Table 3.
Candidate SNPs within DEGs associated with Fast- (F) and Slow- (S) growing phenotypes of P. Margaritifera juveniles from RDA. A cut-off of ± 2.75 SD (P < 0.006) from the mean loading of the first axis (RDA1) was used to identify candidate SNPs from a two-tailed normal distribution where the mean was centered on 0
| Scaffold | Position | Effect | Impact | RDA_loading | Log2FC | Padj | Gene_ID | Description | Up-Regulation |
|---|---|---|---|---|---|---|---|---|---|
| scaffold2377size95048 | 35,421 | synonymous | Low | 0.25 | 1.959 | 1.12E-47 | DYH5_HUMAN | Dynein axonemal heavy chain 5 | F |
| scaffold3047size151625 | 123,277 | synonymous | Low | 0.28 | 2.392 | 6.77E-33 | DYH1_HUMAN | Dynein axonemal heavy chain 1 | F |
| scaffold3047size151625 | 128,652 | synonymous | Low | 0.25 | 2.936 | 2.22E-51 | DYH1_HUMAN | Dynein axonemal heavy chain 1 | F |
| scaffold3333size191570 | 81,288 | synonymous | Low | 0.26 | 3.106 | 3.82E-35 | XM_022477301.1 | dynein cytoplasmic 1 heavy chain 1 | F |
| scaffold3500size108302 | 87,376 | synonymous | Low | 0.28 | -1.947 | 8.12E-04 | NA | S | |
| scaffold4300size113025 | 20,247 | stop_gained | High | -0.29 | 2.502 | 1.85E-19 | SREC_MOUSE | Class F scavenger receptor SR-F1 | F |
| scaffold4300size113025 | 20,254 | missense | Moderate | 0.29 | 2.502 | 1.85E-19 | SREC_MOUSE | Class F scavenger receptor SR-F1 | F |
| scaffold4300size113025 | 20,475 | missense | Moderate | 0.29 | 2.502 | 1.85E-19 | SREC_MOUSE | Class F scavenger receptor SR-F1 | F |
| scaffold4300size113025 | 20,748 | missense | Moderate | 0.29 | 2.502 | 1.85E-19 | SREC_MOUSE | Class F scavenger receptor SR-F1 | F |
| scaffold4300size113025 | 20,520 | missense | Moderate | 0.29 | 0.502 | 1.85E-19 | SREC_MOUSE | Class F scavenger receptor SR-F1 | F |
| scaffold6914size72805 | 36,739 | missense | Moderate | 0.25 | 3.984 | 9.35E-22 | CAS4_EPHMU | Short-chain collagen C4 | F |
| scaffold6914size72805 | 36,752 | synonymous | Low | 0.32 | 3.984 | 9.35E-22 | CAS4_EPHMU | Short-chain collagen C4 | F |
| scaffold6914size72805 | 36,793 | missense | Moderate | -0.32 | 3.984 | 9.35E-22 | CAS4_EPHMU | Short-chain collagen C4 | F |
| scaffold6914size72805 | 38,277 | missense | Moderate | 0.25 | 3.984 | 9.35E-22 | CAS4_EPHMU | Short-chain collagen C4 | F |
| scaffold7129size47494 | 32,807 | synonymous | Low | 0.28 | -2.041 | 1.99E-08 | NA | S | |
| scaffold8696size123454 | 24,578 | splice_region/synonymous | Low | 0.25 | 3.409 | 0.00E + 00 | DYHC_TRIGR | Dynein beta chain | F |