Conservation and genetic analysis of the endangered Martina Franca donkey using pedigree data

Introduction: The Martina Franca donkey is an endangered Italian breed with historical significance in agriculture and therapy. Conservation efforts are crucial due to increasing risks of genetic erosion and inbreeding. Methods: Pedigree data from 2,261 individuals, spanning from 1940 to 2023, were analyzed. Key parameters such as inbreeding coefficients (FPED), effective population size (Ne), and founder contributions were computed using R packages including optiSel, purgeR, and pedigree. Population structure was assessed using demographic and genealogical indicators. Results: The study showed a rise in inbreeding (FPED increased from 0.07 in 2009 to 0.10 in 2020), with low Ne values (as low as 3.06 using complete generations), well below the FAO threshold (Ne > 50). Only 16.6 founders in the total population and 15.1 in the reference population accounted for most of the genetic diversity, indicating a genetic bottleneck. Despite recent demographic growth, mainly due to milk and therapy uses, genetic variability remains critically low. Discussion: These findings highlight the need for immediate conservation strategies, including broadening the breeding base, limiting overuse of sires, and improving pedigree recording. Without intervention, the long-term viability of the breed is at risk.