With an average sequencing coverage of 0.5x the correlation between the two methods was between 0.85 and 0.92 using imputation, depending on the trait. At sequencing coverages between 2X and 4X the correlation between ONT breeding values and SNP array-based breeding values was > 0.92 when imputation was used and > 0.88 when no imputation was used. Here we demonstrate the potential of the later by calculating genomic breeding values for four traits in cattle using low-coverage ONT sequence data and comparing these breeding values to breeding values calculated from SNP arrays. This introduces the potential for in-house clinical genetic disease risk screening in humans or calculating genomic breeding values on-farm in agriculture.
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Oxford Nanopore Technologies' (ONT) portable sequencers have the potential to combine the benefits genotyping-by-sequencing with portability and decreased turnaround time. Recently, genotyping-by-sequencing has become popular, due to lower cost and greater genome coverage (including structural variants). Both fields typically use SNP array genotypes for the analysis. In agriculture, these methods are used to select superior individuals using genomic breeding values in humans these methods are used to quantitatively measure an individual's disease risk, termed polygenic risk scores. Statistical methods to calculate the effect of these loci have been developed and can be used to predict phenotypes in new individuals.
Effects at these loci lie along a continuum ranging from common low-effect to rare high-effect variants that cumulatively contribute to the overall phenotype. Most traits in livestock, crops and humans are polygenic, that is, a large number of loci contribute to genetic variation.
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