Imputation strategies for genomic prediction using nanopore sequencing.

ABSTRACT:

Background

Genomic prediction describes the use of SNP genotypes to predict complex traits and has been widely applied in humans and agricultural species. Genotyping-by-sequencing, a method which uses low-coverage sequence data paired with genotype imputation, is becoming an increasingly popular SNP genotyping method for genomic prediction. The development of Oxford Nanopore Technologies' (ONT) MinION sequencer has now made genotyping-by-sequencing portable and rapid. Here we evaluate the speed and accuracy of genomic predictions using low-coverage ONT sequence data in a population of cattle using four imputation approaches. We also investigate the effect of SNP reference panel size on imputation performance.

Results

SNP array genotypes and ONT sequence data for 62 beef heif

SUBMITTER: Lamb HJ 

PROVIDER: S-EPMC10709982 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature