Molecular diversity assessment of local African pigs using microsatellite (SSRs) markers in Central and Northern Benin

Knowledge of local animal resource diversity is a prerequisite for developing conservation and improvement strategies aimed at sustainable management and food security.This study assessed the genetic differentiation within local African pigs across the Collines and Atacora departments of Benin.A total of 112 local pigs, including 49 from Collines and 63 from Atacora, were genotyped using 16 microsatellite markers.The results revealed a high degree of polymorphism across all loci.The total number of alleles observed was 180, averaging 11.25 alleles per locus.Expected (He) and observed (Ho) heterozygosity rates were estimated at 0.64 and 0.58, respectively.The mean inbreeding coefficient (FIS) was 0.098, while the polymorphic information content (PIC) and Nei's gene diversity (Hs) were 0.61 and 0.64, respectively.Hardy-Weinberg equilibrium testing showed that the population deviated significantly from expectations (p<0.001).Population structure models confirmed an internal subdivision into four distinct genetic subpopulations (K=4), with no geographic differentiation observed among individuals.Individual assignment tests showed that over 71% of the Collines individuals and over 85% of the Atacora individuals were incorrectly assigned to their geographic origins.Analysis of Molecular Variance (AMOVA) indicated that differentiation among individuals accounted for 90% of genetic variability.Quantitative and qualitative bottleneck models revealed no signs of a recent population bottleneck.This high genetic diversity and clear subdivision represent vital assets for driving genetic progress in breeding programmes targeting zootechnical and economic traits to boost pig production in Benin.