Table 4. R genes and FS-related genes detected from chromosomes with PMR and FSI major QTLs, and SNPs in these gene between ‘Arka Manik’ and ‘TS34’.
The genes and SNPs for which PCR markers were developed are underlined.
| Trait | Gene | Gene ID | Location | Gene function annotation | SNP(AM/TS) | ||
|---|---|---|---|---|---|---|---|
| Chr. | Reference genome(bp) | Nucleotide | Position (bp) | ||||
| PMR | R-gene | Cla019831 | 2 | 26750001–26753327 | Disease resistance protein (IPR002182 NB-ARC) | A/G | 26751854 |
| A/C | 26752052 | ||||||
| Cla019844 | 2 | 26582380–26589679 | Cc-nbs-lrr resistance protein (IPR002182 NB-ARC) | C/T | 26583608 | ||
| C/T | 26583793 | ||||||
| T/G | 26584613 | ||||||
| T/A | 26586794 | ||||||
| Cla019850 | 2 | 26501165–26506002 | Resistance protein RGC2 (Fragment) (IPR001611 Leucine-rich repeat) | - | - | ||
| Cla019854 | 2 | 26456943–26459976 | TIR-NBS disease resistance-like protein (IPR000157 Toll-Interleukin receptor) | - | - | ||
| Cla019855 | 2 | 26449200–26453033 | TIR-NBS disease resistance protein (IPR000157 Toll-Interleukin receptor) | T/C | 26449686 | ||
| Cla019856 | 2 | 26439873–26444126 | TIR-NBS disease resistance-like protein (IPR000157 Toll-Interleukin receptor) | - | - | ||
| Cla019857 | 2 | 26432098–26437657 | TIR-NBS disease resistance-like protein (IPR000157 Toll-Interleukin receptor) | - | - | ||
| Cla019863 | 2 | 26383499–26388744 | TIR-NBS disease resistance-like protein (IPR000157 Toll-Interleukin receptor) | - | - | ||
| FSI | WOX | Cla008252 | 3 | 1542265–1543627 | WOX2 (WUSCHEL RELATED HOMEBOX 2); transcription factor | - | - |
| SUN | Cla011257 | 3 | 26846490–26847637 | IQD26 (IQ-domain 26); calmodulin binding | C/T | 26846636 | |
| G/A | 26846820 | ||||||
| C/T | 26847041 | ||||||
| Cla001773 | 3 | 21241760–21249007 | IQD26 (IQ-domain 26); calmodulin binding | C/A | 21243320 | ||
| C/T | 21243489 | ||||||
| C/T | 21245913 | ||||||