Table 2.
Summary of significant marker-trait associations identified by GWAS analysis using two approaches (FarmCPU and MLMM) for all the photosynthetic traits across six categories (A–F) in well-water (WW), water-stress (WS), water-recovery (WR) conditions and for drought stress index (DSI) and drought recovery index (DRI) of traits as a relative measure
| Trait Classification | Marker-Trait | WW | WS | WR | DSI | DRI |
|---|---|---|---|---|---|---|
| (A) Chl fluorescence (Mother trees- Array) | Associations | 63 | 69 | 10 | 41 | 23 |
| Unique SNPs | 50 | 41 | 9 | 35 | 18 | |
| (B) Chl fluorescence (Mother trees- GBS) | Associations | 59 | 64 | 32 | 31 | 9 |
| Unique SNPs | 43 | 45 | 26 | 23 | 5 | |
| (C) Chl fluorescence (Progeny-GBS) | Associations | 51 | 14 | 26 | 14 | 68 |
| Unique SNPs | 38 | 10 | 23 | 13 | 55 | |
| (D) Gas exchange (Mother trees- Array) | Associations | 28 | 15 | 2 | 11 | 1 |
| Unique SNPs | 25 | 14 | 2 | 10 | 1 | |
| (E) Gas exchange (Mother trees- GBS) | Associations | 56 | 38 | 13 | 14 | 24 |
| Unique SNPs | 32 | 29 | 10 | 14 | 21 | |
| (F) Gas exchange (Progeny-GBS) | Associations | 2 | 4 | 5 | - | 8 |
| Unique SNPs | 2 | 4 | 4 | - | 8 | |
| Total associations | Associations | 259 | 204 | 88 | 111 | 133 |
| Unique SNPs | 190 | 143 | 74 | 95 | 108 | |
| Associations detected by the FarmCPU approach | Associations | 71 | 47 | 14 | 24 | 32 |
| Unique SNPs | 53 | 40 | 14 | 24 | 27 | |
| Associations detected by the MLMM approach | Associations | 188 | 157 | 74 | 87 | 101 |
| Unique SNPs | 146 | 115 | 65 | 75 | 88 | |
| SNPs detected by both approaches | Total SNPs | 259 | 204 | 88 | 111 | 133 |
| Unique SNPs | 199 | 155 | 79 | 99 | 115 |