Table 4. A list of candidate genes harbouring missense mutations with ΔAF > 0.7 in two contrasts ‘RJFs vs. Coms’ and ‘BRs vs. LRs’.
| Frequency of variant allelea | ||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Wild | Layers | Broilers | ||||||||||||||||
| Gene | Chr_Pos | Ref | Alt | RJFt | RJFi | BL | WL | RWp | BRA | BRB | BRpD | ΔRJFsComs | ΔRJFsBRs | ΔRJFsLRs | ΔBRsLRs | AA | SIFT | Functionb |
| GLI3 | 2_50876521 | T | C | 0.06 | 0.00 | 1.00 | 0.00 | 1.00 | 0.98 | 0.95 | 0.84 | 0.76 | 0.64 | 0.89 | 0.25 | K/R | Tolerated_low_confidence (1) | Wing development |
| CORIN | 4_67124162 | T | A | 0.12 | 0.06 | 1.00 | 1.00 | 1.00 | 0.85 | 0.98 | 0.93 | 0.87 | 0.91 | 0.83 | 0.08 | S/T | Tolerated (0.4) | Pigmentation |
| KIF7 | 10_12832456 | G | A | 0.06 | 0.00 | 0.54 | 0.88 | 1.00 | 0.9 | 0.8 | 0.83 | 0.79 | 0.77 | 0.82 | 0.04 | V/M | Tolerated (0.17) | Wing development. |
| SPEF2 | Z_10819221 | G | A | 0.03 | NA | 1.00 | 0.88 | 1.00 | 0.84 | 1.00 | 0.21 | 0.79 | 0.93 | 0.65 | 0.28 | S/N | Tolerated (0.36) | Chicken feathering |
| SKIV2L2 | Z_16761767 | C | G | 0.71 | NA | 0.00 | 0.00 | NA | 0.00 | 0.00 | 0.00 | 0.71 | 0.71 | 0.71 | 0.00 | P/A | Tolerated_low_confidence (0.14) | Melanocyte regeneration |
| LEPR | 8_28464218 | T | C | 0.56 | NA | 0.71 | 1.00 | 0.87 | 0.00 | 0.07 | 0.35 | 0.06 | 0.30 | 0.42 | 0.72 | C/R | Deleterious (0.01) | Leptin receptor |
| IGSF10 | 9_23584350 | A | C | 0.10 | NA | 0.61 | 1.00 | 0.84 | 0.02 | 0.07 | 0.00 | 0.32 | 0.72 | 0.07 | 0.78 | I/L | NA | Delayed puberty |
| PLEKHM1 | 27_1768503 | C | G | 0.14 | NA | 0.94 | 0.84 | 0.58 | 0.05 | 0.00 | 0.00 | 0.26 | 0.65 | 0.12 | 0.77 | G/A | Tolerated (1) | Osteoporosis |
| MEGF10 | Z_56413219 | T | C | 0.20 | NA | 0.00 | 0.00 | 0.00 | 0.81 | 0.90 | 0.78 | 0.21 | 0.20 | 0.63 | 0.83 | I/T | Tolerated (0.82) | Muscle generation |
aFrequencies of variant alleles (Alt) are reported for RJFt = red jungle fowl (Thailand), RJFi = red jungle fowl (India), BL = Brown layer, WL = White layer, RWp, Rhode and White pool, BRA = Broiler line A, BRB = Broiler line B and BRpD = Broiler line pool D. AA = Amino acid substitutions, SIFT<0.05 indicates a likely deleterious missense mutation. Sites with ΔAF>0.7 in two contrasts of ‘RJFs vs. Coms’ and ‘BRs vs. LRs’ are in bold.