Supporting data for "Genome-wide definition of selective sweeps reveals molecular evidence of trait-driven domestication among elite goat (Capra species) breeds for the production of dairy, cashmere, and meat"

Domestication of wild goats and subsequent intensive trait-driven crossing, inbreeding, and selection, all have led to dramatic phenotypic purification and intermediate breeds for high-quality production of dairy, cashmere, and meat. Genomic re-sequencing provides a powerful mean for direct identification of trait-associated sequence variations that underlie molecular mechanisms of domestication. Here, we report our effort to define such variations based on data from domestic goat breeds (Capra eagagrus hircus; 5 each) selected for dairy, cashmere, and meat production in referencing to their wild ancestors, Sindh ibex (Capra eagagrus blythi; 2) and Markhor (Capra falconeri; 2). Using ~24 million high-quality single nucleotide polymorphisms (SNPs), ~1.9 million insertions/deletions (indels), and 2,317 copy number variations (CNVs), we define SNP-desert-associated genes (SAGs), domestic-associated genes (DAGs), and trait-associated genes (TAGs), and attempt to associate them with quantitative trait loci (QTL), domestication, and agronomic traits. Surprisingly, a greater majority of SAGs shared by all domestic breeds classified into Gene Ontology categories of metabolism and cell cycle. DAGs, together with some SAGs, are most relevant to behavior, immunity, and trait-specificity, whereas TAGs appear directly involved in growth regulation, such as growth differentiation factor 5 (GDF5) and fibroblast growth factor 5 (FGF5) for bone and hair growth, respectively. When investigating divergence of Capra populations, the sequence variations and candidate genes we have identified provide valuable molecular markers for trait-driven genetic mapping and breeding.