Chapter 2: DNA-based Omics in Food Science

One of the disciplines with a broad interdisciplinary view that in recent years has allowed an increase in the capacity to collect information regarding food is certainly genomics. The advent of high-throughput DNA sequencing (HTS) techniques coupled with powerful computational approaches are revolutionizing food data exploration and have effectively changed approaches to food research. From single-marker species identification to sequencing whole genomes to genomic prediction and genotyping for genome-wide association studies, continuous cost reduction and advances in technology and applications have led to breakthroughs which have changed our point of view in the food sector, especially in food security. As the field of genomics is extremely vast, we have decided to discuss five of the main genomic-based strategies widely applied in food research: (i) whole genome sequencing (WGS) of a single cultured isolate; (ii) single nucleotide polymorphism (SNP) genotyping and multilocus sequence typing (MLST) in genotyping association studies; (iii) shotgun metagenomics, the random shotgun sequencing of the whole genomic content of communities; (iv) amplicon-based sequencing or DNA metabarcoding, consisting of the amplification and sequencing of a specific marker; (v) RNA sequencing for the detection and characterization of only viable organisms and for gene expression analysis. We aim to consider both the potential and the limits of these techniques, with a particular focus on the importance of correct data management and data integration.