The highly significant category was “regulation of protein kinase activity” (GO: 0045859) ( P = 5.95E-8) containing the candidate genes PCK1 and EDN3 ; another significant category was “transmembrane receptor protein tyrosine kinase signaling pathway” (GO: 0007169) ( P = 5.80E-9).
We found that EDN3 was overexpressed in the ovary of dark comb layers ( P = 0.041, ∼2.5-fold increase), suggesting that the genomic duplication close to the EDN3 gene act as an enhancer in regulating the function, whereas an approximate twofold decrease was observed in the expression of BMP7 in the ovary of dark comb layers, but the difference is marginally nonsignificant ( P = 0.061).