Abstract
Oxford Nanopore Technologies’ MinION has proven to be a valuable tool within human and microbial genetics. Its capacity to produce long reads in real time has opened up unique applications for portable sequencing. Examples include tracking the recent African swine fever outbreak in China and providing a diagnostic tool for disease in the cassava plant in Eastern Africa. Here we review the current applications of Oxford Nanopore sequencing in livestock, then focus on proposed applications in livestock agriculture for rapid diagnostics, base modification detection, reference genome assembly and genomic prediction. In particular, we propose a future application: ‘crush-side genotyping’ for real-time on-farm genotyping for extensive industries such as northern Australian beef production. An initial in silico experiment to assess the feasibility of crush-side genotyping demonstrated promising results. SNPs were called from simulated Nanopore data, that included the relatively high base call error rate that is characteristic of the data, and calling parameters were varied to understand the feasibility of SNP calling at low coverages in a heterozygous population. With optimised genotype calling parameters, over 85% of the 10,000 simulated SNPs were able to be correctly called with coverages as low as 6×. These results provide preliminary evidence that Oxford Nanopore sequencing has potential to be used for real-time SNP genotyping in extensive livestock operations.
Highlights
DNA sequencing allows us to examine the underlying genomic information that affects important traits in agriculture
We propose the future application of the MinION sequencer to rapidly on-farm genotype cattle for genomic selection in Australia’s northern beef industry, which we term
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Summary
DNA sequencing allows us to examine the underlying genomic information that affects important traits in agriculture. Sequencing technology can broadly be divided into three distinct generations. First-generation technology, such as Sanger sequencing, was characterised by the use of chain termination, second-generation sequencers, such as Illumina, by high-throughput short reads and third-generation sequencers by high-throughput long reads [1,2]. Two technologies have led third-generation sequencing: Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio). A feature of third-generation sequencing technology is that the native DNA is sequenced directly without amplification. This has the advantage of removing the nucleotide biases and alterations in relative abundance of DNA templates that are observed in some short-read sequence data [1,3,4]
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