| Linkage Group | Locus /Gene Name | Probe, Gene or Gene Product | References | Accession # |
| IX | ANT | mitochondrial ADP/ATP translocator | Sharpe and Day (1993) | X65194 |
| IX | CNA47 | cDNA corresponding to EST 1031051H10 | This study | BI997794 |
| IX | CNA38B | cDNA fragment | This study | |
| IX | PPX1 | protoporphyrinogen oxidase precursor | Randolph-Anderson et al. (1998) | AF068635 |
| IX | HSP70C | 68 kDa heat shock protein | von Gromoff et al. (1989) | |
| IX | UNI2 | UNI2 gene | W-C. Wu and C. Silflow, unpublished results | |
| IX | PF16 | protein in C1 microtubule of flagellar central apparatus | Smith and Lefebvre (1996) | U40057 |
| IX | PSBO | OEE1 protein of photosystem II | Mayfield et al. (1989) | X13826 |
| IX | GP35 | random genomic fragment | This study | AF467704 |
| IX | GP209 | random genomic fragment | This study | |
| IX | CNB6 | cDNA corresponding to EST 1024027D07 | This study | BG849900 |
| IX | CNA36 | cDNA fragment | This study | |
| IX | NIT1 | nitrate reductase | Fernandez et al. (1989) | AH001336 |
| IX | CAH3 | carbonic anhydrase, alpha type | Funke et al. (1997) | U73856 |
| IX | MBO2 | MBO2 gene | Tam and Lefebvre (2002) | AF394181 |
| IX | MBB1 | required for expression of psbB/psbT/psbH | Vaistij et al. (2000) | AJ296291 |
| IX | SC2 | genomic fragment | A. Nguyen and W. Dentler, unpublished results |