Comprehensive Phylogeographic Analysis Using mtDNA, SRY, and SNPs Markers Revealed Genetic Influence on Kyrgyzstan Goats via the Eurasian Steppe and the Oasis Routes

ABSTRACT Kyrgyzstan lies at the merge point of two ancient trade routes (the Eurasian Steppe and the Oasis Routes) and represents a key geographic region associated with probable goat propagation. Our study aimed to clarify goat propagation and the relationship between human activity and goats in Asia by investigating the genetic structure of Kyrgyzstan goats. We analyzed the mtDNA hypervariable region 1, the SRY 3′UTR, and genome‐wide SNPs of 30 Kyrgyzstan goats. The mtDNA sequences were classified into three haplogroups: A ( n = 25/30), D ( n = 3/30), and G ( n = 2/30), similar to that observed in Central Asia. Haplogroup G, mainly reported in the Middle East but absent in Central Asia, suggested a propagation route into Kyrgyzstan along the Oasis Route. For SRY haplotypes, Y1AB ( n = 3/18) and Y2A ( n = 15/18) were identified. The haplotype Y2A, largely distributed in Central Asia, implied genetic influence on Kyrgyzstan goats from the Eurasian Steppe Route. Genome‐wide SNPs revealed that the Kyrgyzstan population formed a geographic cline extending from Russia to East Asia. Our findings reflect combined influences of the Eurasian Steppe and Oasis Routes on the genetic structure of Kyrgyzstan goats and illuminate their migration process through these routes.