Supporting information
Figure S1.(a) SNP density and distribution across the genome (b). Number of novel SNPs vs. those found within the dbSNP database.
Figure S2. Indel density and distribution across the genome.
Figure S3. Biplots showing PC1 vs. PC2, PC1 vs PC3, and PC2 vs PC3.
Figure S4. The CV error associated with each K value.
Figure S5. Venn diagrams showing numbers of genes identified using FST , Pi, and XP-EHH analyses for (a). Baier Yellow Chicken. (b). Beijing You Chicken. (c). Langshan Chicken.
Figure S6. Go term and KEGG analysis for (a). Beijing You Chicken. (b). Baier Yellow Chicken. (c). Langshan Chicken.
Figure S7. (a). Phylogenetic tree constructed using the genome-wide SNPs; (b). Phylogenetic tree constructed using SNPs associated with economic traits. (a). Beijing You chicken. (b). Baier Yellow Chicken. (c). Langshan chicken.
Table S1. Summary statistics for genome sequencing.
Table S2. Summary of genome sequencing and annotation of variants for the three Chinese domestic chicken breeds.
Table S3. Estimation of the pairwise genetic differentiation statistic among breeds (FST ).
Table S4. Effective population size (Ne) estimated for the three breeds in in situ and ex situ conservation programs.
Table S5. Statistical summary of analysis for runs of homozygosity in in situ and ex situ conserved chicken populations.
Table S6. Candidate regions in (a) Baier Yellow chicken. (b). Beijing You chicken. (c). Langshan chicken.
Table 1. Pedigree information of the In-situ and ex-situ conserved chicken populations