| 7 | 11,713,561 | QSTS176 | Indel | GTGGCAGCTTGAGAGCATTC | TTTAATCCAAGCTTAGGCAACC | This study |
| 7 | 13,552,392 | QSTS180 | Indel | GGAGCTCGTACAGAAAAATCG | CCGGAGGTATATTCCTTGTTTG | This study |
| 7 | 17,831,145 | QSTS182 | Indel | GGCAATGGAACTTTTTGATTTG | ATGCACTTTCTGTCTCAGTTTG | This study |
| 7 | 21,243,983 | QSTS191 | Indel | CAGTTTGGCACTGGCCTATC | GCATTTCACTCAAGCAATGG | This study |
| 7 | 28,894,378 | RM1306 | SSR | TGCCAATTACCTTCCCGTAC | TGCTCCGTATTGCTGCTATG | McCouch et al. (2002) |
| 8 | 20,645,571 | RM223 | SSR | GAGTGAGCTTGGGCTGAAAC | GAAGGCAAGTCTTGGCACTG | Chen et al. (1997) |
| 8 | 26,294,879 | QSTS215 | Indel | TCCCTTAACTTGTCAACAAATCC | GCCACGTCAGCTAAAACCTC | This study |
| 8 | 27,898,042 | RM3155 | SSR | GAAAAGGACAGGGGAAAAGC | GATCGTTCGTGTTCGTGTTG | McCouch et al. (2002) |
| 9 | 5,048,789 | QSTS222 | Indel | CAACCAGCGAAACATACTGC | ACGGGAGGAAGATGACCAC | This study |
| 9 | 11,045,262 | QSTS227 | Indel | TTTTTGCTTCTCACCCATTC | TTGCATGAACAGAGGTTTGC | This study |
| 9 | 12,583,087 | QSTS228 | Indel | ATATCATTCCGGTGCCTACC | GTGCGCATGTGTGTGTACTG | This study |
| 9 | 14,644,334 | QSTS229 | Indel | AGTGGATGGATGGATGGATG | CGTCGTCTCTTCCGTTTTTC | This study |
| 9 | 20,246,472 | RM3808 | SSR | CGTTAGCGAAACGAACAGTG | CAGTGGCTCGGTAATCGC | McCouch et al. (2002) |
| 9 | 17,054,142 | RM3600 | SSR | TGCCCACACATGATGAGC | AACGGGCAAGAGATCTTCTG | McCouch et al. (2002) |
| 10 | 2,522,494 | QSTS237 | Indel | GACCAGAGACTGCCCCATC | TCACTTCAAGTCTGTGGTTTCAG | This study |
| 10 | 22,133,218 | QSTS248 | Indel | TGCAATTGACTACTACTCCAAGG | TCAAACAAACAATCGTGAAGC | This study |
| 10 | 17,490,576 | RM6704 | SSR | AATCGAATCTGGATATCTTG | CTTCTACCTAGCTACCGAGA | McCouch et al. (2002) |
| 10 | 15,903,727 | RM5304 | SSR | CATCTTGAATCCTCCTTCGACTCC | GGCAGCGATAGCAGGAAGAGG | McCouch et al. (2002) |
| 11 | 794,611 | QSTS250 | Indel | CGTTGGATAATTAATGGAGATCG | CACAAGCACCAAACCCAAC | This study |
| 11 | 4,484,051 | QSTS255 | Indel | CATTGCTACGAGGCACAATC | CCGCGCACGTAGGTATATG | This study |
| 11 | 7,007,889 | QSTS263 | Indel | ATAAAATCCGGCGAGACAAG | GAAGCGAGTGCTCCTAGCTC | This study |
| 11 | 21,626,773 | RM206 | SSR | CCCATGCGTTTAACTATTCT | CGTTCCATCGATCCGTATGG | Chen et al. (1997) |
| 11 | 28,173,902 | RM144 | SSR | CATGTTGTGCTTGTCCTACTGC | AGCTAGAGGAGATCAGATGGTAGTGC | Temnykh et al. (2000) |
| 12 | 905,092 | RM1080 | SSR | AGAGCCCTCGTAAGCCAAAG | GGTCGTGAATCTCCTCCAAG | McCouch et al. (2002) |
| 12 | 4,919,671 | RM3455 | SSR | TGAATCCACACTCGCAGATC | GCCAGTCCACGATTGGTC | McCouch et al. (2002) |
| 12 | 25,036,187 | RM3739 | SSR | AGTTGCGCAGCTAATCGATC | AAGATCCAACGGGTTCTGTG | McCouch et al. (2002) |
| 12 | 8,828,165 | RM101 | SSR | GTGAATGGTCAAGTGACTTAGGTGGC | ACACAACATGTTCCCTCCCATGC | Temnykh et al. (2000) |
| 12 | 19,156,079 | RM1246 | SSR | AGCTCGATCCCCTAGCTCTC | TTGGAGAAGGTCACCTGCC | McCouch et al. (2002) |
| 12 | 25,067,717 | RM5715 | SSR | GCAGAAGAGAGAAATGAAAG | CTTGTCTACGTAGCATGACA | McCouch et al. (2002) |