Table 3.
Positional candidate genes categorized by function for windows explaining the largest percentage of genetic variation
| Function | Trait | Gene name | Description |
|---|---|---|---|
| Disruption of DNA synthesis, transcription, RNA processing, and translation | BW21 | HHEX | Gallus gallus hematopoietically expressed homeobox (HHEX), mRNA. [Source:RefSeq mRNA;Acc:NM_205252] |
| BT20 | MED9 | Gallus gallus mediator complex subunit 9 (MED9), mRNA. [Source:RefSeq mRNA;Acc:NM_001277637] | |
| BT22 | MED15 | Mediator complex subunit 15 [Source:HGNC Symbol;Acc:HGNC:14248] | |
| BT28-20 | RNF113A | Gallus gallus ring finger protein 113A (RNF113A), mRNA. [Source:RefSeq mRNA;Acc:NM_001004396] | |
| BT28-20 | DDX42 | Gallus gallus DEAD (Asp-Glu-Ala-Asp) box polypeptide 42 (DDX42), mRNA. [Source:RefSeq mRNA;Acc:NM_001030926] | |
| Digestibility | MED31 | Mediator complex subunit 31 [Source:HGNC Symbol;Acc:HGNC:24260] | |
| Breast yield | MRPL42 | Mitochondrial ribosomal protein L42 [Source:HGNC Symbol;Acc:HGNC:14493] | |
| Disruption of progression through the cell cycle | BT22 & BT28 | TBX6 | Gallus gallus T-box 6 (TBX6), mRNA. [Source:RefSeq mRNA;Acc:NM_001030367] |
| BT22 | KLHL22 | Kelch-like family member 22 [Source:HGNC Symbol;Acc:HGNC:25888] | |
| BT28-20 | LIMD2 | Gallus gallus LIM domain containing 2 (LIMD2), mRNA. [Source:RefSeq mRNA;Acc:NM_001006330] | |
| BT28-20 | STRADA | Gallus gallus STE20-related kinase adaptor alpha (STRADA), mRNA. [Source:RefSeq mRNA;Acc:NM_001012844] | |
| Digestibility | KIAA0753 | KIAA0753 [Source:HGNC Symbol;Acc:HGNC:29110] | |
| Increase protein degradation by ubiquitination | BW21 | MARCH5 | Gallus gallus membrane-associated ring finger (C3HC4) 5 (MARCH5), mRNA. [Source:RefSeq mRNA;Acc:NM_001012906] |
| BW28 | PCGF5 | Gallus gallus polycomb group ring finger 5 (PCGF5), mRNA. [Source:RefSeq mRNA;Acc:NM_001277361] | |
| BW28 | HECTD2 | HECT domain containing E3 ubiquitin protein ligase 2 [Source:HGNC Symbol;Acc:HGNC:26736] | |
| BT20 | USP22 | Ubiquitin carboxyl-terminal hydrolase [Source:UniProtKB/TrEMBL;Acc:F1NG36] | |
| Membrane permeability and ions | BW28-21 | GRID2 | Glutamate receptor, ionotropic, delta 2 [Source:HGNC Symbol;Acc:HGNC:4576] |
| BT20 | PEMT | Gallus gallus phosphatidylethanolamine N-methyltransferase (PEMT), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001006164] | |
| BT28-20 | CYB561 | Cytochrome b561 [Source:HGNC Symbol;Acc:HGNC:2571] | |
| BT28-20 | KCNH6 | Potassium voltage-gated channel, subfamily H (eag-related), member 6 [Source:HGNC Symbol;Acc:HGNC:18862] | |
| BT28-20 | CCDC47 | Coiled-coil domain containing 47 [Source:HGNC Symbol;Acc:HGNC:24856] | |
| BT28-20 | MYL4 | Myosin, light chain 4, alkali; atrial, embryonic [Source:HGNC Symbol;Acc:HGNC:7585] | |
| Digestibility | SLC13A5 | Solute carrier family 13 (sodium-dependent citrate transporter), member 5 [Source:HGNC Symbol;Acc:HGNC:23089] | |
| Digestibility | PITPNM3 | PITPNM family member 3 [Source:HGNC Symbol;Acc:HGNC:21043] | |
| Immune system activation | BT20 | TNFRSF13B | Gallus gallus tumor necrosis factor receptor superfamily, member 13B (TNFRSF13B), mRNA. [Source:RefSeq mRNA;Acc:NM_001097537] |
| BT22 | DDT | Gallus gallus D-dopachrome tautomerase (DDT), mRNA. [Source:RefSeq mRNA;Acc:NM_001030667] | |
| BT22 | CABIN1 | Calcineurin binding protein 1 [Source:HGNC Symbol;Acc:HGNC:24187] | |
| BT28 | MIF | Macrophage migration inhibitory factor [Source:UniProtKB/Swiss-Prot;Acc:Q02960] | |
| Breast yield | SOCS2 | Suppressor of cytokine signaling 2 [Source:RefSeq peptide;Acc:NP_989871] | |
| Cell signaling | BW21 | EXOC6 | Exocyst complex component 6 [Source:RefSeq peptide;Acc:NP_001012923] |
| BW28 | PPP1R3C | Protein phosphatase 1, regulatory subunit 3C [Source:HGNC Symbol;Acc:HGNC:9293] | |
| BT20 | COPS3 | Gallus gallus COP9 constitutive photomorphogenic homolog subunit 3 (Arabidopsis) (COPS3), mRNA. [Source:RefSeq mRNA;Acc:NM_001006163] | |
| BT20 | NT5 M | 5′,3′-nucleotidase, mitochondrial [Source:HGNC Symbol;Acc:HGNC:15769] | |
| BT20 | RASD1 | Gallus gallus RAS, dexamethasone-induced 1 (RASD1), mRNA. [Source:RefSeq mRNA;Acc:NM_001044636] | |
| BT22 | CRKL | v-crk avian sarcoma virus CT10 oncogene homolog-like [Source:HGNC Symbol;Acc:HGNC:2363] | |
| BT28-20 | MAP3K3 | Mitogen-activated protein kinase kinase kinase 3 [Source:HGNC Symbol;Acc:HGNC:6855] | |
| BT28-20 | DCAF7 | Gallus gallus DDB1 and CUL4 associated factor 7 (DCAF7), mRNA. [Source:RefSeq mRNA;Acc:NM_001079504] | |
| Apoptosis | Digestibility | XAF1 | XIAP associated factor 1 [Source:HGNC Symbol;Acc:HGNC:30932] |
| Breast yield | CRADD | Gallus gallus CASP2 and RIPK1 domain containing adaptor with death domain (CRADD), mRNA. [Source:RefSeq mRNA;Acc:NM_001030748] | |
| Glucose | BW21 | IDE | Insulin-degrading enzyme [Source:HGNC Symbol;Acc:HGNC:5381] |
| BW28 | TNKS2 | Gallus gallus tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2 (TNKS2), mRNA. [Source:RefSeq mRNA;Acc:NM_204341] | |
| Disruption of cytoskeleton | BW21 | KIF11 | Gallus gallus kinesin family member 11 (KIF11), mRNA. [Source:RefSeq mRNA;Acc:NM_001031230] |
| Free radical damage | BT22 | GSTT1 | Gallus gallus glutathione S-transferase theta 1 (GSTT1), mRNA. [Source:RefSeq mRNA;Acc:NM_205365] |
| Digestibility | TXNDC17 | Thioredoxin domain containing 17 [Source:HGNC Symbol;Acc:HGNC:28218] | |
| Blood vessel development | BT28-20 | ACE | Gallus gallus angiotensin I converting enzyme (peptidyl-dipeptidase A) 1 (ACE), mRNA. [Source:RefSeq mRNA;Acc:NM_001167732] |
All characterized genes within a 200-kb region, i.e. 100 kb upstream and 100 kb downstream of the SNP which was most frequently included in the MCMC iterations (post-burn-in), and is in the window explaining the largest amount of genetic variation for each trait
Body temperature (BT) measured on days 20, 22, 28, and the differential 28-20; body weight (BW) measured on days 21, 28, and the differential 28-21; digestibility, measured from ileal content, on day 28; percent of breast weight, calculated from percent of total body weight, and measured on day 28