breed purity test analysis

Question

[m90]

Hello everyone,

I have set of animals and I want to do purity test analysis for them, to assign each set to their true breed using bioinformatics tools. Has anyone worked on a topic like this or has scripts for this task? I searched in GitHub and I didn't find any repository working on this topic

Answer 1

[Michael]

You need some genetic information, e.g. SNP markers to check for alleles either from genome sequencing or genotyping (SNP) arrays, or other easier-to-use genetic markers (inter-simple sequence repeat (ISSR)) (For dogs it is described in Kriangwanich et al. 2020). Then you also need a panel (genetic information of the different breeds to map out representative alleles for each breed) to compare the test alleles to. But it all depends on what kind of data you can produce for your samples. On SNP data you could run ADMIXTURE or STRUCTURE, and produce a phylogenetic tree.