Breedbase

Breedbase provides a database and analysis platform for plant breeding that stores phenotypic and high-density genotypic data, supports genotyping sample collection and field layout design, and performs Genomic Selection analyses and predictions.

Key Features:

• Field layout design: Supports field layout design for breeding trials.
• Phenotypic data collection: Collects phenotypic data via tablets.
• Genotyping sample collection: Manages genotyping sample collection workflows.
• Genotypic data storage: Stores high-density genotypic information.
• Genomic Selection: Performs Genomic Selection analyses and predictions.
• BrAPI compliance: Adheres to the BrAPI standard to facilitate interoperability within the plant breeding community.
• Integration of "waves": Integrates the R package "waves" for analysis of visible and near-infrared (vis-NIRS) spectroscopy data.
• vis-NIRS support: Analyzes vis-NIRS spectral data to support increased phenotyping throughput.
• Spectrometer compatibility: Supports various spectrometer models.
• Spectral processing: Provides visualization, filtering, and aggregation of spectral data.
• Cross-validation: Forms cross-validation sets and implements several cross-validation schemes relevant to breeding programs.
• Model training and prediction: Performs model training and prediction to associate spectra with reference measurements and assess predictive accuracy.
• Spectral data management: Supports storage and management of spectral data alongside other breeding data.

Scientific Applications:

• High-throughput phenotyping: Use of vis-NIRS analysis to increase phenotyping throughput in breeding programs.
• Spectral calibration and prediction: Associating vis-NIRS spectra with reference measurements for prediction and calibration.
• Genomic selection support: Enabling genomic selection by combining phenotypic and high-density genotypic data for prediction of breeding values.
• Data interoperability: Facilitating data interoperability and exchange among breeding databases via BrAPI.
• Cross-crop analyses: Application across a broad range of crop species for spectral and breeding analyses.

Methodology:

Integration of the R package "waves" for visualization, filtering, and aggregation of vis-NIRS spectral data, formation of cross-validation sets, model training and prediction using several cross-validation schemes to assess predictive accuracy, storage and management of spectral and high-density genotypic data, and adherence to the BrAPI standard.