Accuracy of Imputation of Microsatellite Markers from a 50K SNP Chip in Spanish Assaf Sheep.

ABSTRACT: Transitioning from traditional to new genotyping technologies requires the development of bridging methodologies to avoid extra genotyping costs. This study aims to identify the optimum number of single nucleotide polymorphisms (SNPs) necessary to accurately impute microsatellite markers to develop a low-density SNP chip for parentage verification in the Assaf sheep breed. The accuracy of microsatellite marker imputation was assessed with three metrics: genotype concordance (C), genotype dosage (length r2), and allelic dosage (allelic r2), for all imputation scenarios tested (0.5-10 Mb microsatellite flanking SNP windows). The imputation accuracy for the three metrics analyzed for all haplotype lengths tested was higher than 0.90 (C), 0.80 (length r2), and 0.75 (allelic r2), indicating str

SUBMITTER: Marina H 

PROVIDER: S-EPMC7824810 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature