Tracing the genetic legacy of Malabari goats through complete mitogenome sequencing: evidence of maritime exchange via the historic spice route.

The Malabari goat of South India is one of the most efficient dual-purpose breeds, exhibiting exceptional adaptability to humid tropical stressors. This study aimed to characterize the complete mitochondrial genome of Malabari goats and to decipher their maternal phylogenetic relationships, thereby providing insights into lineage divergence, domestication origins and genetic connectivity with global caprine populations. Whole-genome sequencing of pooled DNA from 20 unrelated Malabari goats revealed a complete mitogenome comprising 37 genes, including 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs) and two ribosomal RNAs (rRNAs), in addition to a hypervariable non-coding displacement loop (D-loop) region. A total of 45 single nucleotide polymorphisms (SNPs) and two indels were identified, of which 21 SNPs were detected in PCGs-six of them non-synonymous. Importantly, we report the first tRNA mutation described in goats: a novel heteroplasmic substitution (11693 T>C) in the MT-TL2 gene coding for tRNALeuCUN. The mitochondrial genome analysis of Malabari goats revealed their closest genetic affinity with Iraqi Meriz goats and Arabian goat populations, highlighting significant maternal contributions via ancient maritime trade networks, distinct from most Indian breeds that predominantly belong to haplogroup A. The whole mitogenome phylogenetic analysis revealed that Malabari goats cluster in a monophyletic group together with local goats from Vietnam, domestic goats from Malaysia and domestic goats from Russia. Phylogenetic reconstruction based on mitochondrial D-loop placed Malabari goats within haplogroup B1 along with goats from Iraq, Oman and Gujarat in India. Mitogenome analysis of Malabari goats provides genetic evidence of their genetic roots shaped by maritime exchanges along the ancient Spice Route.