Genetic diversity, inbreeding dynamics, and reproductive fitness in Algerian Arabian racehorses: a 35-year longitudinal study

This 35-year longitudinal study investigated genetic diversity, inbreeding, and reproductive fitness in 972 Algerian Arabian racehorses (1984–2019) genotyped at 14 microsatellite markers and partitioned into six birth cohorts (C1–C6). Genetic diversity indices, inbreeding coefficients (FIS), effective population size (Ne), and pairwise differentiation (FST) were estimated, and the effects of inbreeding on age at first foaling, foaling interval, and foaling success were evaluated using mixed-effects models. Genetic diversity peaked in cohort C4 (2002–2007), coinciding with the importation of foreign breeding stock (mean number of alleles per locus, Na=6.3; allelic richness, Ar=5.40; expected heterozygosity, He=0.71; Ne=185). Following import cessation, allelic richness declined (Ar=5.10 in C6), while heterozygosity remained stable (He=0.68–0.71). Contrary to expectations, FIS values were consistently negative (mean FIS=−0.011±0.004), indicating avoidance of consanguineous matings. Nevertheless, significant inbreeding depression was detected: each unit increase in FIS was associated with delayed age at first foaling (β=+0.84 months; P=0.018), prolonged foaling intervals (β=+1.12 months; P=0.011), and reduced foaling success (OR=0.91; P=0.023). Effective population size declined to Ne=38 in the most recent cohort, which is below the recommended threshold. These findings demonstrate that despite active outbreeding, the population remains vulnerable to genetic erosion and inbreeding depression. The direct association between inbreeding and reproductive impairment underscores the need for integrating genetic monitoring into routine veterinary management to preserve the long-term viability of this historically important population.