Genes associated with SNP outliers and DMRs, and gene ontology analyses
We investigated whether genomic outliers and DMRs overlapped genes in 5 kb upstream and downstream regions using BEDTools v2.28.0 (Quinlan & Hall, 2010). Gene ontology analyses were performed with the R package topGO (Alexa & Rahnenführer, 2009), with GO referenced for the chickenGallus gallus (ggallus_gene_ensembl), to identify potential statistically enriched genes ontologies among the lists of genes extracted. In order to take into account hierarchy and non-independence in GO terms we used the “weight01” algorithm with a “fisher” statistic (options algorithm=“weight01” andstatistics=“fisher” of the runTest() function). GO terms were considered significantly enriched when having a weightFisher < 0.05.