RAPPORT: An Open-Source R Shiny Application for Breeding Program Management with Integrated Pedigree-Based Genetic Monitoring

Managers of closed or semi-closed animal breeding programs must balance production targets with the preservation of genetic diversity, yet they often lack training in population genetics and access to integrated, user-friendly tools. RAPPORT (Relatedness Analysis and Population Planning, Organisation, Reporting and Tracking) is a freely available, open-source R Shiny application that combines pedigree-based genetic monitoring with operational breeding management in a single no-code interface. The application computes inbreeding coefficients and pairwise kinship, estimates rate of inbreeding (ΔF) and effective population size (Ne), and visualises inbreeding trends with forward projections. Production planning tools include dam scheduling, litter projections, and phenotype-integrated breeder selection with mean kinship ranking. Mating recommendations are filtered by a per-mating inbreeding increase threshold and user-defined health criteria. Pedigree and phenotypic data are uploaded in Excel format, and any user-defined traits are automatically incorporated into downstream analyses. Using a test case with anonymised data from a Belgian assistance dog breeding program (852 pedigree entries, 65 litters), the numerical correctness of RAPPORT’s pedigree-based genetic metrics was compared and confirmed against established R packages, and RAPPORT’s capacity to identify a production shortfall and support breeding decisions integrating genetic and phenotypic criteria was illustrated. RAPPORT makes population-level genetic management accessible to non-specialist breeding program managers.