Table 3 Summary of candidate gene analysis for seven traits in different seasons and environments validated for genes and qDTY regions
Trait | MTA/ QTL detected | QTL span (Mb) | SNP start (chrom_pos (bp)) | SNP end (chrom_pos (bp)) | Env | Season | Locus name (MSU 7.0) / Drought QTL (qDTY) |
|---|---|---|---|---|---|---|---|
BMDW | – | – | S2_17808669 | S2_17808669 | LL_N | DS | LOC_Os02g30270 |
BMDW | qBMDW8–1 | 0.075 | S8_00466752 | S8_00541934 | LL_S | WS,DS | – |
BMDW | qBMDW-NBP9–1 | 2.021 | S9_19316065 | S9_20944019 | LL_N | WS,DS | LOC_Os09g36290, LOC_Os09g36330 |
DTF | qDTF6–1 | 0.138 | S6_07611279 | S6_07749410 | LL_N | WS,DS | – |
DTF | qDTF6–2 | 0.832 | S6_09539728 | S6_10,371,528 | LL_N | WS,DS | – |
DTF | – | – | S7_19,598,023 | S7_19,598,023 | LL_N | WS | LOC_Os07g32800 |
DTF | – | – | S7_20,159,780 | S7_20,159,780 | LL_N | DS | LOC_Os07g32820 |
DTF | – | – | S9_13934171 | S9_13934171 | LL_S | DS | qDTY9.1 |
DTF | qDTF11–1 | 0.691 | S11_06525213 | S11_07215940 | LL_S | WS,DS | – |
DTF | – | – | S11_18836588 | S11_18836588 | LL_S | DS | LOC_Os11g31980 |
GY | qGY1–1 | 0.351 | S1_03473291 | S1_03824622 | LL_S,UL_S | WS,DS | – |
GY | – | – | S1_24304274 | S1_24304274 | UL_S | DS | LOC_Os01g43450 |
GY | qGY1–2 | 0.403 | S1_39987434 | S1_40390527 | LL_S,UL_S | WS,DS | qDTY1.1 |
GY | qGY2–1 | 4.271 | S2_18794394 | S2_23065933 | UL_S | WS,DS | LOC_Os02g33620, LOC_Os02g36190 |
GY | qGY2–2 | 3.18 | S2_25979458 | S2_29167141 | UL_S | WS,DS | qDTY2.3 |
GY | – | – | S3_28646420 | S3_28646420 | UL_S | WS | LOC_Os03g49650 |
GY | – | – | S4_01441702 | S4_01441702 | UL_S | WS | LOC_Os04g25400 |
GY | – | – | S4_25920763 | S4_25920763 | LL_S | DS | LOC_Os04g37410 |
GY | – | – | S4_31088649 | S4_31088649 | LL_S | DS | LOC_Os04g50150 |
GY | qGY5–1 | 0.365 | S5_04502747 | S5_04505637 | UL_S | WS | – |
GY | – | – | S5_12494100 | S5_12494100 | UL_S | WS | LOC_Os05g20900 |
GY | – | – | S5_19224697 | S5_19224697 | LL_S | DS | LOC_Os05g32660 |
GY | qGY5–2 | 5.205 | S5_24708194 | S5_29913640 | UL_S | WS | OsRPK1, OsCCaMK, OsHAP3B, OsTPS1, OsSTN8 |
GY | – | – | S6_06025083 | S6_06025083 | UL_S | WS | LOC_Os06g11540 |
GY | – | – | S6_22794237 | S6_22794237 | UL_S | WS | LOC_Os06g37850 |
GY | – | – | S6_23132086 | S6_23132086 | UL_S | WS | LOC_Os06g39690 |
GY | – | – | S6_27655258 | S6_27655258 | UL_S | WS | LOC_Os06g47030 |
GY | – | – | S6_31179920 | S6_31179920 | UL_S | WS | LOC_Os06g49910 |
GY | – | – | S7_13019061 | S7_13019061 | UL_S | DS | LOC_Os07g23450 |
GY | – | – | S7_16180595 | S7_16180595 | UL_S | WS | LOC_Os07g27900 |
GY | – | – | S7_16181810 | S7_16181810 | UL_S | WS | |
GY | – | – | S7_16183053 | S7_16183053 | UL_S | WS | |
GY | – | – | S9_03032058 | S9_03032058 | UL_S | WS | LOC_Os09g06650 |
GY | – | – | S9_05467194 | S9_05467194 | UL_S | WS | LOC_Os09g10300 |
GY | – | – | S11_16248710 | S11_16248710 | UL_S | WS | qGP-11, qGI-11, yld11.1, gpl11.1, gl11.1 |
GY | – | – | S11_20668615 | S11_20668615 | UL_S | WS | LOC_Os11g35310 |
GY | – | – | S11_21311326 | S11_21311326 | UL_S | WS | LOC_Os11g36200 |
GY | – | – | S12_02835650 | S12_02835650 | UL_S | DS | LOC_Os12g06020 |
GY | qGY12–1 | 0.941 | S12_18165164 | S12_19106346 | UL_S | WS,DS | qDTY12.1 |
GY / HI | qGY5–1 | 0.365 | S5_04140355 | S5_04266313 | UL_S | DS | – |
HI | – | – | S2_24797737 | S2_24797737 | LL_N | DS | LOC_Os02g40920 |
HI | – | – | S2_25205930 | S2_25205930 | LL_N | DS | LOC_Os02g42020 |
HI | – | – | S5_05891992 | S5_05891992 | LL_N | DS | LOC_Os05g10700 |
HI | – | – | S11_10053723 | S11_10053723 | UL_S | DS | LOC_Os11g18366 |
HI | – | – | S11_10351950 | S11_10351950 | LL_N | DS | LOC_Os11g19230 |
HI | – | – | S11_23022593 | S11_23022593 | LL_N | DS | – |
HI | – | – | S12_23250434 | S12_23250434 | LL_N | WS | LOC_Os12g37850 |
NBP | – | – | S1_37770897 | S1_37770897 | LL_N | DS | qDTY1.1 |
NBP | qBMDW-NBP9–1 | 2.021 | S9_20908000 | S9_21337553 | LL_N | WS,DS | – |
PH | qPH1–1 | 0.982 | S1_33,418,648 | S1_34,400,345 | LL_N, LL_S, UL_S | WS,DS | LOC_Os01g53670, LOC_Os01g59760 |
PH | qPH1–2 | 1.085 | S1_37,960,019 | S1_39,044,781 | LL_N, UL_S | WS,DS | qDTY1.1 |
PH | – | – | S3_33,600,040 | S3_33,600,040 | LL_S | WS | LOC_Os03g58220 |
PH | – | – | S3_33,600,989 | S3_33,600,989 | LL_S | WS | |
PH | – | – | S6_13439145 | S6_13439145 | LL_N | WS | OsPT9, OsPT1055,OsGLK1, nyc3 |
PH | qPH9–1 | 2.731 | S9_13,423,222 | S9_16,154,337 | LL_N,UL_S | WS,DS | qDTY9.1 |
PH | – | – | S11_20,143,839 | S11_20,143,839 | LL_N | DS | LOC_Os11g34364 |
PH | – | – | S11_22175365 | S11_22175365 | UL_S | DS | qGP-11,qGl-11, yld11.1, gpl11.1, gw11.1 |
SPKFT | – | – | S6_28876857 | S6_28876857 | UL_S | DS | LOC_Os06g49060 |
SPKFT | qSPKFT9–1 | 2.411 | S9_09426722 | S9_11838142 | LL_N | WS,DS | – |