Table 2.
SNPs found in 3000 rice genomes at the EBEs of known TAL effector targets in rice.
| TAL | Xo Strain | Reference | Gene | Effector binding element (EBE) sequence | SNPs EBE | SNPs promoter | SNPs gene |
|---|---|---|---|---|---|---|---|
| PthXo3 | PXO61 | Yang and White (2004) | LOC_Os11g31190 (SWEET14) | TATATAAACCCCCTCCAACCAGGTGCTAAG | 2 | 20 | 28 |
| AvrXa7 | PXO86 | Antony et al. (2010) | LOC_Os11g31190 (SWEET14) | TATATAAACCCCCTCCAACCAGGTGCT | 2 | 20 | 28 |
| Tal3b | BLS256 | Cernadas et al. (2014) | LOC_Os07g36430 | TATAAGAAGCCCTCACTCG | 1 | 22 | 3 |
| Tal9b | BLS256 | LOC_Os01g51040 | TAGAAACTGCTCTTCCT | 1 | 2 | 22 | |
| TalC | BAI3 | Yu et al. (2011) | LOC_Os11g31190 (SWEET14) | CATGCATGTCAGCAGCTGGTCAT | 0 | 20 | 28 |
| Tal5 | MAI1 | Streubel et al. (2013) | LOC_Os11g31190 (SWEET14) | TAAGCTCATCAAGCCTTCA | 0 | 20 | 28 |
| PthXo6 | PXO99A | Sugio et al. (2007) | LOC_Os09g29820 (OsTFX1) | TATAAAAGGCCCTCACCAACCCAT | 0 | 5 | 3 |
| PthXo7 | PXO99A | LOC_Os01g73890 (OsTFIIAγ1) | TATAATCCCCAAATCCCCTCCTC | 0 | 8 | 8 | |
| PthXo1 | PXO99A | Yang et al. (2006) | LOC_Os08g42350 (SWEET11) | TGCATCTCCCCCTACTGTACACCAC | 0 | 8 | 17 |
| Tal9A | PXO99A | Moscou and Bogdanove (2009) | LOC_Os07g06970 (HEN1) | TCCCTTCCCTAAACCCCACTT | 0 | 4 | 20 |
| Tal1c | BLS256 | Moscou and Bogdanove (2009) | LOC_Os07g06970 (HEN1) | TCCCCCTCGCTTCCCTT | 0 | 4 | 20 |
| Tal2c | BLS256 | Cernadas et al. (2014) | LOC_Os03g03034 | TCCGGCCCCTCTCCCCCCGCCACCTGAC | 0 | 5 | 25 |
| Tal2d | BLS256 | LOC_Os04g49194 | TATTCCCTCGCGTGATC | 0 | 18 | 78 | |
| Tal3b | BLS256 | LOC_Os02g34970 | TATAAGTAGCACTCGCTCA | 0 | 4 | 9 | |
| Tal3b | BLS256 | LOC_Os05g27590 | TATAAATAGCCCTCACTCT | 0 | 3 | 0 | |
| Tal4a | BLS256 | LOC_Os03g37840 | TATATATCTCGGTCAGGCCAGGCCCCT | 0 | 12 | 28 | |
| Tal3c | BLS256 | LOC_Os03g07540 | TACACGTTCCCTCCACC | 0 | 3 | 9 | |
| Tal3c | BLS256 | LOC_Os02g47660 | TACACATTAGCTACCAT | 0 | 2 | 11 | |
| Tal6 | BLS256 | LOC_Os09g29100 | TACAAAGAGAACGCATCCCCC | 0 | 11 | 24 | |
| Tal6 | BLS256 | LOC_Os12g42970 | TAAAAGCGAAACCCTCCCTCC | 0 | 16 | 8 | |
| Tal5a | BLS256 | LOC_Os02g15290 | TAAATCCCCCCTGCACAGGAAAGCT | 0 | 31 | 2 | |
| Tal2g | BLS256 | LOC_Os01g52130 | TGGCCCGTAGCCTCTCCT | 0 | 0 | 89 | |
| Tal2g | BLS256 | LOC_Os06g46500 | TGGCAAGTGACCTCAGCT | 0 | 9 | 14 | |
| Tal4c | BLS256 | LOC_Os06g37080 | TATAAAACCTGGACAAGCCTCTCT | 0 | 7 | 46 | |
| Tal4b | BLS256 | LOC_Os09g32100 | TGTATAGTATCCCCT | 0 | 14 | 14 |
SNPs found elsewhere in the promoter regions (1 kb upstream TSS) and the genes (including intrond) are also indicated. Position of the SNPs in the EBE sequences is indicated by bold and underlined nucleotides. SNP data were obtained from the Rice SNPseek database (Alexandrov et al., 2015).