Current challenges and future potential of tomato breeding using omics approaches

Abstract

As tomatoes are one of the most important vegetables in the world, improvements in the quality and yield of tomato are strongly required. For this purpose, omics approaches such as metabolomics and transcriptomics are used not only for basic research to understand relationships between important traits and metabolism but also for the development of next generation breeding strategies of tomato plants, because an increase in the knowledge improves the taste and quality, stress resistance and/or potentially health-beneficial metabolites and is connected to improvements in the biochemical composition of tomatoes. Such omics data can be applied to network analyses to potentially reveal unknown cellular regulatory networks in tomato plants. The high-quality tomato genome that was sequenced in 2012 will likely accelerate the application of omics strategies, including next generation sequencing for tomato breeding. In this review, we highlight the current studies of omics network analyses of tomatoes and other plant species, in particular, a gene coexpression network. Key applications of omics approaches are also presented as case examples to improve economically important traits for tomato breeding.

Exploiting the Genetic Diversity of Maize Using a Combined Metabolomic, Enzyme Activity Profiling, and Metabolic Modeling Approach to Link Leaf Physiology to Kernel Yield

“…More recently, these approaches have been extended to a wider range of plants including cereals such as rice (Oryza sativa) and maize (Kusano et al, 2011;Lisec et al, 2011;Amiour et al, 2014;Riedelsheimer et al, 2012a). Thus, interesting perspectives have arisen concerning the use of metabolome-assisted breeding techniques to narrow the genotype/phenotype gap of complex traits, such as yield and biomass production (DellaPenna and Last, 2008;Fernie and Shauer, 2009;Lisec et al, 2011;Kusano and Fukushima, 2013;Wen et al, 2015).…”

Dissecting a QTL into Candidate Genes Highlighted the Key Role of Pectinesterases in Regulating the Ascorbic Acid Content in Tomato Fruit

“…Significant advances have been made in the sequencing and annotation of the tomato genome since our laboratory first reported the transcriptional profiling of the introgression line IL12‐4 (Di Matteo et al, 2010). In addition to the expanding genomic resources, a number of “omics” tools have become available for tomato (Kusano and Fukushima, 2013). These allow for the linkage of phenotypic traits to genomic sequences, transcripts, or proteins, as demonstrated in species such as Arabidopsis , legumes, and cereals (Lysenko et al, 2009; Borrill et al, 2014; Feuillet et al, 2012; Pratap et al, 2014).…”

Integrated bioinformatics to decipher the ascorbic acid metabolic network in tomato

“…A major contribution to dissect these aspects can be provided by a suitable integration of data and resources today available for tomato (Chiusano et al 2008;Tomato Genome Consortium 2012;Shearer et al 2014;Bostan and Chiusano 2015). Driven by the recent increase of the ''omics'' data in tomato (Kusano and Fukushima 2013) the aim of this work is to gain insights into the AsA network architecture providing a complete gene survey for the biosynthetic, the recycling and the translocation pathways based on the current annotation of the tomato genome (iTAG2.40). The bioinformatics approach herein employed, integrating also gene expression data, provided a comprehensive view on the functionality of the genes in the AsA network in physiological conditions, highlighting the pivotal role of some components.…”