Table 1 The mapped QTLs for rice cold tolerance at seedling stage
From: Genome-wide Association Mapping of Cold Tolerance Genes at the Seedling Stage in Rice
QTLs | Chromosome | linked SNP locia | linked tolerant SNP marker | LOD | Phenotype contribution | Candidate genes |
|---|---|---|---|---|---|---|
qCTS1-1 | 1 | 7392085 | CC | 3.13 | 5.15 | NA |
qCTS1-2 | 1 | 19180885 | TT | 3.99 | 5.14 | NA |
qCTS1-3 | 1 | 20261058 | AA | 3.27 | 4.16 | NA |
qCTS1-4 | 1 | 41385263 | TT | 3.28 | 4.43 | NA |
qCTS1-5 | 1 | 41859177 | AA | 3.88 | 4.92 | NA |
qCTS1-6 | 1 | 42438945 | CC | 3.23 | 4.11 | OsDREB1F, LOC_Os01g73770 |
qCTS2-1 | 2 | 74241 | GG | 4.05 | 5.45 | NA |
qCTS2-2 | 2 | 4797319 | AA | 3.12 | 3.85 | NA |
qCTS2-3 | 2 | 15096404 | AA | 3.54 | 4.44 | NA |
qCTS2-4 | 2 | 35929494 | TT | 3.84 | 5.07 | NA |
qCTS3-1 | 3 | 604512 | CC | 3.54 | 4.47 | qLTG3-1, LOC_Os03g01320 Chr03:219977-221070 |
qCTS3-2 | 3 | 995211 | TT | 3.52 | 4.62 | NA |
qCTS3-3 | 3 | 1243161 | AA | 3.99 | 5.12 | NA |
qCTS3-4 | 3 | 2110407 | TT | 3.81 | 4.83 | NA |
qCTS3-5 | 3 | 2680925 | CC | 4.88 | 8.20 | NA |
qCTS3-6 | 3 | 3032938 | TT | 3.44 | 4.43 | NA |
qCTS3-7 | 3 | 3211019 | CC | 3.91 | 5.60 | NA |
qCTS3-8 | 3 | 3668304 | CC | 4.68 | 6.14 | NA |
qCTS3-9 | 3 | 3763778 | GG | 4.43 | 5.74 | Osryh1, LOC_ Os03g019140 |
qCTS3-10 | 3 | 8192574 | AA | 3.26 | 4.04 | NA |
qCTS3-11 | 3 | 22540833 | TT | 3.14 | 3.90 | NA |
qCTS3-12 | 3 | 27608937 | AA | 3.69 | 5.96 | NA |
qCTS3-13 | 3 | 31924530 | AA | 3.19 | 3.97 | NA |
qCTS4-1 | 4 | 5850082 | TT | 3.65 | 4.59 | NA |
qCTS5-1 | 5 | 1970193 | GG | 3.03 | 4.44 | NA |
qCTS5-2 | 5 | 6171822 | CC | 3.58 | 4.51 | NA |
qCTS5-3 | 5 | 8040996 | AA | 3.29 | 4.51 | NA |
qCTS5-4 | 5 | 24616513 | GG | 3.33 | 4.18 | NA |
qCTS5-5 | 5 | 25098060 | TT | 4.56 | 6.25 | NA |
qCTS5-6 | 5 | 25154581 | AA | 4.82 | 6.39 | NA |
qCTS5-7 | 5 | 25720662 | AA | 3.1 | 4.00 | NA |
qCTS5-8 | 5 | 26092015 | TT | 5.05 | 6.77 | NA |
qCTS5-9 | 5 | 29432186 | TT | 3.84 | 4.97 | NA |
qCTS6-1 | 6 | 4733861 | TT | 3.39 | 4.25 | NA |
qCTS6-2 | 6 | 6228690 | AA | 3.18 | 4.02 | NA |
qCTS6-3 | 6 | 10452388 | CC | 3.46 | 5.81 | NA |
qCTS6-4 | 6 | 10964887 | GG | 3.6 | 4.55 | NA |
qCTS6-5 | 6 | 23876111 | TT | 3.52 | 4.42 | OsSPX1, LOC_Os06g40120 |
qCTS7-1 | 7 | 914685 | CC | 3.3 | 4.13 | NA |
qCTS7-2 | 7 | 17875297 | GG | 3.09 | 3.82 | NA |
qCTS7-3 | 7 | 18202939 | CC | 4.67 | 7.06 | NA |
qCTS7-4 | 7 | 23783174 | CC | 3.12 | 3.92 | NA |
qCTS7-5 | 7 | 29220680 | AA | 4.08 | 5.34 | OsFAD8 LOC_Os07g49310 |
qCTS8-1 | 8 | 8883364 | AA | 3.44 | 4.34 | NA |
qCTS8-2 | 8 | 10142772 | CC | 4.21 | 5.48 | NA |
qCTS8-3 | 8 | 10506862 | GG | 3.16 | 3.91 | NA |
qCTS8-4 | 8 | 20385371 | AA | 3.82 | 4.97 | NA |
qCTS9-1 | 9 | 1141448 | CC | 3.49 | 4.40 | OsCYL4a, LOC_Os09g02270 |
qCTS9-2 | 9 | 1706118 | CC | 3.25 | 4.33 | NA |
qCTS9-3 | 9 | 3375476 | CC | 3.29 | 4.97 | NA |
qCTS9-4 | 9 | 3869544 | GG | 3.11 | 4.57 | NA |
qCTS9-5 | 9 | 4289803 | GG | 3.56 | 4.48 | NA |
qCTS9-6 | 9 | 4767843 | TT | 3.04 | 4.20 | NA |
qCTS9-7 | 9 | 6403821 | AA | 3.06 | 4.65 | NA |
qCTS9-8 | 9 | 16181745 | CC | 3.26 | 4.04 | NA |
qCTS9-10 | 9 | 17697057 | GG | 3.15 | 3.89 | NA |
qCTS10-1 | 10 | 5690202 | CC | 3.59 | 4.63 | NA |
qCTS11-1 | 11 | 5902436 | AA | 3.25 | 4.15 | NA |
qCTS11-2 | 11 | 6478793 | GG | 3.6 | 5.02 | NA |
qCTS11-3 | 11 | 7249274 | GG | 3.64 | 4.61 | NA |
qCTS11-4 | 11 | 9163345 | GG | 3.45 | 4.33 | NA |
qCTS11-5 | 11 | 17519565 | AA | 3.27 | 4.68 | NA |
qCTS11-6 | 11 | 19897968 | AA | 3.49 | 4.95 | NA |
qCTS11-7 | 11 | 21779484 | AA | 3.87 | 6.75 | NA |
qCTS11-8 | 11 | 22115297 | GG | 3.21 | 5.11 | NA |
qCTS11-9 | 11 | 24958836 | CC | 3.67 | 4.68 | NA |
qCTS11-10 | 11 | 25432012 | CC | 4.52 | 6.48 | NA |