SNP15_C14_13_06 | 72.17 | −1.5592 | 0 | 22.6 | 16.5896 |
| Merredin2017 | 100–seed weight | salSWqtl.3 | CaLG04 | SNP14_C14_12_74(C) | 71.61 | SNP15_C14_13_06 | 72.17 | −1.5393 | 0 | 34.4 | 22.3099 |
| Merredin2017 | Seed yield | salSYqtl.1 | CaLG05 | DArT595 | 97.52 | DArT553 | 111.41 | 0.3222 | 0 | 17.9 | 4.3667 |
| Merredin2017 | Seed yield | salSYqtl.2 | CaLG04 | SNP201 | 27.87 | SNP2_ Ca4_75 | 29.89 | 0.3865 | 0 | 22 | 5.1227 |
| Glasshouse | Seed yield | salSYqtl.3 | CaLG06 | SNP246 | 131 | SNP259(C) | 133.94 | 0.3113 | 0 | 13.2 | 3.5456 |
| Glasshouse | Water use efficiency | salWUEqtl.1 | CaLG01 | DArT85 | 27.79 | DArT78(C) | 28.07 | 484.6509 | 0 | 46.3 | 4.167 |
| Glasshouse | X30AGR | salX30AGRqtl.1 | CaLG01 | SNP5 | 12.46 | DArT1786 | 15.7 | 1.4136 | 0 | 28.7 | 4.0182 |
| Glasshouse | X34AGR | salX34AGRqtl.1 | CaLG01 | SNP5 | 12.46 | DArT1786 | 15.7 | 1.5533 | 0 | 29.2 | 3.735 |
| (B) | |||||||||||
| Glasshouse | Number of filled pods | conFPqtl.1 | CaLG07 | DArT1204(C) | 43.73 | SNP286(C) | 46.27 | −1.7159 | 0 | 19.6 | 3.7095 |
| Merredin2017 | Number of filled pods | conFPqtl.2 | CaLG04 | SNP14_C14_12_74(C) | 71.61 | SNP15_C14_13_06 | 72.17 | 1.8559 | 0 | 39.3 | 14.0499 |
| Merredin2018 | Sodium | conNaqtl.1 | CaLG04 | SNP201 | 27.87 | SNP2_ Ca4_75 | 29.89 | 0.1007 | 0 | 17 | 4.3069 |
| Glasshouse | Seed number | conSNqtl.1 | CaLG07 | DArT1046 | 40.32 | DArT1204(C) | 43.73 | −2.5513 | 0 | 19.1 | 4.0558 |
| Glasshouse | Seed number | conSNqtl.2 | CaLG04 | SNP14_C14_12_74(C) | 71.61 | SNP15_C14_13_06 | 72.17 | 2.1867 | 0 | 14.3 | 3.5923 |
| Merredin2017 | Seed number | conSNqtl.3 | CaLG04 | SNP14_C14_12_74(C) | 71.61 | SNP15_C14_13_06 | 72.17 | 2.1157 | 0 | 22.2 | 6.5191 |
| Merredin2017 | Seed number | conSNqtl.4 | CaLG04 | SNP202(C) | 93.61 | DArT1740(C) | 103.27 | 1.7592 | 0 | 13.8 | 4.0847 |
| Merredin2017 | Seed number | conSNqtl.5 | CaLG08 | DArT1753 | 48.59 | SNP393(C) | 55.61 | 1.2955 | 0 | 8.5 | 3.776 |
| Merredin2017 | 100-seed weight | conSWqtl.1 | CaLG05 | DArT595 | 97.52 | DArT553 | 111.41 | 1.411 | 0 | 17.5 | 13.2902 |
| Glasshouse | 100-seed weight | conSWqtl.2 | CaLG04 | SNP14_C14_12_74(C) | 71.61 | SNP15_C14_13_06 | 72.17 | −1.9649 | 0 | 35.2 | 23.9314 |
| Merredin2017 | 100–seed weight | conSWqtl.3 | CaLG04 | SNP14_C14_12_74(C) | 71.61 | SNP15_C14_13_06 | 72.17 | −1.9341 | 0 | 39.7 | 31.4225 |
| Glasshouse | 100-seed weight | conSWqtl.4 | CaLG06 | SNP246 | 131 | SNP259(C) | 133.94 | 0.9269 | 0 | 8.3 | 5.5955 |
| Merredin2018 | Seed yield | conSYqtl.1 | CaLG05 | DArT523 | 126.94 | DArT1040 | 137.75 | −0.1348 | 0 | 39.5 | 4.1562 |
| Merredin2017 | Seed yield | conSYqtl.2 | CaLG04 | DArT419 | 88.67 | DArT417 | 88.95 | 0.2063 | 0.0001 | 11.3 | 3.0544 |
| Merredin2017 | Seed yield | conSYqtl.3 | CaLG01 | DArT63(C) | 24.06 | SNP24(C) | 26.68 | −0.2385 | 0 | 14.2 | 4.0241 |
| Glasshouse | Water use | conWUqtl.1 | CaLG04 | SNP14_C14_12_74(C) | 71.61 | SNP15_C14_13_06 | 72.17 | −2.5546 | 1.00E-04 | 22.1 | 3.0077 |
| Glasshouse | Water use efficiency | conWUEqtl.1 | CaLG04 | SNP14_C14_12_74(C) | 71.61 | SNP15_C14_13_06 | 72.17 | −2.71E+02 | 0 | 18.7 | 4.0655 |
| Glasshouse | Water use efficiency | conWUEqtl.2 | CaLG01 | DArT1786 | 15.7 | DArT1798 | 15.97 | 284.3119 | 0 | 21 | 4.6183 |
| Glasshouse | X30AGR | conX30AGRqtl.1 | CaLG04 | DArT417 | 88.95 | SNP203 | 90.37 | −2.6217 | 0 | 64.1 | 7.6002 |
| Glasshouse | X34AGR | conX34AGRqtl.1 | CaLG04 | DArT417 | 88.95 | SNP203 | 90.37 | −3.0783 | 0 | 64 | 7.8203 |
X30AGR-Absolute growth rate at 30 days after sowing, X34AGR- Absolute growth rate at 34 days after sowing. Allele effects contributed by Rupali are denoted by negative effect size while the positive effect size is contributed by Genesis836.