Table 3. Contributions of seven SNPs in genes potentially related to eggshell ultrastructure.
| SNP |
rs15301807 | rs313822026 | rs314985144 | rs316011750 | rs314546938 | rs313308902 | |
|---|---|---|---|---|---|---|---|
| Gene | KCNJ8 | WNK1 | ABCC9 | ITPR2 | ITM2C | KNDC1 | |
| Consequence | Intron variant | Intron variant | Intron variant | Intron variant | Downstream gene variant | Downstream gene variant | |
| Chromosome | 1 | 1 | 1 | 1 | 9 | 6 | |
| Position (bp) | 67106463 | 60604387 | 67055169 | 67859289 | 4863515 | 21070589 | |
| EA/AA | A/C | G/C | G/A | C/T | T/C | C/A | |
| MAF | 0.472 | 0.478 | 0.473 | 0.453 | 0.344 | 0.116 | |
| EST | beta (SE)a | −0.347 (0.058) | −0.348 (0.059) | −0.361 (0.058) | −0.277 (0.059) | – | – |
| CPV (%) | 5.52 | 5.50 | 6.09 | 3.23 | – | – | |
| ET | beta (SE) | −0.329 (0.056) | −0.365 (0.056) | −0.366 (0.055) | −0.290 (0.057) | – | – |
| CPV (%) | 4.88 | 6.16 | 6.28 | 3.63 | – | – | |
| MT | beta (SE) | – | – | – | – | −0.276 (0.053) | – |
| CPV (%) | – | – | – | – | 3.34 | – | |
| MD | beta (SE) | – | – | – | – | – | −0.440 (0.081) |
| CPV (%) | – | – | – | – | – | 3.91 | |
Abbreviations: EA = effect allele (minor allele); AA = alternative allele (major allele); MAF = minor allele frequency; CPV = contribution to phenotypic variance (%); EST = eggshell thickness; ET = effective layer thickness; MT = mammillary layer thickness; MD = mammillary density.
abeta is the estimated allelic substitution effect per copy of the effect allele (EA) based on an inverse-normal transformed scale under an additive model, expressed in SD unit/allele; SE = standard error of the beta.