Uncovering Functional Genetic Variation in the Indigenous Greek Eghoria Goat: An Integrative Genome-Wide Discovery and Validation Approach

Abstract

The Eghoria goat constitutes the major indigenous goat population in Greece and represents an important genetic resource. Despite its significance, genomic information remains scarce. This study aimed to investigate coding variation in the Eghoria goat using whole-genome sequencing (WGS), with particular focus on missense single nucleotide polymorphisms (SNPs) and coding insertions/deletions (indels). Whole-genome sequencing was performed on Eghoria goats (n = 6), followed by bioinformatic processing and variant filtering. Functional characterization was conducted through Gene Ontology (GO) and KEGG pathway analyses (FDR < 0.05). Normalized variant density metrics identified highly polymorphic genes. Selected missense SNPs were validated in an independent population (n = 54) using MassARRAY genotyping. Whole-genome analysis identified 10,796,211 SNPs and 1,022,779 indels. After prioritization, 15,949 missense SNPs and 861 indels were retained. Functional enrichment analyses highlighted pathways related to metabolism, ion transport, calcium signaling, immune function, transcriptional regulation, and environmental adaptation. Genes exhibiting elevated polymorphism density included olfactory receptor family members, and loci associated with metabolic regulation. Validation analyses confirmed the presence of selected variants in the Eghoria goat population. The study expands current knowledge of genomic diversity in the indigenous Eghoria goat and provides valuable resources for future genetic improvement, conservation, and breeding programs.