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Mapping The Tomato Genome Promises A Tastier Future

The EU Tomato Genome Sequencing Consortium has announced that they have completed sequencing the genome of “Heinz 1706″ as well as it’s wild relative Solanum pimpinellifolium. The sequence will be published tomorrow (May 31st) in Nature. The hopes are that having access to the tomato genome will make breeding easier, and hopefully lead to tastier tomatoes. Currently tomato breeding is one of the most complex and interwoven processes that most Americans have no clue is even happening. As it stands most commercial tomatoes have to be completely rebred every couple of years just to be the same consistent tomato that we are familiar with. The publishing of the tomato genome will hopefully not only make the whole process easier, but also help producers to emphasize genes that enhance flavor and not just appearance, yield, and durability.

From “Tomato genome sequence bears fruit” By Rebecca Hill

According to the leaders of the UK arm of the Tomato Genome Consortium, Graham Seymour at the University of Nottingham and Gerard Bishop, formerly of Imperial College London, the sequence will make precision breeding possible not just in tomatoes, but also in other crop species from the Solanaceae family, such as aubergines (Solanum melongena) and peppers (Capsicum spp.).

They also hope it will help in the development of tomatoes that can survive pests, pathogens and even climate change, as well as high-yield crops that still have a good flavour. “It’s really all about making a better tomato,” says Allen Van Deynze, a molecular geneticist at the Seed Biotechnology Center at the University of California, Davis. “This work enables a lot of things we just couldn’t do before.”

Launched in 2003, the project has taken some time to get results, but it has produced an “amazingly complete” sequence, the leaders say. With more than 80% of the genome sequenced, and more than 90% of the genes within it identified, and refinements still taking place, the group hopes to make this a gold-standard reference sequence. “It’s one of the better genomes out there,” says Van Deynze.

From Nature Editorial “You Say Tomato

The scientists have analysed many more traits in these variants than just taste. They have built up a phenotypic resource that details all the desirable (and undesirable) properties you might want to see in a tomato — from pest-resistance to speed of ripening. The resource will be extremely valuable for those who want to exploit the tomato genome, the sequence of which we publish this week (seepage 635). The paper reports the sequences of both the inbred tomato strain Heinz 1706 — generated by the company whose founder Henry Heinz changed the world of tomato ketchup — and its wild ancestorSolanum pimpinellifolium. (Among the many aphorisms ascribed to Heinz is this fitting one: to improve the product in glass or can, you must improve it while it is still in the ground.)

Plant genomes are more challenging to sequence than those of animals because they tend to be larger and more complicated. But at around 900 megabases — just over one-quarter of the size of the human genome — the tomato genome proved manageable. Still, more than 300 scientists from 90 institutes across 14 countries have been slaving away at the task since 2003. It is a fabulous effort that has the potential to radically advance plant science. First, however, the biology behind the genome needs to be understood.

Understanding the basis of tomato genomics is important for three reasons. First, it will help scientists to unravel the extraordinary diversity of the tomato plant, and of the natural world in general. The tomato belongs to one of the planet’s most diverse plant genera — Solanum, which includes more than 1,000 species ranging from the potato (Solanum tuberosum) to woody nightshade (Solanum dulcamara). Comparing sequences may help researchers to understand evolutionary processes

From “Tomato Genome Sequenced” from Science Daily

Tomato is a member of the Solanaceae or nightshade family, and the new sequences are expected to provide reference points helpful for identifying important genes in tomato’s Solanaceae relatives. The group includes potato, pepper, eggplant and petunia and is among the world’s most important vegetable plant families in terms of both economic value and production volume.

Beyond improvement of the tomato, the genome sequence also provides a framework for studying closely related plants, such as potato, pepper, petunia and even coffee. These species all have very similar sets of genes, yet they look very different.

How can a similar set of “genetic blueprints” empower diverse plants with different adaptations, characteristics and economic products? This challenging question is being explored by comparing biodiversity and traits of tomato and its relatives.

The Tomato Genome Consortium started its work in 2003, when scientists analyzed the DNA sequence of tomato using the most modern equipment available at the time. Fortunately, with the recent introduction of so-called “next generation sequencing” technologies, the speed of data output increased 500-fold and enabled the project to move on efficiently to its conclusion.

“The tomato genome sequence provides insights into fleshy fruit evolution”  The Tomato Genome Consortium Sato et al.

Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanumpimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

The genes shown represent a fruit ripening control network regulated by transcription factors (MADS-RINCNR) necessary for production of the ripening hormone ethylene, the production of which is regulated by ACC synthase (ACS). Ethylene interacts with ethylene receptors (ETRs) to drive expression changes in output genes, including phytoene synthase (PSY), the rate-limiting step in carotenoid biosynthesis. Light, acting through phytochromes, controls fruit pigmentation through an ethylene-independent pathway. Paralogous gene pairs with different physiological roles (MADS1/RINPHYB1/PHYB2ACS2/ACS6ETR3/ETR4PSY1/PSY2), were generated during the eudicot (γ, black circle) or the more recent Solanum (T, red circle) triplications. Complete dendrograms of the respective protein families are shown in Supplementary Figs 16 and 17.

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