Table 1.
Results from PERMANOVA of gene expression of one‐week‐old F1‐juveniles
| One‐week‐old | Total | Residuals | F0‐bacteria | F1‐bacteria | F0‐sex | F0‐bacteria × F1‐bacteria | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| DF | Df | Df | F.Model | Pr(>F) | sig | Df | F.Model | Pr(>F) | sig | Df | F.Model | Pr(>F) | sig | Df | F.Model | Pr(>F) | sig | |
| Immune genes [29] | 299 | 284 | 2 | 10.21 | 0.001 | *** | 2 | 6.63 | 0.001 | *** | 1 | 5.76 | 0.001 | *** | 4 | 0.82 | ns | |
| Innate immune genes [13] | 299 | 284 | 2 | 11.88 | 0.001 | *** | 2 | 6.28 | 0.001 | *** | 1 | 2.72 | 0.001 | *** | 4 | 0.78 | ns | |
| Innate & adaptive genes [5] | 299 | 284 | 2 | 12.37 | 0.001 | *** | 2 | 7.18 | 0.001 | *** | 1 | 16.97 | 0.001 | *** | 4 | 1.12 | ns | |
| Adaptive immune genes [8] | 299 | 284 | 2 | 7.42 | 0.027 | * | 2 | 1.16 | 0.059 | • | 1 | 3.54 | 0.027 | * | 4 | 0.65 | ns | |
| Complement component genes [3] | 299 | 284 | 2 | 10.68 | 0.001 | *** | 2 | 19.40 | 0.001 | *** | 1 | 2.56 | 0.001 | *** | 4 | 1.28 | ns | |
| Epigenetic genes [15] | 299 | 284 | 2 | 1.77 | 0.001 | *** | 2 | 2.04 | 0.001 | ** | 1 | 5.68 | 0.001 | *** | 4 | 0.89 | ns | |
| DNA‐methylation genes [5] | 299 | 284 | 2 | 1.50 | 0.003 | ** | 2 | 1.28 | 0.037 | * | 1 | 11.03 | 0.003 | ** | 4 | 0.67 | ns | |
| Histone de/methylation genes [4] | 299 | 284 | 2 | 1.34 | 0.001 | *** | 2 | 2.67 | 0.003 | ** | 1 | 2.63 | 0.001 | *** | 4 | 0.79 | ns | |
| Histone de/acetylation genes [5] | 299 | 284 | 2 | 2.86 | 0.001 | *** | 2 | 2.95 | 0.001 | *** | 1 | 2.40 | 0.001 | *** | 4 | 1.33 | 0.006 | ** |
| Total | Residuals | F0‐bacteria × F0‐sex | F0‐sex × F1‐bacteria | F0‐bacteria × F1‐bacteria × F0‐sex | Size covariate | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| DF | df | Df | F.Model | Pr(>F) | sig | Df | F.Model | Pr(>F) | sig | Df | F.Model | Pr(>F) | sig | Df | F.Model | Pr(>F) | sig | |
| Immune genes [29] | 299 | 284 | 1 | 6.68 | 0.001 | *** | 2 | 1.51 | 0.002 | ** | 2 | 0.95 | ns | 1 | 4.27 | ns | ||
| Innate immune genes [13] | 299 | 284 | 1 | 8.79 | 0.001 | *** | 2 | 1.65 | 0.003 | ** | 2 | 0.66 | ns | 1 | 5.99 | ns | ||
| Innate & adaptive genes [5] | 299 | 284 | 1 | 7.16 | 0.012 | * | 2 | 1.15 | ns | 2 | 0.84 | ns | 1 | 3.35 | 0.043 | * | ||
| Adaptive immune genes [8] | 299 | 284 | 1 | 5.23 | 0.005 | ** | 2 | 0.97 | ns | 2 | 1.17 | 0.047 | * | 1 | 1.31 | ns | ||
| Complement component genes [3] | 299 | 284 | 1 | 0.94 | 0.001 | *** | 2 | 2.05 | 0.039 | * | 2 | 1.00 | ns | 1 | 6.58 | ns | ||
| Epigenetic genes [15] | 299 | 284 | 1 | 5.84 | 0.001 | *** | 2 | 1.94 | 0.003 | ** | 2 | 0.60 | ns | 1 | 6.06 | ns | ||
| DNA‐methylation genes [5] | 299 | 284 | 1 | 1.56 | 0.008 | ** | 2 | 2.20 | 0.008 | ** | 2 | 0.68 | ns | 1 | 8.24 | 0.035 | * | |
| Histone de/methylation genes [4] | 299 | 284 | 1 | 5.23 | 0.005 | ** | 2 | 3.09 | 0.005 | ** | 2 | 0.99 | ns | 1 | 7.93 | 0.049 | * | |
| Histone de/acetylation genes [5] | 299 | 284 | 1 | 13.95 | 0.003 | ** | 2 | 0.47 | ns | 2 | 0.34 | ns | 1 | 1.14 | ns | |||
Multivariate PERMANOVA to assess the effect and interaction of the three fixed factors F0‐parents, F0‐sex, and F1‐offspring, size as covariate and family as strata term on relative gene expression values (−∆Ct values). Each analysis was based on a Bray–Curtis distance matrix with P‐values obtained by 999 permutations. Significant P‐values are marked in bold letters (significance code: <0.001***, 0.001**, 0.01*, 0.1> P‐value ≥0.05 trend •), whereas “ns” indicates no statistical difference.