TABLE 4.
Significant associations between marker genotypes and bacterial load sustained 28 hr after infection with each of four bacteria
| Serratia marcescens | Providencia burhodogranaria | Enterococcus faecalis | Lactococcus lactis | |
|---|---|---|---|---|
| PGRP-SC1A | ||||
| Marker 3771856 | ||||
| A/G, 800 bp 3′ of stop | 0.002** | 0.370 | 0.266 | 0.452 |
| A (56.6%)a | 10.375 (0.155) | 10.226 (0.823) | 10.836 (0.424) | 11.316 (0.218) |
| G (43.4%)a | 10.799 (0.161) | 10.566 (0.828) | 10.841 (0.430) | 11.284 (0.223) |
| % variance explained | 26.9 (4.6) | 0.8 (0.3) | 0 (0) | 0 (0) |
| PGRP-SC2 | ||||
| Marker 3777783 | ||||
| Val/Ile G/A, codon 24 | 0.607 | 0.661 | 0.267 | 0.044* |
| G (26.4%) | 10.521 (0.179) | 10.334 (0.844) | 10.465 (0.455) | 10.954 (0.251) |
| A (73.6%) | 10.563 (0.129) | 10.389 (0.813) | 10.908 (0.419) | 11.385 (0.220) |
| % variance explained | 0 (0) | 0 (0) | 5.2 (1.2) | 18.9 (4.8) |
| SR-CI | ||||
| Marker 4115944 | ||||
| Silent G/T, codon 475 | 0.367 | 0.046* | 0.331 | 0.420 |
| G (53.3%) | 10.483 (0.136) | 10.077 (0.829) | 10.796 (0.462) | 11.263 (0.227) |
| T (46.7%) | 10.631 (0.133) | 10.614 (0.826) | 10.832 (0.458) | 11.314 (0.224) |
| % variance explained | 0.6 (0.1) | 3.7 (1.3) | 0 (0) | 0 (0) |
| SR-CII | ||||
| Marker 7274975 | ||||
| Silent C/G, codon 252 | 0.015* | 0.488 | 0.075 | 0.002** |
| G (74.5%) | 10.666 (0.145) | 10.348 (0.905) | 10.876 (0.426) | 11.433 (0.257) |
| C (25.5%) | 10.211 (0.177) | 10.462 (0.933) | 10.684 (0.457) | 10.830 (0.280) |
| % variance explained | 28.7 (5.3) | 0 (0) | 0 (0) | 33.8 (9.3) |
| Marker 7274899 | ||||
| 28-bp indel, intron 2 | 0.678 | 0.666 | 0.146 | 0.001** |
| Insertion (86.2%) | 10.565 (0.134) | 10.412 (0.824) | 10.876 (0.450) | 11.399 (0.219) |
| Deletion (13.8%) | 10.428 (0.211) | 10.100 (0.895) | 10.478 (0.514) | 10.460 (0.283) |
| % variance explained | 0 (0) | 28.7 (5.3) | 2.5 (0.6) | 61.3 (22.7) |
| Marker 7276155 | ||||
| 60-bp indel, 313 bp 5′ of start | 0.013* | 0.603 | 0.197 | 0.344 |
| Insertion (93.9%)a | 10.622 (0.135) | 10.338 (0.803) | 10.803 (0.420) | 11.297 (0.272) |
| Deletion (6.1%)a | 9.992 (0.281) | 10.576 (0.962) | 11.024 (0.574) | 11.341 (0.375) |
| % variance explained | 43.8 (9.6) | 0 (0) | 0 (0) | 0 (0) |
| SR-CIII | ||||
| Marker 4113576 | ||||
| Silent A/G, codon 195 | 0.398 | 0.031* | 0.906 | 0.196 |
| A (92.0%) | 10.597 (0.127) | 10.453 (0.815) | 10.844 (0.417) | 11.311 (0.209) |
| G (8.0%) | 10.314 (0.251) | 9.750 (0.935) | 10.785 (0.571) | 11.226 (0.316) |
| % variance explained | 4.8 (0.7) | 5.3 (1.9) | 0 (0) | 0 (0) |
| Marker 4114081 | ||||
| GT/AG, 70–71 bp 3′ of stop | 0.049* | 0.105 | 0.305 | 0.446 |
| GT (18.9%) | 10.613 (0.209) | 9.860 (0.920) | 10.469 (0.485) | 11.454 (0.272) |
| AG (81.1%) | 10.536 (0.141) | 10.445 (0.870) | 10.888 (0.417) | 11.267 (0.218) |
| % variance explained | 0 (0) | 3.9 (1.5) | 3.1 (0.7) | 0 (0) |
| SR-CIV | ||||
| Marker 3515646 | ||||
| Presence/absence of intron 2 | 0.589 | 0.925 | 0.269 | 0.004** |
| Presence (67.3%) | 10.584 (0.165) | 10.420 (0.867) | 10.937 (0.437) | 11.425 (0.226) |
| Absence (32.7%) | 10.527 (0.189) | 10.260 (0.885) | 10.668 (0.453) | 11.046 (0.242) |
| % variance explained | 0 (0) | 0 (0) | 1.6 (0.4) | 16.1 (3.9) |
| Tehao | ||||
| Marker 13423404 | ||||
| Noncoding G/A, 1231 bp 5′ of start | 0.841 | 0.837 | 0.942 | 0.047* |
| G (27.8%) | 10.498 (0.194) | 10.418 (0.791) | 10.876 (0.477) | 11.172 (0.230) |
| A (72.2%) | 10.586 (0.154) | 10.321 (0.754) | 10.865 (0.438) | 11.345 (0.198) |
| % variance explained | 0 (0) | 0 (0) | 0 (0) | 0 (0) |
| Marker 13423843 | ||||
| T/A, 778 bp 5′ of start | 0.194 | 0.597 | 0.048* | 0.014* |
| T (42.6%) | 10.431 (0.158) | 10.194 (0.829) | 11.196 (0.440) | 11.548 (0.208) |
| A (57.4%) | 10.688 (0.145) | 10.471 (0.823) | 10.645 (0.431) | 11.139 (0.201) |
| % variance explained | 8.9 (1.4) | 0 (0) | 10.2 (2.5) | 20.5 (4.8) |
| Marker 13424088 | ||||
| G/A, 533 bp 5′ of start | 0.251 | 0.714 | 0.018* | 0.396 |
| G (65.3%) | 10.493 (0.138) | 10.351 (0.815) | 11.076 (0.436) | 11.316 (0.206) |
| A (34.7%) | 10.730 (0.161) | 10.370 (0.833) | 10.463 (0.453) | 11.311 (0.222) |
| % variance explained | 6.4 (1.0) | 0 (0) | 12.2 (3.1) | 0 (0) |
| Marker 13426961 | ||||
| Cys/Tyr G/A, codon 406 | 0.117 | 0.349 | 0.045* | 0.814 |
| G (75.3%) | 10.607 (0.123) | 10.445 (0.843) | 10.751 (0.423) | 11.312 (0.211) |
| A (24.7%) | 10.312 (0.171) | 10.111 (0.878) | 11.087 (0.459) | 11.268 (0.244) |
| % variance explained | 12.0 (1.9) | 1.4 (0.6) | 1.1 (0.3) | 0 (0) |
| Marker 13427284 | ||||
| Synonymous G/A, codon 512 | 0.576 | 1.000 | 0.441 | 0.022* |
| G (35.7%) | 10.516 (0.149) | 10.401 (0.802) | 10.932 (0.429) | 11.402 (0.209) |
| A (65.3%) | 10.657 (0.165) | 10.405 (0.815) | 10.724 (0.444) | 11.128 (0.222) |
| % variance explained | 0 (0) | 0 (0) | 0 (0) | 0 (0.6) |
| 18-wheeler | ||||
| Marker 15174292 | ||||
| 10-bp indel, 1.5 kb 5′ of start | 0.006** | 0.303 | 0.092 | 0.521 |
| Insertion (91.2%) | 10.607 (0.152) | 10.423 (0.731) | 10.829 (0.430) | 11.303 (0.237) |
| Deletion (8.8%) | 10.065 (0.318) | 10.386 (0.911) | 10.522 (0.548) | 11.032 (0.319) |
| % variance explained | 2.7 (0.6) | 0 (0) | 0 (0) | 2.7 (0.6) |
| Marker 15179526 | ||||
| Silent T/C, codon 1210 | 0.257 | 0.035* | 0.201 | 0.482 |
| C (38.6%) | 10.508 (0.163) | 10.254 (0.807) | 10.834 (0.401) | 11.226 (0.236) |
| T (61.4%) | 10.762 (0.174) | 10.818 (0.821) | 10.916 (0.415) | 11.350 (0.247) |
| % variance explained | 6.5 (1.2) | 3.7 (1.3) | 3.7 (1.3) | 0 (0) |
| Marker 15179232 | ||||
| Silent G/A, codon 1212 | 0.495 | 0.613 | 0.022* | 0.044* |
| G (82.7%) | 10.583 (0.148) | 10.495 (0.807) | 10.991 (0.489) | 11.275 (0.221) |
| A (13.3%) | 10.846 (0.259) | 10.240 (0.896) | 10.066 (0.557) | 11.211 (0.289) |
| % variance explained | 2.8 (0.5) | 0 (0) | 0 (0) | 0 (0) |
| Marker 15179676 | ||||
| 12-bp indel, codons 1361–1364 | 0.222 | 0.842 | 0.001** | 0.357 |
| Insertion (5.1%) | 10.010 (0.450) | 10.549 (1.042) | 9.472 (0.715) | 10.790 (0.497) |
| Deletion (94.9%) | 10.504 (0.154) | 10.252 (0.830) | 10.984 (0.537) | 11.291 (0.337) |
| % variance explained | 12.4 (3.1) | 2.8 (0.5) | 65.8 (22.3) | 11.7 (3.1) |
| DIF | ||||
| Marker 17392491 | ||||
| 10-bp indel, intron 6 | 0.837 | 0.163 | 0.044* | 0.497 |
| Deletion (73.1%) | 10.449 (0.174) | 10.656 (0.835) | 11.265 (0.469) | 11.434 (0.261) |
| Insertion (26.9%) | 10.546 (0.128) | 10.229 (0.799) | 10.646 (0.428) | 11.218 (0.228) |
| % variance explained | 0 (0) | 0 (0) | 0 (0) | 2.6 (0.6) |
| ik2 | ||||
| Marker 20644684 | ||||
| 6-bp indel, 1.3 kb 5′ of start | 0.788 | 0.240 | 0.009** | 0.954 |
| Deletion (4.9%) | 10.774 (0.359) | 9.507 (1.096) | 9.583 (0.590) | 11.339 (0.434) |
| Insertion (95.1%) | 10.527 (0.160) | 10.437 (0.915) | 10.883 (0.419) | 11.291 (0.217) |
| % variance explained | 0 (0) | 6.0 (2.6) | 43.8 (13.8) | 0 (0) |
Markers that are nominally significant at P < 0.05 against at least one bacterium are listed. Markers are identified by their position in Release 3.1 of the D. melanogaster complete genome assembly, as well as by their position in the relevant candidate gene. The ancestral state for each polymorphism is listed first, with the frequency of each allelic state in parentheses. Each marker/bacterium entry contains the nominal P-value of the association, the least-squares mean (SE) load sustained by each genotype, and the percentage of the observed nonerror (total) phenotypic variance explained by the marker. L. lactis loads reported are those obtained after 100-fold dilution of the Drosophila homogenates and therefore are smaller than the true loads sustained (see materials and methods). *P < 0.05, **P < 0.01.
a
The ancestral states could not be reliably determined for the two sites in SR-CII and PGRP-SC1A.