New Insights into Genetic Diversity and Differentiation of 11 Buffalo Populations Using Validated SNPs for Dairy Improvement

TL;DR

This study explores genetic differences among 11 buffalo populations to better understand their diversity and support future breeding and conservation efforts.

Contribution

The study identifies key genetic markers (DGAT1 and CSN3) that distinguish buffalo types and provides insights into their genetic structure.

Findings

River and swamp buffaloes show significant genetic differentiation (p < 0.001).

DGAT1 and CSN3 are key loci for distinguishing buffalo types.

The Italian Mediterranean buffalo has the highest genetic diversity, while Indonesian, Chinese, and Vietnamese populations show low heterozygosity.

Abstract

Background/Objectives: Buffalo populations exhibit distinct genetic variations influenced by domestication history, geographic distribution, and selection pressures. This study investigates the genetic structure and differentiation of 11 buffalo populations, focusing on five loci related to milk protein (CSN1S1 and CSN3) and fat metabolism (LPL, DGAT1 and SCD). The aim is to assess genetic variation between river, swamp, and wild-type buffaloes and identify key loci contributing to population differentiation. Methods: Genetic diversity was analyzed through allele frequency distribution, the Hardy−Weinberg equilibrium testing, and observed (Ho) and expected heterozygosity (He) calculations. Population structure was assessed using principal component analysis (PCA), FST statistics, and phylogenetic clustering (k-means and UPGMA tree). The silhouette score (SS) and the Davies−Bouldin index (DBI) were applied to determine optimal population clustering. Results: Significant genetic differentiation was observed between river and swamp buffaloes (p < 0.001). DGAT1 and CSN3 emerged as key markers distinguishing buffalo types. The Italian Mediterranean buffalo exhibited the highest genetic diversity (Ho = 0.464; He = 0.454), while the Indonesian, Chinese, and Vietnamese populations showed low heterozygosity, likely due to selection pressures and geographic isolation. The global FST (0.2143; p = 0.001) confirmed moderate differentiation, with closely related populations (e.g., Nepal and Pakistan) exhibiting minimal genetic divergence, while distant populations (e.g., Egypt and Indonesia) showed marked differences, and the Romanian population showed a unique genetic position. Conclusions: These findings contribute to a deeper understanding of buffalo genetic diversity and provide a valuable basis for exploiting the potential of this species in the light of future breeding and conservation strategies specific for each buffalo type.

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