IonBreeders

IonBreeders provides conversion, preprocessing, imputation, and genomic-prediction plugins to support genomics-assisted breeding using next-generation sequencing (NGS)-derived genotyping data.

Key Features:

• Format conversion (ABH plugin): Converts NGS-derived genotyping data into the ABH format compatible with R/qtl, MapMaker, and AntMap.
• Data preprocessing and imputation (IMPUTATION plugin): Filters non-informative markers and imputes missing marker genotypes.
• Genomic prediction (GENOMIC PREDICTION plugin): Implements four statistical methods for constructing genomic prediction models considering target traits, quantitative trait locus (QTL) effects, and marker numbers.
• VCF support: Handles genotype data in Variant Call Format (VCF).
• Torrent Suite integration: Operates within the Torrent Suite environment.

Scientific Applications:

• Genome-wide marker-assisted breeding: Enables end-to-end analysis from genotyping to genomic prediction for marker-assisted selection.
• Genomic selection and prediction: Supports building prediction models from NGS-derived polymorphism data for trait selection.
• Crop improvement and variety development: Facilitates use of polymorphism information to accelerate crop improvement programs and development of new plant varieties with desirable traits.

Methodology:

Conversion of genotyping data to ABH format; filtering of non-informative markers and imputation of missing marker genotypes; genomic prediction using four statistical methods; operation within the Torrent Suite environment and handling of Variant Call Format (VCF) genotype files; format conversion via free software or scripts provided by NARO.