‘Omics’ approaches in tomato aimed at identifying candidate genes for ascorbic acid accumulation in the fruit

Abstract

Tomato (Solanum lycopersicum) is one of the most important vegetables in the world with significant importance for human health and nutrition. This species has long served as model system for plant genetics, development, physiology, pathology, and fleshy fruit ripening, resulting in the accumulation of many genetic and genomic resources. In addition, the tremendous development of high-throughput technologies, such as transcriptomics, metabolomics and proteomics, collectively denoted as ‘omics’ technologies, has led to a huge collection of data and platforms today available on the net. Nowadays, identifying all the components of a single biological system is within our means; however, assigning function to genes, proteins and metabolites is still a daunting task. Major challenges include interpretation and integration of large datasets to understand the principles underlying the regulation of genes, metabolites and proteins, and how their combined interactions associate with variation in phenotype. In this review, we will focus on the role of the different high-throughput technologies in enhancing tomato breeding particularly for fruit quality traits. We also describe how two ‘omics’ approaches could be combined in order to identify candidate genes for the genetic control of ascorbic acid accumulation in tomato fruit. We report the example of transcriptomic and genomic approaches established on the use of different high-throughput platforms available for tomato.

Key words: Tomato, introgression lines, quality trait, genomics, transcriptomics, candidate gene, single nucleotide polymorphism (SNPs).