PlantBreedingSuite: an integrated open-source r shiny dashboard for genetic diversity analysis, multi-environment trial stability, and multi-trait selection in crop breeding programmes

PlantBreedingSuite is an open-source R Shiny web application that integrates three core analytical workflows—genetic diversity analysis, multi-environment trial (MET) stability assessment, and multi-trait index selection—within a single browser-based, no-code platform. The application comprises three modules: (i) D² Genetic Diversity Analyser (Mahalanobis D² distances, Tocher clustering, MANOVA, PCA, and Pearson correlation); (ii) MET Stability Suite (classical stability estimators, AMMI, WAAS index, and GGE biplots); and (iii) Multi-Trait Selection Suite (MTSI, MGIDI, FAI-BLUP, Smith–Hazel index, coincidence index, and four-way Venn analysis). Implemented in R using shinydashboard, the application integrates analytical methods from the metan, biotools, and FactoMineR packages through an intuitive graphical user interface. PlantBreedingSuite accepts appropriately formatted replicated phenotypic datasets in CSV or Excel format with interactive column mapping and provides publication-ready tables and figures for downstream analyses. A wheat case study comprising 36 genotypes evaluated across six environments for 11 traits demonstrates the functionality of all analytical modules. By integrating multiple statistical workflows within a single interface, PlantBreedingSuite substantially simplifies data analysis and eliminates the need for extensive R scripting, thereby improving accessibility for plant breeders and researchers without programming expertise. The software is freely available under the MIT License.