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Table 5 List of candidate genes close to the significant markers determined based on function or expression pattern

From: Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam

QTL ID Chr Position of QTL Trait(s) Gene in rice Gene in Arabidopsis Function References
q48 1 2710978-2880907 NR_T Os01g05820 no Specifically expressed in lateral root initiation zone [25]
q48 1 2710978-2880907 NR_T Os01g06010 no Specifically expressed in lateral root initiation zone [25]
q48 1 2710978-2880907 NR_T Os01g06060 no Specifically expressed in root cap [25]
q73 1 5851606 DWB60, DRW Os01g10900 At04g18640 Arabidopsis MRH1, root hair development [44]
q73 1 5851606 DWB60, DRW Os01g11010 no Specifically expressed in lateral root initiation zone [25]
q84 1 6404307 DRP Os01g11860 no Specifically expressed in root cap [25]
q49 1 10299033 NR_T Os01g18360 no OsIAA4, crown roots formation in response to auxin [34]
q36 1 28579082 NCR Os01g49690 At01g50370 Arabidopsis FYPP1, post transductional, PIN protein regulation [32]
q50 1 42706214 NR_T Os01g73700 no Specifically expressed in root cap [25]
q50 1 42706214 NR_T Os01g73720 no Specifically expressed in root cap [25]
q66 2 5015093 DW2040 Os02g09760 no Specifically expressed in root cap [25]
q64 2 25990556 DW0020 Os02g43 120 no Specifically expressed in root cap [25]
q74 2 30762847 DWB60 Os02g50372 no Candidate gene for a root mass at depth QTL [45]
q38 2 31652149 NCR Os02g51710 At04g39730 Arabidopsis PLAT1, regulation of lateral root development [41]
q59 3 35166421 THK Os03g63970 At05g51810 OsGA20ox1, underlies a QTLs for early vigor [47]
q51 5 16205923-16458100 NR_T Os05g27920 At05g58440 Arabidopsis SNX2, endocellular transport of PIN2 [33]
q60 6 4 649 357 THK Os06g09280 At01g26370 Arabidopsis RID1, root development [46]
q76 6 15 865 171 DWB60 Os06g27980 At03g05390 Specifically expressed in root cap [25]
q42 7 474 875 NCR Os07g01820 no OsMADS15, crown roots development [39, 40]
q61 7 15 424 576 THK Os07g26740 no OsRR7, cytokinin signaling [49, 57]
q61 7 15 424 576 THK Os07g26740 no Specifically expressed in lateral root initiation zone [25]
q53 7 22174085-22175036 NR_T Os07g37010 At04g03270 Arabidopsis CYCLIN D6;1 lateral root initiation [38]
q71 12 1 185 335 DW4060 Os12g03110 no Arabidopsis MIF1, root development [43]
q71 12 1 185 335 DW4060 Os12g03150 At01g08810 Arabidopsis MYB60, root development [42]