TABLE 6.
Genotype-to-transcript-level associations*
| Phenotype | Marker | Frequency of “fit” allele | Marker typea | Adjusted r2b | Other associationsc |
|---|---|---|---|---|---|
| Acp26Aa | Acp33s1559** | 0.91 | GAT(pref.):GAC(un.) | 0.05 | None |
| CG8137 | CG8137s2957** | 0.50 | GGA(un.):GGT(un.) | 0.08 | 29, 33 (−): 36 (+) |
| Acp29AB | CG17331s2065**** | 0.70 | AAC(pref.):AAT(un.) | 0.15 | P1 (+) |
| CG31872 | None | NA | NA | NA | NA |
| Acp32CD | None | NA | NA | NA | NA |
| Acp33A | Acp29s2633*** | 0.95 | Downstream | 0.10 | 32, 8137 (+) |
| CG17331 | CG17331s486*** | 0.33 | Upstream | 0.08 | 53 (+) |
| Acp36DE | CG8137s2957** | 0.50 | GGA(un.):GGT(un.) | 0.07 | 29, 33 (−): FecO, 8137 (+) |
| Acp36s2084** | 0.52 | CUA(un.):GUC(un.) | 0.09 | None | |
| Acp36Indel2623**** | 0.47 | LLREAQQK pos. 253 | 0.12 | None | |
| PEBs1155*** | 0.44 | Upstream | 0.11 | None | |
| Acp53Ea | Acp26s2193*** | 0.29 | AGC(pref.):AGT(un.) | 0.11 | 26, 33, 36, 31872 (+) |
| Acp26s2201** | 0.28 | ATA(I):AGC(S) | 0.07 | P2 (−) | |
| PEBII | Acp53s1760** | 0.91 | ACC(pref.):ACT(un.) | 0.10 | None |
| Acp53s1766** | 0.70 | CGT(un.):CGC(pref.) | 0.08 | 26, 29, 33, 31872 (+) |
Comparisonwise P < 0.05,
P < 0.01,
P ≤ 0.001,
Experimentwise P < 0.05. NA, not applicable.
High-fitness codon shown on the left with its amino acid for nonsynonymous changes or usage; preferred (pref.) and unpreferred (un.) for synonymous changes indicated in parentheses.
Calculated using a simple linear regression considering only the individually significant marker (see text).
“Other associations” indicates other phenotypes that were associated with that marker. Significant associations are underlined. Antagonistic associations indicated by (−) and protagonistic associations indicated by (+). Markers associated with both phenotype and expression were considered protagonistic if the same allele produced higher fitness and higher transcript abundance. Genes are listed excluding the “CG” or “Acp” prefix.