Reduced Inbreeding Seed Orchard Engine: A Web-Based Application for Optimising Seed Orchard Layouts

Abstract In advanced seed orchards, factors such as shared clone origins and uneven planting densities heighten the chances of inbreeding. The RISE tool advances beyond traditional minimum-inbreeding and quadratic assignment frameworks by incorporating comprehensive coancestry data, gap-filling for plant losses, variable clone counts, and dynamic features like distance graphs and selectable clone emphasis in an online environment. This research describes an innovative browseraccessible program that creates efficient orchard arrangements for practical forest management, employing a preliminary placement strategy paired with a streamlined annealing process to reduce the inbreeding indicator, dₘin. The system accommodates custom grid setups, the number of clones, clonal replicates, and sibling links, producing arrangements through spreadsheet exports and engaging visual displays. Relative to arbitrary configurations, the program yields notably reduced dₘin levels (an indicator of mating hazards). It provides statistical analysis of the resulting orchard, such as paired t-test, Kolmogorov-Smirnov test and Levene’s test, validating improvements across cases. It can handle complex pedigrees and co-ancestry estimates from marker based genomic studies. The tool suits forestry practitioners, delivering an effective option for orchards of diverse scales. The program's architecture, approach, and forestry applications are explored, underscoring its role in advancing orchard oversight.