Table 2.
Putative candidate genes in the close vicinity of significantly associated GWAS peaks. Regarding names for QTLs, PPQ stands for potentially pleiotropic QTL, which are the GWAS peaks listed in Table S7 that are significantly associated with 2 or more root traits.
| Name of QTL | Locus | Chr | Pos | Distance from putative candidate gene | Putative candidate gene |
|---|---|---|---|---|---|
| QDIM_8DAT_03 | 1_49305802 | 1 | 49305802 | 8,238 | Serine/threonine phosphatases (PP2C) |
| QTRL_8DAT_01 | 2_8678721 | 2 | 8678721 | Genic | WRKY transcription factor-like protein (Lazy 1) |
| PPQ02(TRL_8DAT, TSA_8DAT) | 2_9448766 | 2 | 9448766 | 1,061 | Eukaryotic aspartyl protease |
| PPQ04(TRL_8DAT, TSA1_8DAT) | 2_8593061 | 2 | 8593061 | 4,307 | Uncharacterized protein |
| PPQ06(TSA_8DAT, TRV_8DAT) | 2_9883206 | 2 | 9883206 | 6,277 | UDP-glucosyltransferase71c5 |
| QTCA_8DAT_04 | 4_47068983 | 4 | 47068983 | 3,199 | DNA-directed DNA polymerase |
| QTRL_8DAT_04 | 4_47283354 | 4 | 47283354 | Genic | Mitogen-activated protein kinase kinase kinase (MAP3KA) |
| QCOPM_8DAT_01 | 4_48983360 | 4 | 48983360 | 2,554 | DOF AFFECTING GERMINATION 1 |
| QDIM_8DAT_05 | 5_34851234 | 5 | 34851234 | 8,287 | Serine/threonine protein phosphatase 2A (PP2A-3) |
| QTCA_8DAT_09 | 6_6108102 | 6 | 6108102 | 3,832 | CALMODULIN LIKE 42 |
| QTRV_5DAT_04 | 7_4869847 | 7 | 4869847 | Genic | 1-Phosphatidylinositol 4-kinase and ubiquitin-like |
| QTRT_8DAT_01 | 9_37109514 | 9 | 37109514 | 1,317 | F-box protein Phloem Protein 2-A13 |
| QTRV_8DAT_02 | 11_7681279 | 11 | 7681279 | Genic | Peptidyl-prolyl cis-trans isomerases; P-loop containing nucleoside triphosphate hydrolase |
| QTRL_8DAT_05 | 11_17101313 | 11 | 17101313 | 2,387 | TCP-1/cpn60 chaperonin family protein |
| PPQ12(TSA3_8DAT, TRV_8DAT) | 12_33823378 | 12 | 33823378 | 3,989 | ZF-HD homeobox like protein |
| QTRT_5DAT_28 | 14_30641451 | 14 | 30641451 | 9,781 | Gibberellin 20 oxidase 3-like |
| QDIM_8DAT_08 | 19_42651593 | 19 | 42651593 | 319 | F-box like 17 protein containing LRR |
| QSOL_5DAT_02 | 20_2376802 | 20 | 2376802 | 8,485 | O-FUCOSYL TRANSFERASE 1 |
| QCOPM_8DAT_12 | 20_31095132 | 20 | 31095132 | 7,620 | SUGAR WILL EVENTUALLY BE EXPORTED TRANSPORTER (SWEET) |
| PPQ11(TSA3_8DAT, TRV_5DAT, TSA3_5DAT) | 20_42450695 | 20 | 42450695 | 4,424 | EDF1 |
| PPQ08(TSA3_5DAT, TRV_5DAT) | 20_42464855 | 20 | 42464855 | Genic | C2H2 zinc finger (DOT-5) |