Population genomic characterization and detection of selection signatures in livestock using SNP genotype data

다국어 초록 (Multilingual Abstract)

Selective sweep approaches are widely used in livestock population genomics to identify genomic regions associated with positive selection, adaptation, and breed-specific evolutionary history. With the increasing availability of genome-wide SNP genotype data, various population genomic approaches have been applied to investigate genetic structure, genomic differentiation, haplotype diversity, and homozygosity patterns in domestic animals. However, integrated and reproducible workflows for selective sweep studies using livestock SNP genotype data remain limited. In this protocol, we introduce a step-by-step workflow for population genomic characterization and selective sweep studies using publicly available goat SNP genotype data. Representative goat breeds were used to demonstrate procedures for genotype quality control, linkage disequilibrium pruning, principal component analysis (PCA), ancestry estimation using ADMIXTURE, fixation index (FST), cross-population extended haplotype homozygosity (XP-EHH), and runs of homozygosity (ROH). This workflow provides practical guidance for livestock population genomic studies using genome-wide SNP genotype data and can be applied to various livestock and companion animal populations.