Supplemental Material for Bakovic et al., 2022

Supplementary figures and tables for the publication titled "Genomic and gene expression associations to morphology of a sexual ornament in the chicken".

Table S1. Gene expression data generated using NimbleGen 12 x 135k custom gene expression arrays. Each row represents a single probeset and its expression profile for 39 male chicken individuals (Gallus gallus). 

Table S2. An R/qtl cross file consisting of all the phenotypes measurements and genotypes of chicken (Gallus gallus) samples used in this study. (Column descriptions are attached)

Table S3. Results of the QTL analysis performed a F8 intercross population generated by breeding the domestic chicken with the Red Junglefowl. (Column descriptions are attached)

Table S4. The results of a eQTL analysis conducted on a F8 intercross population generated by mixing domestic breeds of chicken with the Red Junglefowl. Gene expression data from over 35,000 probesets were used as the phenotype in this interval mapping analysis. eQTL found within 50cM of its underlying QTL were considered CIS, while those found over 50Kb away were considered TRANS. p values under 0.05 were considered significant, while those under 0.2 were considered suggestive. (Column descriptions are attached)

Table S5. Overlap between QTL and eQTL detected in this study. Overlap regions are established where the confidence intervals of underlying QTL and eQTL overlap.

Table S6. Overlap between QTL confidence intervals and selective sweep regions identified in Qanbari et al., 2020.

Figure S1. Mean comb shape as defined by Principal Components 1 to 10 and 2 standard deviations in both directions for each, depicting the different aspects of comb shape captured by the different axes. Note PCs 1 and 2 were used for analyses performed in this study.

Figure S2. Proportion of variance explained by Principal Components 1 to 10. Bars represent the amount of variation explained by each component, whereas numbers above bars are cumulative figures.