Genotyping of SNPs in bread wheat at reduced cost from pooled experiments and imputation

In this study, we propose to combine pooling and imputation and demonstrate this by simulating a hypothetical microarray for genotyping a population of recombinant inbred lines in a cost-effective and accurate manner, even for rare variants. We show that with an adequate imputation model, it is feasible to accurately predict the individual genotypes at lower cost than sample-wise genotyping and time-effectively. Moreover, we provide code resources for reproducing the results presented in this study in the form of a containerized workflow.PMID:38243086 | PMC:PMC10799138 | DOI:10.1007/s00122-023-04533-5

Source: TAG. Theoretical and Applied Genetics - January 19, 2024 Category: Genetics & Stem Cells Authors: Camille Clouard Carl Nettelblad Source Type: research