The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock

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.

Current research and emerging tools to improve fresh red meat quality

“…Although not as accurate as short read sequencing, they seemed to be fast and sequencing reads are long (10-60 kb), hence they are leading to progress with livestock genome projects at the forefront, for example, goat (Bickhart et al, 2017) and water buffalo (Low et al, 2019) genome builds which each surpassed the human genome in contiguity. These technologies have high relevance in microbiome and pathogen sequencing and the Nanopore MinION technology has the capability to bring genome sequencing at the slaughterhouse level and to countries with more limited infrastructure for genome sequencing (Lamb et al, 2020).…”

The Promise of Genetics and Genomics for Improving Invasive Mammal Management on Islands

“…R. et al, 2015), can provide scalable, rapid and costeffective tools for informing the design, implementation and evaluation of eradication operations (Sjodin et al, 2020a), even when paired with non-invasive genetic sampling (Schmidt et al, 2020; see Figure 2 for a generalized workflow for GTseq SNP panel design). Further advances in DNA sequencing technologies have enabled portable genotyping in the field (e.g., Oxford Nanopore MinION; Lamb et al, 2020); although not yet opertionalized within the context of IMS eradication or control programs, this technology holds great promise if paired with pre-eradication inventories (e.g., Macdonald et al, 2019) for informing management operations in real-time.…”

Tracing Viral Transmission and Evolution of Bovine Leukemia Virus through Long Read Oxford Nanopore Sequencing of the Proviral Genome

“…The developed workflow could also be a valuable tool for resolving transmission patterns of Human T Lymphotropic Virus type 1 (HTLV-1) in the central regions of Australia where disease prevalence has been estimated at 33% within indigenous populations [35] as this virus most similarity related to BLV. Furthermore, this tool could be used to resolve structural variation within several genomic loci at once to extend GWAS-based approaches that identify highly associated SNPs with a given phenotype within humans and livestock [36,37].…”