Table 4.
Functional annotations of the associated SNPs located within the candidate genes for chlorophyll fluorescence parameters measured under drought stress and recovery in the first and second year experiments
| Method | Model | SNP | Position | Chrom | Trait | P.value | maf | R2 | Sequence Description |
Blast Top Hit E-Value |
Blast Top Hit Accession |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MGBS | MLMM FarmCPU |
S1_3 020 891 | 3 020 891 | Chr1 | FV_WR22 FM_WR22 FI_WR22 FJ_WR22 |
9.05E-25 1.21E-12 7.61E-11 5.66E-06 9.40E-05 6.79E-05 1.29E-05 2.56E-05 |
0.09 | 0.25 0.29 0.30 0.26 |
probable receptor-like protein kinase At1g30570 | 2.90E-09 | XP_018822983 |
| MGBS | MLMM FarmCPU |
S7_4 088 661 | 4 088 661 | Chr7 | FM/F0_DSI21 FV/F0_DSI21 φPav_WS21 PIABS_WS21 |
1.07E-19 3.89E-19 1.18E-08 4.25E-10 |
0.08 | 0.29 0.28 0.32 0.25 |
vacuolar sorting protein 39 | 9.30E-10 | KAF5463988 |
| PGBS | MLMM | S8_15 239 273 | 15 239 273 | Chr8 | PIABS_WW21 | 1.00E-13 | 0.42 | 0.16 | protein CELLULOSE SYNTHASE INTERACTIVE 3-like | 8.90E-08 | XP_018830259 |
| MArray | MLMM | AX-171212226 | 25 226 489 | Chr16 | FV/F0_WS21 FM/F0_WS21 |
1.04E-13 1.04E-13 |
0.32 | 0.16 0.16 |
cyclase-associated protein 1-like | 1.20E-08 | XP_018807064 |
| PGBS | MLMM | S13_30 285 764 | 30 285 764 | Chr13 | DI0/RC_WW21 | 1.58E-09 | 0.07 | 0.09 | glucan endo-1,3-beta-glucosidase | 1.10E-09 | XP_018824600 |
| MArray | MLMM | AX-171174023 | 10 769 441 | Chr13 | FI_DSI21 | 1.85E-07 | 0.45 | 0.24 | ubiquinone biosynthesis protein COQ4 homolog, mitochondrial-like | 8.20E-11 | KAF5449503 |
| MArray | FarmCPU | AX-171179454 | 7 717 597 | Chr1 | FJ_WS21 TR0/RC_WS21 FI_WS21 FM_WS21 FV_WS21 FV/FM_DSI21 FM/F0_WS21 FV/F0_WS21 |
1.98E-05 3.24E-05 3.55E-05 3.81E-05 4.77E-05 5.46E-05 9.81E-05 9.81E-05 |
0.23 | 0.27 0.26 0.25 0.24 0.25 0.25 0.23 0.23 |
LRR receptor-like serine/threonine-protein kinase RPK2 | 5.00E-08 | XP_018816677 |
| PGBS | MLMM | S4_1 477 560 | 1 477 560 | Chr4 | FM_WS21 FI_WS21 |
5.78E-07 6.45E-07 |
0.39 | 0.08 0.07 |
BAG family molecular chaperone regulator 4 | 1.70E-08 | KAF5471506 |
| MGBS | FarmCPU | S12_21 754 474 | 21 754 474 | Chr12 | DI0/RC_DSI21 | 1.62E-06 | 0.28 | 0.01 | pentatricopeptide repeat-containing protein At5g19020, mitochondrial | 1.00E-08 | XP_018840533 |
| MArray | FarmCPU | AX-171177765 | 1 333 358 | Chr2 | DI0/RC_WS21 ABS/RC_WS21 ABS/RC_DSI21 φD0_WS21 FV/FM_WS21 FV/FM_DSI21 DI0/RC_DSI21 N_DSI21 φPav_WS21 PC1_WS21 |
2.32E-06 2.39E-06 5.31E-06 8.26E-06 8.26E-06 9.33E-06 9.34E-06 2.46E-05 2.97E-05 3.57E-05 |
0.48 | 0.34 0.35 0.32 0.3 0.3 0.29 0.29 0.26 0.27 0.26 |
cyclin-dependent kinase G-2-like isoform X1 | 6.90E-09 | XP_018822176 |
| MArray | FarmCPU | AX-171176298 | 17 931 021 | Chr4 | ET0/RC_WR22 VI_WS21 φD0_DRI22 FV/FM_DRI22 N_DSI21 FV_DRI22 |
3.29E-06 1.63E-05 2.42E-05 3.05E-05 3.10E-05 4.87E-05 |
0.05 | 0.3 0.24 0.25 0.26 0.26 0.26 |
leucine-rich repeat receptor-like serine/threonine-protein kinase BAM3 | 7.50E-10 | XP_018814580 |
| MArray | FarmCPU MLMM |
AX-171200020 | 13 088 532 | Chr2 | VI_DRI22 | 3.34E-06 7.97E-06 |
0.23 | 0.28 | glucan endo-1,3-beta-glucosidase-like | 1.20E-08 | KAF5447740 |
| MArray | FarmCPU MLMM |
AX-171218271 | 3 371 396 | Chr6 | F0_DSI11 | 7.35E-06 1.17E-05 |
0.23 | 0.19 | wall-associated receptor kinase-like 1 | 4.00E-06 | XP_018812976 |
| PGBS | FarmCPU | S6_3 429 326 | 3 429 326 | Chr6 | TR0/RC_DRI22 | 6.15E-06 | 0.16 | 0.28 | wall-associated receptor kinase 2-like | 1.40E-09 | XP_035546447 |
| MArray | FarmCPU | AX-171217577 | 28 076 649 | Chr11 | F0_DSI21 | 1.56E-05 | 0.44 | 0.29 | glutathione S-transferase-like | 3.30E-10 | KAF5455705 |
| MArray | MLMM | AX-171180361 | 19 366 994 | Chr7 | ABS/RC_WS21 | 1.91E-05 | 0.14 | 0.01 | 9-cis-epoxycarotenoid dioxygenase NCED6, chloroplastic | 3.50E-11 | XP_018817253 |
| MArray | FarmCPU | AX-171192601 | 9 713 679 | Chr13 | TR0/RC_DSI21 F0_DSI21 |
1.934E-05 5.72E-05 |
0.36 | 0.30 0.26 |
pentatricopeptide repeat-containing protein At3g04130, mitochondrial | 4.40E-10 | XP_018857296 |
| MArray | FarmCPU MLMM |
AX-171166172 | 18 425 461 | Chr1 | ψ0_DRI22 | 2.13E-05 3.19E-05 |
0.49 | 0.27 | beta-amylase-like | 6.10E-09 | XP_018846417 |
| MGBS | FarmCPU | S11_4 360 438 | 4 360 438 | Chr11 | φE0_WW21 VJ_WW21 ψ0_WW21 ET0/RC_WW21 |
2.66E-05 2.69E-05 2.69E-05 4.34E-05 |
0.35 | 0.25 0.26 0.26 0.26 |
protein FAR1-RELATED SEQUENCE 5-like | 5.10E-10 | KAF5454297 |
| PGBS | MLMM FarmCPU |
S11_10 333 165 | 10 333 165 | Chr11 | F0_WS21 | 3.13E-05 3.33E-05 |
0.1 | 0.24 | zinc finger BED domain-containing protein DAYSLEEPER-like | 1.60E-07 | XP_035547471 |
| MArray | MLMM FarmCPU |
AX-171195135 | 42 508 998 | Chr1 | VJ_WR22 ψ0_WR22 |
3.20E-05 3.20E-05 3.27E-05 3.27E-05 |
0.2 | 0.26 0.24 |
cytochrome P450 94A2-like | 1.10E-09 | KAF5482357 |
| MArray | FarmCPU MLMM |
AX-171206801 | 1 322 756 | Chr15 | Fv_WS11 | 5.06E-06 3.81E-05 |
0.17 | 0.19 | calcium-dependent protein kinase 32-like | 7.30E-11 | XP_018834447 |
| MArray | MLMM | AX-171141014 | 11 272 317 | Chr11 | TR0/RC_WW21 | 3.67E-05 | 0.18 | 0.01 | protein FAR-RED IMPAIRED RESPONSE 1-like | 6.10E-07 | XP_035546226 |
| MArray | FarmCPU | AX-171159752 | 37 390 204 | Chr10 | DI0/RC_WW21 | 4.37E-05 | 0.11 | 0.2 | glucose-6-phosphate 1-dehydrogenase, chloroplastic-like isoform X3 | 6.60E-12 | XP_035550548 |
| MArray | FarmCPU | AX-171199574 | 16 297 096 | Chr8 | φPav_DRI22 | 6.96E-05 | 0.43 | 0.21 | 2-alkenal reductase (NADP(+)-dependent)-like | 3.30E-09 | KAF5462701 |
| PGBS | FarmCPU MLMM |
S1_20 893 964 | 20 893 964 | Chr1 | FV/FM_WS12 F0_WS12 |
5.06E-06 1.21E-05 9.81E-06 3.45E-05 |
0.11 | 0.14 0.12 |
G-type lectin S-receptor-like serine/threonine-protein kinase LECRK1 | 3.30E-11 | XP_018859482 |
| MArray | MLMM | AX-170695720 | 2 303 269 | Chr11 | FV_WS12 | 1.82E-05 | 0.29 | 0.14 | acyl-CoA-binding domain-containing protein 4 | 4.70E-09 | XP_018850062 |
| MArray | MLMM FarmCPU |
AX-171197482 | 2 063 855 | Chr10 | FV/F0_WS12 | 1.95E-05 4.49E-05 |
0.28 | 0.16 | protein KINESIN LIGHT CHAIN-RELATED 2-like | 2.00E-08 | KAF5457244 |
CHR: chromosome; MAF: minor allele frequency; R2 (%): proportion of variation explained by an SNP.
WW: well-water; WS: water-stress; DSI: drought stress index; and DRI: drought recovery index.
11: moderate drought stress in the first year; 12: severe drought stress in the first year; 21: severe drought stress in the second year; and 22: recovery condition in the second year.