BIGapp

BIGapp streamlines genomic data processing for plant breeding programs to facilitate quantitative trait locus (QTL) identification and accelerate breeding cycles.

Key Features:

• Genomic Data Processing: Processes genomic data for breeding populations regardless of species ploidy.
• Genome-Wide Association Studies (GWAS): Identifies quantitative trait loci (QTLs) associated with target traits.
• Genomic Prediction: Evaluates predictive ability for traits to support selection decisions.
• DArTag Marker Panel Integration: Supports genotyping with the 3K DArTag marker panel.

Scientific Applications:

• QTL Mapping in Alfalfa: Identified three QTLs for creeping rootedness, including one major QTL on chromosome 6.1 in a population of 648 alfalfa (Medicago sativa L.) lines.
• Genomic Prediction for Creeping Rootedness: Achieved moderate predictive ability (r = 0.68) for this horizontal root growth trait in alfalfa breeding.
• Alfalfa Breeding Program Support: Integrates genomics into existing breeding programs for cultivar development with improved productivity and persistence against biotic and abiotic stresses.

Methodology:

BIGapp is implemented as an R Shiny application. The published study used genome-wide association studies (GWAS) and genomic prediction with a 3K DArTag marker panel on 648 alfalfa lines.