CRUMBLER

CRUMBLER is a software tool that estimates the breed composition of cattle using genotype data. It is particularly useful for analyzing admixed animals crossbred from different purebred ancestors. CRUMBLER utilizes existing public software, ADMIXTURE, and SNPweights, along with a defined reference panel of purebred individuals to determine the proportions of an animal's genome originating from different ancestral breeds.

The tool was developed to address the lack of an automated or semi-automated ancestry estimation platform for cattle. It simplifies estimating breed composition for livestock genomics researchers by providing a streamlined pipeline that handles data processing and file format conversions.

The developers created the reference panel using a large cattle genotype dataset and breed association pedigree information. They performed iterative analyses to identify representative purebred individuals for each breed. They also evaluated the number of markers necessary for accurate breed composition estimation.

CRUMBLER extracts a subset of genotypes common to all commercially available genotyping platforms, processes the data into the required file formats, and predicts admixture proportions using the reference population allele frequencies. Although developed and tested on cattle, the pipeline is species-agnostic and can be applied to other livestock with complex ancestries.

The tool has various applications, including estimating genomic breeding values for crossbred animals, determining quantitative trait locus effects, and assessing heterosis and heterosis retention in advanced-generation composite animals.