Phylogeny and genetic diversity analysis in Chhattisgarhi, Chilika, and Kalahandi buffaloes of Central and Eastern India through the High-density SNP Array

¹ Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, 173234, Himachal Pradesh, India
² Department of Animal Genetics, ICAR NBAGR, Karnal, 132001, Haryana, India

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Abstract

The genetic diversity and evolutionary pattern of the Indian buffalo groups can only be understood to come up with the effective conservation and breeding measures. This paper investigates the genomic composition and population structure of three regional buffalo populations, namely Chhattisgarhi (CG), Chilika (CH) and Kalahandi (KH) by high-density SNP genotyping. The analyses showed the general low-to-moderate population genetic variation. The pairwise FST estimates showed a moderate level of differentiation between Chilika and other two groups (0.044-0.049) but strong level of similarity between Chhattisgarhi and Kalahandi buffaloes (0.010). Principal component analysis (PCA) revealed that Chilika buffaloes had a higher number of internal diversity, whereas the Chhattisgarhi and Kalahandi buffaloes displayed a close clustering pattern, which corresponded to their proximity in the geographical location and the exchange of genes. Three genetically consistent groups were found to have a shared ancestry with phylogenetic relationships and identity-by-state (IBS) heatmaps Patterns of linkage disequilibrium suggest a moderate level of genetic diversity with indications of a recent decline in the effective population size. These findings would highlight the need to keep genetic uniqueness and adaptability to preserve diversity and make the buffalo genetic resources more productive, which would sustain the long-term viability of buffalo genetic resources in India.