Genome-wide variation reveal that goats were introduced into Asia via multiple migrations

Abstract

In recent world-wide studies on the autosomal genetic diversity of goats, Asian goats were represented only by Southwest Asian, Pakistani and Chinese breeds. We have collected 55 K genome-wide SNP genotypes for 12 South/Southeast Asian and 2 central Asian goat populations, and inferred the origin and evolutionary history of Asian goats based on the population genomic analyses. Breed relationships, diversity clines, and coancestry patterns revealed two distinct migration routes separated by the Himalayan mountains: a northern route (Kazakhstan–Mongolia–Xinjiang) and a southern route (Bangladesh–Indochina). These routes tentatively parallel major human migration events across Eurasia. The migrations of goats converge into the Indochina goat populations, which then became the ancestors of the Philippine and Indonesian goats. Previous data on Y-chromosomal haplogroups indicate within the first group a separate migration of cashmere goats in eastern and northern China. Similarly, the southern route has been followed by two subsequent waves of goats, the first carrying the mitochondrial B haplogroup and in eastern Indochina associated with that Katjang type, and a later wave carrying exclusively the mitochondrial A haplogroup and associated in western Indochina with the Indian lop-eared trait with a roman convex facial profile. Haplogroup B in Indochina and Indonesia seems to be associated with tropical adaptation, whereas the Y1AB haplotype in northern China occurs at high frequency in cashmere goats, suggesting potential adaptation to arid environments. Together, these patterns point to a complex demographic history and diverse adaptive trajectories in Asian goats. Supplementary Information The online version contains supplementary material available at 10.1038/s41598-025-29204-x.