Aunt Ruby’s Got Good Genes

Few edible plants inspire the nostalgia or controversy that a tomato does; a quick Google search uncovers hundreds of articles and blog posts whose authors covet the tomatoes of yore, and admonish modern day supermarket–bound tomato handling practices like forced ethylene gas ripening, or the abominable, flavor-depleting refrigeration. Few garden staples can lend themselves more to the myriad of possibilities, raw or cooked, sliced, sauced or roasted, salsa-ed or gazpachoed or bloody mary-ed, that a tomato can. In perhaps its finest incarnation, still warm from the summer sun, with only a drizzle of olive oil and a sprinkle of salt, it is, quite literally, the stuff of poetry (see Pablo Neruda’s Ode to the Tomato). For me, it was this same longing, disdain, and appeal that made one genome publication among a plethora of genome publications stand out. The Tomato Genome.

Jason Waskey, Small Heirloom Tomato and Salt, oil on linen, 2009.

Indeed, as reported in Nature this May, an extensive, global team of scientists has successfully sequenced the genomes of the domesticated tomato, Solanum lycopersicum (specifically, the Heinz 1706 cultivar), as well as its closest wild relative, Solanum pimpenellifolium. The massive project has been ongoing since 2003. The information generated from these efforts is of particular significance given the evolutionary history of the Solanum lineage—which is among the world’s most diverse plant genera— and its ability to shed light on the mysteries of eudicot evolution. Also, because tomatoes are such an important food crop, scientists, breeders, farmers, and consumers may benefit from a greater understanding of the molecular and genetic architecture of tomato strains if that knowledge is used to produce superior fruits.

The authors, who are collectively referred to as the “Tomato Genome Consortium,” made two important discoveries when comparing their sequenced tomato genome to the grape genome. First, their data supported the hypothesis a whole-genome triplication occurred in the common eudicot ancestor and second, an additional polyploidy event occurred in the tomato lineage following divergence from grapes, and is shared with the potato genome (Sato et al., 2012). These triplications likely contributed to the major eudicot lineages, and may help to explain, at least partially, what continues to be a hotly debated topic since Darwin reflected on it centuries ago— the rapid diversification of angiosperms on the planet (Stockey et al. 2009).

Figure 2a. from Soto et al. below.

Speciation and polyploidization in eudicot lineages. Confirmed whole-genome duplications and triplications are shown with annotated circles, including ‘T’ (this paper) and previously discovered events α, β, γ. Dashed circles represent one or more suspected polyploidies reported in previous publications that need further support from genome assemblies. Grey branches indicate unpublished genomes. Black and red error bars bracket indicate the likely timings of divergence of major asterid lineages and of ‘T’, respectively.

The result of polyploidy events are the generation of new gene families that, in the case of tomatoes, have had important functions in the plant’s fruit. For example, scientists determined (using orthology and synteny analyses) that gene families mediating functions such as fruit ripening and lycopene (antioxidant) biosynthesis were generated during such genome duplications. Interestingly, these evolutionary outcomes have impacted the loss of fruit functions as well, with important implications for their viability as a food source— gene subfamilies connected to the production of toxic compounds in ancestral lineages have either been completely lost in tomatoes, are not expressed (Sato et al., 2012). Texture is another key characteristic that determines how appetizing a tomato is. Genes sequenced during this project show that cell wall structure and composition largely affect fruit texture, with over fifty differentially-expressed genes encoding proteins involved in altering the structure of the cell wall.

Then how might this extensive data set be applied to the tomato breeding industry? By identifying traits that are associated with fruit development, might we manipulate genetics (through breeding) to select for desirable traits such as taste, texture, color, pest-resistance, speed of ripening, shelf life, pathogen susceptibility, or even levels of antioxidant and disease-fighting phytochemicals?

In a chapter of Genetic Diversity of Plants devoted to the tomato, authors Bauchet and Causse (2012) note that tomato bottlenecks that were artificially generated through domestication, leading to a drastic reduction of genetic diversity, followed by diversification in domestic types by selective breeding. Prized in modern CSA culture, tomato ‘heirlooms’ were pollinated from the seeds farmers saved from the previous year’s harvest; new genotypes arose either from spontaneous mutations, natural hybridization or purposeful recombination of tomato plants with varied traits.

Colorful ‘heirloom’ tomatoes in a variety of shapes and sizes.

A great challenge for breeders has been the ability to ‘unlink’ favorable and unfavorable traits (You say tomato, 2012) i.e. optimal taste and pest attractiveness. Now, scientists can help them conquer this by knowing not only what trait a particular gene codes for, but also how its placement within the genome may influence the expression of neighboring genes. The tomato genome project has generated millions of SNPs (Sato et al., 2012) that can be used  for biodiversity-based breeding, a traditional alternative to the production of genetically-modified “frankenfoods,” which consumers are generally wary of.

Sequence comparison of the Heinz 1706 genes to those of the wild relative, S. pimpenellifolium, revealed that a number of gains and losses of stop codons may have significantly altered gene function in the domesticated tomato. However, Sato et al. found several chromosomal segments in cultivated tomatoes, especially the small “cherry” variety, that are more closely related to the wild species than to Heinz 1706, and attribute this to gene pool mixing through breeding. With both genomes sequenced, greater opportunity arises for new varieties to be cultivated based on wild-type genes, with the potential of reintroducing alleles that were lost during domestication (Bauchet & Causse, 2012). For the likes of farmers, gardeners and foodies everywhere, I hope the resulting traits will render tomatoes as tasty and as healthful as ever.

References:

Bauchet, G. & Causse, M. (2012). Genetic diversity in tomato (Solanum lycopersicum) and its wild relatives Genetic Diversity in Plants DOI: 10.5772/33073

Sato, S. & The Tomato Genome Consortium (2012). The tomato genome sequence provides insights into fleshy fruit evolution Nature DOI: 10.1038/nature11119

Stockey, R.A., Graham, S.W. & Crane. P.R. (2009) Introduction to the Darwin special issue: the abominable mystery. Am. J. Bot. 96: 3-4.

Anon. (2012). You say tomato Nature DOI: 10.1038/485547a

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