Table 2.
Differentially-methylated windows between the selection lines
| Chr | Window start (bp) | CpGs | logFC | Adjusted p value | Gene symbol | Gene description |
|---|---|---|---|---|---|---|
| 1 | 121,257,001 | 4 | − 1.33 | 9.52e − 02 | AP1S2 | Adaptor related protein complex 1 sigma 2 subunit [Source:HGNC Symbol;Acc:HGNC:560] |
| 1 | 142,947,001 | 4 | − 0.93 | 5.87e − 02 | NALCN | Sodium leak channel, non-selective [Source:CGNC Symbol;Acc:12660] |
| 1 | 174,158,001 | 7 | − 0.90 | 9.52e − 02 | ||
| 1 | 188,959,001 | 7 | 1.40 | 5.14e − 02 | DLG2 | Discs, large homolog 2 (Drosophila) [Source:CGNC Symbol;Acc:12965] |
| 1 | 192,474,001 | 5 | 1.35 | 3.27e − 07 | CAPN5 | Calpain 5 [Source:CGNC Symbol;Acc:479] |
| 2 | 73,558,001 | 3 | − 2.75 | 8.12e − 02 | ||
| 2 | 85,911,001 | 12 | 0.80 | 9.52e − 02 | ||
| 3 | 9,149,001 | 7 | 1.11 | 3.22e − 02 | EHBP1 | EH domain binding protein 1 [Source:CGNC Symbol;Acc:6763] |
| 3 | 53,750,001 | 7 | 1.31 | 2.73e − 02 | ARFGEF3 | ARFGEF family member 3 [Source:CGNC Symbol;Acc:10361] |
| 3 | 106,780,001 | 5 | 1.70 | 4.83e − 03 | MTMR9 | Myotubularin related protein 9 [Source:CGNC Symbol;Acc:12476] |
| 4 | 27,239,001 | 3 | − 0.98 | 9.24e − 02 | ||
| 5 | 30,875,001 | 3 | − 0.80 | 3.22e − 02 | ||
| 5 | 57,981,001 | 7 | 1.12 | 7.28e − 02 | C5h14orf166 | Gallus gallus chromosome 5 open reading frame, mRNA. [Source:RefSeq mRNA;Acc:NM_205369] |
| 5 | 58,733,001 | 12 | 0.99 | 7.79e − 02 | ||
| 11 | 16,608,001 | 16 | − 1.29 | 5.91e − 02 | ||
| 14 | 5,936,001 | 11 | − 0.83 | 8.12e − 02 | ||
| 15 | 6,629,001 | 22 | 1.13 | 3.22e − 02 | USP30 | Ubiquitin specific peptidase 30 [Source:CGNC Symbol;Acc:50370] |
| 17 | 1,582,001 | 8 | 1.87 | 8.12e − 02 | MRPL41 | Mitochondrial ribosomal protein L41 [Source:CGNC Symbol;Acc:6639] |
| 17 | 1,582,001 | 8 | 1.87 | 8.12e − 02 | PNPLA7 | Patatin-like phospholipase domain containing 7 [Source:CGNC Symbol;Acc:6632] |
| 18 | 10,927,001 | 23 | 0.89 | 5.14e − 02 | ARMC7 | Armadillo repeat containing 7 [Source:CGNC Symbol;Acc:6023] |
| 19 | 58,001 | 3 | − 0.95 | 1.01e − 02 | DDX25 | DEAD-box helicase 25 [Source:HGNC Symbol;Acc:HGNC:18698] |
| 20 | 11,544,001 | 11 | 1.15 | 3.22e − 02 | ||
| 23 | 3,692,001 | 5 | 1.38 | 7.28e − 02 | GNL2 | Guanine nucleotide binding protein-like 2 (nucleolar) [Source:CGNC Symbol;Acc:1398] |
Comparison between HFH and LFH red junglefowl individuals resulted in 22 differentially-methylated 1-kb windows at FDR-corrected p < 0.1. Of these, 13 aligned within genes or promoter regions of genes. The log fold changes (logFC) are based on the comparison between HFH and LFH birds, with HFH birds set as reference in the MEDIPS analysis