Groundbreaking research in food science is shifting from classical methods to novel analytical approaches in which high-throughput techniques have a key role. Among these techniques, RNA-Seq in combination with bioinformatics is applied to investigate topics in food science that were not approachable few years ago. Relevant applications of transcriptomics in modern food science include transcriptome characterization and analysis of gene-expression levels in food crops, foodborne pathogens, and fermenting microorganisms. The aim of the present chapter is to provide an overview of the recent progress in RNA-Seq techniques discussing their advantages and drawbacks. Besides, relevant applications of these technologies will be highlighted in the context of food science to illustrate their impressive potential. Besides, some ideas of the foreseen technological advances and potential applications of these fast-evolving techniques are also provided. © 2014 Elsevier B.V.

This work was supported by AGL2011-29857-C03-01 project (Ministerio de Economía y Competitividad, Spain), and CSD2007-00063 FUN-C-FOOD (Programa CONSOLIDER, Ministerio de Educación y Ciencia, Spain). A.V. thanks the Ministerio de Economía y Competitividad for his FPI pre-doctoral fellowship.

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