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Table 3 Summary of candidate gene analysis for seven traits in different seasons and environments validated for genes and qDTY regions

From: Genome-Wide Association Study for Yield and Yield Related Traits under Reproductive Stage Drought in a Diverse indica-aus Rice Panel

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