Genetic Diversity and Population Structure of Egyptian and Crossbred Buffaloes Using Microsatellite Markers

The Egyptian buffalo (Bubalus bubalis) is a key livestock species in Egypt, contributing substantially to national milk and meat production. Although high-throughput genomic technologies have advanced livestock genetic characterization, baseline knowledge of genetic diversity in Egyptian buffalo-particularly in comparison with crossbred populations-remains limited. This study aimed to establish foundational information on the genetic diversity and population structure of pure Egyptian and Egyptian-Italian crossbred buffaloes using a panel of microsatellite markers. Blood samples were collected from 129 buffaloes (93 pure Egyptian and 36 Egyptian-Italian crossbreds). Genomic DNA was extracted and genotyped using 20 microsatellite markers, 14 of which were polymorphic. Genetic analyses were conducted in R using adegenet, pegas, poppr, hierfstat, and ape. Evaluated parameters included allele number, observed and expected heterozygosity, PIC, Principal Coordinate Analysis (PCoA), Analysis of Molecular Variance (AMOVA), Wright’s F-statistics, and Nei’s genetic distances. Allelic counts ranged from 2 to 8 per locus. Egyptian buffaloes showed a higher mean allele number (4.43) than crossbreds (4.00). Mean observed heterozygosity was 0.45 in Egyptians and 0.34 in crossbreds, while expected heterozygosity was 0.55 and 0.44, respectively. PIC values were also higher in pure Egyptians (0.45) compared to crossbreds (0.37), indicating greater genetic variability. STRUCTURE analysis identified two genetic clusters (K=2), separating pure and crossbred groups. PCA supported this distinction, with PC1 and PC2 explaining 10.32% and 6.94% of variance. AMOVA showed that 85% of variation occurred within populations and 15% between them, and the low Fst value (0.014) indicated minimal differentiation. Pure Egyptian buffaloes retain greater genetic diversity than Egyptian-Italian crossbreds. These baseline findings highlight the importance of conserving indigenous genetics and provide essential groundwork for future high-resolution genomic studies and sustainable breeding strategies.