The Donkey Genome: From Evolutionary Insights to Sustainable Breeding Strategies

Donkeys (Equus asinus) are economically and ecologically important livestock species whose genetic potential remains underexplored. This review synthesizes recent advances in donkey genomics, tracing their evolutionary history while evaluating current applications in selective breeding, conservation genetics, and agricultural management. By integrating evidence from population genomics, functional genomics, and comparative evolutionary studies, we summarize major genomic discoveries and identify persistent knowledge gaps, with a focus on translating genomic information into practical breeding outcomes. High-quality reference genomes, population resequencing, and ancient DNA analyses have clarified the African origin, global dispersal history, and environmental adaptation of donkeys. Genome-wide approaches, including GWAS, QTL mapping, and multi-omics analyses, have further identified genes and regulatory pathways associated with thermotolerance, metabolism, reproduction, and milk production. Nevertheless, progress is still limited by small sample sizes, variable sequencing depth, and inconsistencies in phenotyping and bioinformatic pipelines, which constrain cross-population comparisons and practical applications. Addressing these challenges through standardized phenotyping, improved data integration, and collaborative research frameworks will lay the groundwork for effective conservation strategies and sustainable genomic breeding of global donkey populations.