Fig. 2: Comparative genomic analysis revealed selective regions and genes related to layer breed formation.
a Phylogenetic tree analysis of different breeds. b Principal component analysis of different breeds. c Linkage disequilibrium decay analysis of different breeds. d Selective signals of layer vs. RJF, layer vs. native and native vs. RJF based on ZFST analysis. The horizontal red dashed lines correspond to the top 5% threshold. e Venn diagram of potential selected genes (PSGs) in three comparison groups. f Venn diagram of the intersection of GWASGs and PSGs. g Selective signals of CAMK2D in the three comparison groups. h SNPs and haplotypes in CAMK2D significantly associated with egg production traits in Gushi chicken. Chi-square test and F-test were performed to access the association significance in CCA-based GWAS and haplotype-based GWAS, respectively. CS represents clutch size, MCS represents maximum clutch size, and ACS26-30w represents average clutch size from 31 to 43 weeks of age. i The genotype pattern of SNPs located in the promoter and intron regions of CAMK2D. j Tissue expression pattern of CAMK2D in 30-week-old Hy-line layers and native chickens (n = 3 for the expression in different tissues; n = 8 for the expression in different breeds). Layer: WL (White Leghorn) and RIR (Rhode Island Red). Native chicken breeds: Gushi (GS), Lushi (LS), Xichuan Black Bone (XCBB), Zhengyang San Huang (ZYSH) and Henan Gamecock (HNG) chickens. Wild breed: RJF (Red Jungle Fowl). The data for (j) are presented as the mean ± SEM, and the indicated P values (*P < 0.05, **P < 0.01) are based on two-tailed unpaired t-test. Source data are provided as a Source Data file.
