ArticleMammalian genome : official journal of the International Mammalian Genome Society2025
Unraveling the maternal heritage: identifying the complex origins of indigenous Indian horse and pony breeds through mitochondrial genome analysis.
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3 citing papers in PubMed.
- Whole Mitochondrial Genome Analysis Highlights India's Role in Pig Domestication and Maternal Lineage Diversification.Biochemical genetics · 2026Article
- Advances in Equine Genomics: Decoding the Genetic Architecture of Morphology, Performance, Behavior, and Adaptation.Molecular biotechnology · 2026Review
- Mitochondrial genome assembly of the Peruvian Paso horse through PacBio long-read sequencing.Scientific reports · 2025Article
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Abstract
This study explored the maternal genetic diversity of six indigenous Indian horse and pony breeds (Bhutia, Kathiawari, Manipuri, Marwari, Spiti, and Zanskari) using comprehensive mitochondrial genome (mitogenome) analysis. Blood samples from 53 horses across diverse agro-climatic zones of India were analyzed, revealing 36 distinct haplotypes, with a haplotype diversity of 0.889 and nucleotide diversity of 0.00347. These indices suggest significant maternal genetic diversity in Indian equines. A median-joining (MJ) network, based on the hypervariable region of the D-loop along with sequences of Indian equids retrieved from the NCBI, identified 55 haplotypes, including shared haplotypes across 2-5 breeds. Hierarchical AMOVA analysis revealed that 95.20% of genetic variation was within populations, while only 4.80% was among different groups, indicating minimal genetic structuring based on geographic distribution. Phylogenetic analysis of these mitogenomes, alongside global sequences, revealed significant genetic variability without clear geographic clustering, highlighting extensive gene flow and interbreeding across regions. Median-Joining network based on D-loop sequence revealed that Indian horses conform to seven of the 18 globally recognized haplogroups (A, B, G, J, L, M, and P), with haplogroup A being the most frequent. This research contributes to the broader understanding of equine genetic diversity, aligning with global patterns of extensive maternal haplotype diversity, and underscores the intricate genetic backgrounds resulting from historical breeding practices.
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