AMBP

AMBP integrates haplotype reference panels and analytical pipelines for aquaculture genomics to enable genotype imputation, population-structure inference, and performance-trait genetic analysis to support breeding program decision-making.

Key Features:

• Haplotype Reference Panels: AMBP integrates extensive haplotype reference panels for 18 aquaculture species to improve genotype imputation accuracy.
• Genetic Structure Inference: Provides tools to infer population structure within aquatic species to dissect genetic architectures of performance traits.
• Performance Trait Analysis: Supports dissection of genetic bases underlying performance traits, including estimation of breeding values and prediction of optimum contributions.
• Data Compatibility and Automation: Supports VCF and PLINK (PED and MAP) file formats and includes automated pipelines for format transformation and visualization.
• Demonstrated Applications: Applied to Pacific white shrimp and Atlantic salmon datasets to inform practical breeding program analyses.

Scientific Applications:

• Population structure and diversity analysis: Understand population structures and genetic diversity within aquaculture species.
• Marker identification for traits: Identify genetic markers associated with economically important performance traits.
• Breeding strategy development: Develop informed breeding strategies to enhance performance and sustainability in aquaculture species.

Methodology:

Computational methods explicitly include genotype imputation using integrated haplotype reference panels for 18 aquaculture species, population-structure inference, statistical analyses for performance-trait dissection including breeding-value estimation and optimum-contribution prediction, and automated format transformation and visualization for VCF and PLINK (PED/MAP) files.