TABLE 2.
Details of the PCR amplicons used for genotyping
| Amplicon positiona |
|||||
|---|---|---|---|---|---|
| Amplicon name | cM | Cytology | bp | Accessions (ref)b | SNPsc |
| Coarse mapping | |||||
| or.05d | 1–0.4 | 1F1 | X:1121968 … 1123024 | AJ781891–AJ781902 (3) | 4 |
| or.17d | 1–4.2 | 3F3 | X:3686040 … 3687112 | AJ782000–AJ782012 (3) | 5f |
| sq.01 | 1–15.3 | 5E1 | X:6069264 … 6070310 | DQ450201–DQ450214 (1) | 5 |
| dx.01 | 1–16.5 | 6B1 | X:6378577 … 6379621 | AY863446–AY863461 (2) | 5 |
| ct.01d | 1–20.8 | 7B4 | X:7457973 … 7459036 | AY863490–AY863504 (2) | 3f |
| or.38d | 1–24.1 | 7F9 | X:8465992 … 8467050e | AJ782244–AJ782255 (3) | 6 |
| or.45d | 1–28.9 | 8F10 | X:9552097 … 9553189 | AJ782285–AJ782297 (3) | 5 |
| ds.02 | 1–34.4 | 10B4 | X:11200585 … 11201662 | AY863535–AY863550 (2) | 3 |
| or.65 | 1–43.5 | 11F1 | X:13186028 … 13187124 | AJ782504–AJ782516 (3) | 5 |
| or.84 | 1–55.6 | 15D1 | X:16835989 … 16837079 | AJ782696–AJ782704 (3) | 4 |
| bx.02 | 1–59.2 | 17C3 | X:18369702 … 18370755 | AY863512–AY863527 (2) | 5 |
| ru.01 | 1–64.1 | 19E2 | X:20502610 … 20503644 | DQ450325–DQ450339 (1) | 5 |
| Fine-mapping X-tip | |||||
| or.05d | 1–0.4 | 1F1 | X:1121968 … 1123024 | AJ781891–AJ781902 (3) | 4 |
| pr.01 | 1–1.4 | 3B2 | X:2548289 … 2549339 | AY047980–AY048009 (4) | 5 |
| hr.92 | 1–1.6 | 3C3 | X:2791175 … 2792052 | AY495930–AY495947 (4) | 5 |
| no.01 | 1–2.0 | 3C9 | X:3031507 … 3032543 | AY795911–AY795925 (5) | 5 |
| ss.00 | 1–3.0 | 3D6 | X:3407851 … 3408901 | DQ450247–DQ450262 (1) | 4 |
| or.17d | 1–4.2 | 3F3 | X:3686040 … 3687112 | AJ782000–AJ782012 (3) | 4f |
| Fine-mapping X-middle | |||||
| ct.01d | 1–20.8 | 7B4 | X:7457973 … 7459036 | AY863490–AY863504 (2) | 4f |
| aa.00 | 1–22.0 | 7D2 | X:7873740 … 7874837 | DQ450231–DQ450246 (1) | 3 |
| hh.00 | 1–22.5 | 7D18 | X:8045887 … 8046959 | DQ450340–DQ450355 (1) | 4 |
| or.38d | 1–24.1 | 7F9 | X:8465932 … 8467025e | AJ782244–AJ782255 (3) | 6 |
| cc.00 | 1–24.7 | 8B1 | X:8642024 … 8643083 | DQ450263–DQ450278 (1) | 4 |
| dd.00 | 1–25.1 | 8B3 | X:8693463 … 8694533 | DQ450279–DQ450294 (1) | 5 |
| qq.00 | 1–25.4 | 8C1 | X:8782776 … 8783838 | DQ450295–DQ450310 (1) | 5 |
| lz.01 | 1–27.0 | 8D5 | X:9135950 … 9136999 | DQ450311–DQ450324 (1) | 5 |
| ff.00 | 1–27.9 | 8E3 | X:9334410 … 9335472 | DQ450215–DQ450230 (1) | 4 |
| om.17 | 1–28.4 | 8F2 | X:9461187 … 9462280 | AM001875–AM001886 (6) | 4 |
| or.45d | 1–28.9 | 8F10 | X:9552097 … 9553189 | AJ782285–AJ782297 (3) | 5 |
For each amplicon, the physical position (in base pairs) within the Drosophila melanogaster genome (release 4.2.1) is presented, along with the cytological position and the genetic position in centimorgans (on the standard D. melanogaster map).
GenBank accessions are given for the sequences used to identify polymorphisms. The sequences were first described in (1) this study, (2) Macdonald and Long (2005), (3) Orengo and Aguadé (2004), (4) Harr et al. (2002), (5) DuMont and Aquadro (2005), and (6) Ometto et al. (2005).
The number of SNPs successfully genotyped within each PCR amplicon.
PCR amplicons used for both coarse- and fine-mapping work.
PCR primers used to amplify the or.38 amplicon were altered slightly between the coarse- and fine-mapping experiments.
One of the SNPs we successfully genotyped in amplicon or.17 for the coarse-mapping work failed to yield high-quality genotypes during fine mapping, and one SNP successfully genotyped in ct.01 for fine mapping failed in the coarse mapping.