Simple Summary
Breeding programs, such as for assistance dogs, must produce enough healthy animals to meet demand while also keeping the population genetically diverse. When these animals become too closely related, their offspring are more likely to inherit health problems. However, many program managers lack formal training in genetics and struggle with software that is either too technical or only addresses part of the problem. We developed RAPPORT, a free, open-source computer application that brings together genetic monitoring and day-to-day breeding management in one easy-to-use interface. Users simply upload their records in spreadsheet format, and the application automatically calculates how related the animals are, tracks trends in genetic diversity over time, and projects future changes. It also helps plan which animals to breed and when, it suggests pairings that keep relatedness low, and incorporates health and trait information into those recommendations. We verified RAPPORT’s genetic calculations against independent tools and found them to be identical. A test case using data from a Belgian assistance dog breeding program illustrated that RAPPORT could identify upcoming production shortfalls, and support informed breeding decisions. By making these tools accessible to non-specialists, RAPPORT helps breeding programs produce healthier animals while safeguarding long-term population health.
Abstract
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.