A comprehensive genome-wide analysis for signatures of selection in goat (genus Capra) revealed new candidate genes for environmental adaptation and productive traits

Background: The species Capra hircus encompasses numerous breeds that exhibit a high level of phenotypic and genetic variability, resulting from environmental adaptation and artificial selection for meat, milk, and fiber production. Today, the global domestic goat population is steadily increasing, primarily due to their ability to adapt to harsh environments. Their worldwide distribution offers the opportunity to study how different environmental conditions and farming systems have shaped the goat genome. In this work, 194 whole-genome sequencing data sets from wild, feral, and domestic goats have been used to detect Runs of Homozygosity (ROH) and study Extended Haplotype Homozygosity (EHH) to identify the so-called 'Signatures of Selection' that uniquely characterize each goat population. Results: Common signals of selection have been identified in CCSER1 and ADAMTSL3, two genes associated with body development, which were under selection in feral and wild goats, and in Angora and Boer breeds, respectively. Similarly, both feral and cashmere breeds exhibited selection signals in PCDH15, a gene linked to environmental adaptation. Selection in wild and feral goats was primarily observed at loci related to environmental adaptation and immune response. Moreover, selection signals related to productive traits such as milk and meat production were still detectable in feral populations. The Angora goat genome showed selective pressure mainly targeting efficient reproduction and body development, with relatively low pressure related to environmental adaptation. The four cashmere breeds studied displayed selection signals predominantly in genes involved in environmental adaptation, immune response, and hair follicle biology. Several signatures of selection related to environmental adaptation were also observed in both meat- and milk-producing goats, as well as in genes associated with reproduction, milk, and meat production. Conclusion: These findings suggest that, despite long-term domestication, natural and environmental selection have shaped the goat genome more than artificial selection. Identifying genes linked to adaptation and fitness is vital for future livestock production amid climate change. Our study highlights genetic loci related to environmental adaptation and disease resistance, offering a foundation for targeted breeding and conservation strategies to enhance resilience and sustainability in goat populations.