Additional file 1 of Genomic analysis of the Ixworth chicken: insights into a local dual-purpose breed

Additional file 1: Figure S1. Principal component analysis of chicken populations. The first five principal components are shown, explaining 7.94 %, 5.35 %, 4.74 %, 4.54 %, and 3.99 % of the total genotypic variance. Figure S2. Heatmap of chromosome-wise fixation index (weighted $$F_{ST}$$ ) estimations between chicken populations. Figure S3. Cross-validation error for ADMIXTURE runs with increasing number of clusters (k). The lowest cross-validation error is reached at $$k = 6$$ . Figure S4. Heatmap of chromosome-wise nucleotide diversity ( $$\pi$$ ) estimations within chicken populations. Figure S5. The strongest signatures of selection according to $$|XP-EHH|_w$$ between the Ixworth chicken population and (a) commercial broiler line A, (b) commercial broiler line B, (c) commercial brown layers, (d) commercial white layers, and (e) red junglefowl. Strong selective sweeps are indicated by the red lines according to the top 0.1 %: (a) $$|XP-EHH|_w> 3.32$$ , (b) $$|XP-EHH|_w> 3.46$$ , (c) $$|XP-EHH|_w> 3.10$$ , (d) $$|XP-EHH|_w> 2.92$$ , and (e) $$|XP-EHH|_w> 3.71$$ , respectively. Figure S6. Directional distribution of $$XP-EHH_w$$ between the Ixworth chicken population and (a) commercial broiler line A, (b) commercial broiler line B, (c) commercial brown layers, (d) commercial white layers, and (e) red junglefowl. A positive direction represents a selective sweep in the Ixworth chicken population (reference) while a negative direction indicates selective sweeps in the other populations. File S1. Relationship between the inbreeding coefficients F and $$F_{ROH}$$ . Pearson’s correlation coefficient and linear regression are estimated separately for each population. File S2. Chromosome-wise estimations of LD decay for each chicken population. File S3. Distribution of iHS values within the strongest signatures of selection in the Ixworth chicken. A positive direction represents a selective sweep on the ancestral allele while a negative direction indicates selective sweeps on the derived allele of the Ixworth chicken. File S4. Distribution of XP-EHH values within the strongest signatures of selection in the comparison of Ixworth and broiler line A. File S5. Distribution of XP-EHH values within the strongest signatures of selection in the comparison of Ixworth and broiler line B. File S6. Distribution of XP-EHH values within the strongest signatures of selection in the comparison of Ixworth and brown layer. File S7. Distribution of XP-EHH values within the strongest signatures of selection in the comparison of Ixworth and white layer. File S8. Distribution of XP-EHH values within the strongest signatures of selection in the comparison of Ixworth and red junglefowl. Table S1. Alignment and variant calling statistics. Parameters are calculated as means for each chicken population. Table S2. Genomic location of the strongest signatures of selection (in 40 kb windows) according to the top 0.1 % of the empirical distributions of $$|XP-EHH|_w$$ and $$|iHS|_w$$ . Directly adjacent windows were merged and intersected with genes. Annotations for gene symbols marked by asterisks (“*”) were annotated by BLAST.