Chapter 18 - Nanopore sequencing in agricultural and food applications

Abstract

Biotechnology has greatly contributed to the improvement of productivity and quality of agricultural and food products. A particularly powerful approach in molecular tools has been genome sequencing and sequencing of individual genes and markers. Genomic tools have been used to explain the genetic basis of variation underlying important traits such as quality of food, yield, and tolerance to biotic and abiotic stress. Nanopore technologies offer a unique way to sequence deoxyribonucleic acid (DNA) and allow for very long strands of DNA to be processed into long-sequence reads. These long reads have several advantages that can be leveraged to improve crop and stock species as well as provide some unique DNA testing methods to identify the species origin of food products or detect locations of genetic modification. Nanopore sequencing involves passing the DNA through the nanopore and detecting each base as it passes through. Types of nanopore that are being investigated are solid-state nanopores and protein-based nanopores, with protein-based nanopores being the only type that is commercially available. In this chapter, we discuss the history of sequencing technologies, the background of nanopore sequencing, and its applications in agriculture and food testing that are currently used for de novo genome assembly, genotyping, transcriptomics, metagenomics, and targeted sequencing.