CRUMBLER

CRUMBLER estimates breed composition of cattle from genotype data to quantify proportions of an individual's genome derived from ancestral pure breeds for downstream analyses such as genomic breeding value estimation, quantitative trait locus identification, and heterosis assessment.

Key Features:

• Breed composition estimation: Estimates breed composition in admixed cattle using genotype data and allele frequencies from a defined reference panel.
• Focus on admixed animals: Targets ancestry estimation in crossbred and advanced-generation composite animals.
• Genotype extraction across platforms: Extracts a specified subset of single nucleotide polymorphism (SNP) genotypes common across commercially available genotyping platforms.
• SNP marker evaluation: Evaluates the number of SNP loci required for precise breed composition estimation.
• Integration of ADMIXTURE and SNPweights: Implements ADMIXTURE and SNPweights methodologies within the pipeline for ancestry inference.
• Reference panel construction: Constructs reference panels from large cattle genotype datasets combined with breed association pedigree information and iterative identification of representative purebred individuals.
• File format processing: Processes extracted genotypes into the required file formats for analysis software.
• Simulation of composite genotypes: Simulates genotypes for advanced-generation composite animals to assess precision of estimates.
• Species-agnostic pipeline: Uses a species-agnostic pipeline adaptable to species beyond cattle.

Scientific Applications:

• Genomic breeding value estimation: Supports estimation of genomic breeding values for crossbred animals using inferred breed proportions.
• QTL identification: Facilitates identification and interpretation of quantitative trait locus effects in admixed populations.
• Heterosis assessment: Assesses heterosis and its retention in advanced-generation composite animals.
• Cross-species ancestry estimation: Can be applied to ancestry estimation studies in species other than cattle.

Methodology:

Extracts common SNP subsets from genotyping platforms, converts genotypes to analysis file formats, predicts admixture proportions using allele frequencies from a specified reference panel, integrates ADMIXTURE and SNPweights for inference, constructs reference panels using genotype data plus breed association pedigrees with iterative selection of representative purebreds, evaluates marker counts, and simulates composite genotypes to assess precision.