Advances in tomato research in the post-genome era

Abstract

The tomato (Solanum lycopersicum) draft genome, along with a draft of the wild relative, Solanum pimpinellifolium, were released in 2012, almost a decade after the International Tomato Genome project was initiated. Tomato is an important domesticated crop species, as well as a model organism for many aspects of plant biology such as fleshy fruit development, ripening, disease resistance, plant architecture, and compound leaf development. For these reasons, there has been a substantial effort for producing a high quality reference genome that will serve as an anchor for tomato species, and for closely related Solanaceae plants. The utility of this genome has already been demonstrated by a relatively large number of studies that have been published since the release of the sequence, covering a wide range of topics including gene expression, genetic diversity, phylogeny, comparative genomics, and epigenetics. With the availability of the potato genome, it is now possible to perform detailed comparative genomic analysis of gene families in the Solanaceae, facilitated by conservation and synteny between their genomes. A large number of ongoing efforts will result in the sequencing of hundreds of wild and domesticated tomato accessions from various populations, uncovering the breeding history of tomatoes and introducing new genomic technologies to accelerate breeding processes. In this review, we provide an overview of the origins of tomato and its position in the wider Solanaceae, and demonstrate the impact of the tomato genome sequence on Solanaceae research on the basis of recent literature that has made use of this new resource.

Genome-wide identification, phylogeny, and expression analysis of the SWEET gene family in tomato

“…Bioinformatics studies based on the tomato sequence, which serves as a reference genome for other Solanaceae species, have demonstrated that the tomato genome may serve as a true reference genome for closely related Solanaceae and may enable studies of orthologous genes and gene families both within tomato and among more divergent plants (Menda et al, 2013). Systematic analysis of the phylogeny and expression of these genes during reproductive developmental stages in tomato will be helpful for mining candidate genes for subsequent detailed characterization.…”

Genetic Diversity and Population Structure of Tomato (<i>Solanum lycopersicum</i>) Germplasm Developed by Texas A&M Breeding Programs

“…Among them, the largest number of SNPs were observed in chromosome 12, followed by chromosome 1 and 10 ( Figure 1). The existence of unanchored scaffolds (Chr00) and the large [2]. It also highlights the importance of identifying new intraspecific SNPs in the tested tomato breeding lines.…”

Advances and Challenges in Bacterial Spot Resistance Breeding in Tomato (Solanum lycopersicum L.)

“…For example, molecular markers (SNP and InDels) were developed based on whole-genome re-sequencing of two tomato lines (Caimanta and LA0722) and using those markers in a segregating population; eventually, BS disease resistance lines were developed [59]. Menda et al [60] have reviewed the various genomics resources that can be used in tomato improvement.…”