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Table 3 Summary of reported QTLs and candidate genes from GWA mapping associated with salt tolerance that are co-located to these segments

From: Genome-wide association study for salinity tolerance at the flowering stage in a panel of rice accessions from Thailand

Chr QTL (Marker) QTL Trait Fragment (Mb) Co-QTL Co-QTL Trait Fragment (Mb) SNP No. Loc Number
1 qSES1, qPH1, qPN1, qPS1, qGPP1 [73] (RM582-RM8094) SES, PH, PAN, UFG, GPP 2.1 qSKC-1 [75]
(C1211-S2139)
SKC 1.4 1 LOC_Os01g18850
1 qSTR-1 [77] (RM9-RM128) STR 7.4 qSKC1.1 [74]
(RM488-RM473)
SKC 3.3 10 LOC_Os01g45120, LOC_Os01g45520, LOC_Os01g59020
qPH1.1, qPL1.2, qPF1.5 [107] (RM128-RM472) PH, PL, PF 7.2
qSDS-1, 99SL [75, 78]
(C813-C86)
DSS, RNC, SHL 3.8
1 qPH1.1 s, qPL1.1 s [58]
(RM246-RM431)
PH, PL 11.6 qST1 [76] (RG109-RZ14) SES 1.2 3 LOC_Os01g66740, LOC_Os01g66760, LOC_Os01g66800
2 qDSS2.1 [74] (RM109-RM110) DSS 1.1    19 LOC_Os02g02120, LOC_Os02g02390, LOC_Os02g02410, LOC_Os02g02424, LOC_Os02g02540, LOC_Os02g02640, LOC_Os02g02690, LOC_Os02g02750, LOC_Os02g02930, LOC_Os02g02990
2 qGY2.1 s [58] (RM555-RM324) GY 7.1 qSST2 [74] (RM211-RM71) SES 6.7 10 LOC_Os02g09340, LOC_Os02g09420, LOC_Os02g10090, LOC_Os02g10100, LOC_Os02g10200, LOC_Os02g10230, LOC_Os02g19220
qSDW-2 [56]
(RM279-RM6911)
SDW 6.1
qFRSP2.1 s, qSPFR2.1 s [58] (RM423-RM174) FRSP, SPFR 2.7
qPL2.1 s [58]
(RM174-RM424)
PL 4.4
2 qPL-2 2 [80] (RM5699-RM262) PL 11.1    3 LOC_Os02g25630, LOC_Os02g27690, LOC_Os02g32480
2 qNAK-2 [77] (RM262-RM318) RNAK 8.8 00SW [78] (C560B-C1408) TIL 7.2 9 LOC_Os02g40120, LOC_Os02g40410, LOC_Os02g40420
3 qDSS3 [74] (RM489-RM7) DSS 5.5    2 LOC_Os03g11280
3 qST3 [76] (RZ585-RG179) SES 7 qFWRO-3b [80]
(RM6283-RM6832)
RFW 5.4 2 LOC_Os03g30510, LOC_Os03g35340
3 qPH3.1 s [58] (RM487-RM130) PL 11.4 qNAUP-3 [80]
(RM5626-RM416)
NAUP 6.4 1 LOC_Os03g49860
3 qGP-3 [57] (RM49-RM6712) GP 7.1 qPL3.1 s [58]
(RM520-RM570)
PL 4.7 28 LOC_Os03g58764, LOC_Os03g61080, LOC_Os03g61110, LOC_Os03g61130, LOC_Os03g61140, LOC_Os03g61150, LOC_Os03g61220, LOC_Os03g62388, LOC_Os03g62400, LOC_Os03g62430, LOC_Os03g63250, LOC_Os03g63680
qSHL-3 [80]
(RM7000-RM7389)
SHL 2.4
4 TEL4S-RM261 [19] SKC 6.6    3 LOC_Os04g08749
4 RG190-RG449 [110] SNC, SKC 9.1 qDSRs4–2 [108]
(RM307-RM471)
DSR 5.9 2 LOC_Os04g28170, LOC_Os04g28190
5 qDTF5 [73] (RM430-RM274) HD 8.2 qDWRO-5b [80]
(RM440-RM480)
RDW 7.4 11 LOC_Os05g37870, LOC_Os05g44290, LOC_Os05g44320, LOC_Os05g44330, LOC_Os05g44370
qSST5 [74] (RM161-RM3476) SES 2.9
qSDM5–5 [109] (RZ70-RZ225) BM 2.9
5 QTL44 [106] (M233B-RM334) SES 4.7    9 LOC_Os05g47670, LOC_Os05g47690, LOC_Os05g47770, LOC_Os05g47780, LOC_Os05g47790
6 qSES6, qTN, qPN6, qGPP6, qTGW6, qGY6 [73] (RM586-RM253) SES, TIL, PAN, GY, 1000GW 4.0    1 LOC_Os06g04190
6 qDRW6 [79] (RM5531-RM3183) RDW 5.3 qTN6, qGY6 [73]
(RM253-RM527)
TIL, GY 4.4 5 LOC_Os06g16400, LOC_Os06g18980, LOC_Os06g19300, LOC_Os06g21210, LOC_Os06g21230
7 qPH7.1, qTNI7.2 [107]
(RM51-RM1243)
PL, TIL 3.35    6 LOC_Os07g04220, LOC_Os07g04270, LOC_Os07g04290, LOC_Os07g04310
8 qSTW8.1 s [58] (RM407-RM310) STDW 4.6    6 LOC_Os08g02050, LOC_Os08g07400, LOC_Os08g07430
8 qSNK-8 [56] (RM3572-RM404) SNK 11.5 qTN8.1, qBM8.2 [107]
(RM3215-RM44)
TIL, BM 3.2 11 LOC_Os08g09200, LOC_Os08g09260, LOC_Os08g09715, LOC_Os08g10330, LOC_Os08g10430, LOC_Os08g10440, LOC_Os08g10570, LOC_Os08g10630, LOC_Os08g16880
8 qSTR-8 [56] (RM7027-RM8264) STR 4    100 LOC_Os08g30730, LOC_Os08g30740, LOC_Os08g30770, LOC_Os08g30780, LOC_Os08g30790, LOC_Os08g30800, LOC_Os08g30810, LOC_Os08g30820, LOC_Os08g30870, LOC_Os08g30900, LOC_Os08g30910, LOC_Os08g30930, LOC_Os08g31000, LOC_Os08g31040, LOC_Os08g31080, LOC_Os08g31110, LOC_Os08g31120, LOC_Os08g31130, LOC_Os08g31180, LOC_Os08g31320, LOC_Os08g31340, LOC_Os08g31410, LOC_Os08g31420, LOC_Os08g31450, LOC_Os08g31460, LOC_Os08g31470, LOC_Os08g31550, LOC_Os08g31600, LOC_Os08g31620, LOC_Os08g31690, LOC_Os08g31700, LOC_Os08g31740, LOC_Os08g31800, LOC_Os08g31814, LOC_Os08g31840, LOC_Os08g31980
9 qGP-9 [57] (RM219-RM7048) SG 8.5 qRL-9 [56] (RM219-RM7038) RL 3.4 1 LOC_Os09g18530
9 RZ206-RG358 [110] LWC 10.1 qIR-9 [57] (RM3320-RM2144) IR 4.7 2 LOC_Os09g34110, LOC_Os09g36976
10 qPS10, qGPP10 [73]
(RM184-RM590)
UFG, GPP 6.7 qDTF10.1 s, qSPFR2.10s, qTGW10.1 s [58]
(RM271-RM484)
DTF, SPFR, 1000GW 6.7 2 LOC_Os10g35436, LOC_Os10g38020
qDTF10.1, qTGW10 [73] (RM184-RM228) HD, 1000GW 5.9
qSDM-10 [109]
(RZ625-RZ500)
BM 4.4
qSKC-10b [56]
(RM258-RM333)
SKC 4.4
11 qDSS11 [74] (RM167-RM3428) DSS 9.4    1 LOC_Os11g11510
11 qDRW11 [79] (RM6091-RM229) RDW 4.5    2 LOC_Os11g29970, LOC_Os11g30220
11 RG16-RG1109 [110] LWC 5 RG16-CDO365 [110] LWC 1.4 5 LOC_Os11g31480, LOC_Os11g31810, LOC_Os11g33230, LOC_Os11g33942
11 qTN11, qPN11, qGPP11, qGY11 [73] (RM457-RM254) TIL, PAN, GPP, GY 4.7    2 LOC_Os11g39330, LOC_Os11g40420
12 qGY12.1 [107] (RM519-RM1103) GY 3.7    33 LOC_Os12g35770, LOC_Os12g35820, LOC_Os12g35850, LOC_Os12g35920, LOC_Os12g36630, LOC_Os12g38051, LOC_Os12g37920, LOC_Os12g36690, LOC_Os12g37720, LOC_Os12g37740 LOC_Os12g37760, LOC_Os12g37770, LOC_Os12g37860, LOC_Os12g37870, LOC_Os12g37890