Brightsurf Science News and Current Science News Events
 
Email a Friend Send to a friend
Printer Friendly Print The 21st century tomato

The 21st century tomato

June 30, 2008

Using systems biology to model the metabolic networks in tomato fruit development

When tomatoes ripen in our gardens, we watch them turn gradually from hard, green globules to brightly colored, aromatic, and tasty fruits. This familiar and seemingly commonplace transformation masks a seething mass of components interacting in a well-regulated albeit highly complex manner. For generations, agriculturalists and scientists have bred tomatoes for size, shape, texture, flavor, shelf-life, and nutrient composition, more or less, one trait at a time. With the advent of molecular biology, mutagenesis and genetic transformation could produce tomatoes that were more easily harvested or transported or turned into tomato paste. Frequently, however, optimizing for one trait led to deterioration in another. For example, improving flavor could have a negative effect on yield.




The revolution in genomics, with a wealth of data emerging from sequencing and simultaneous expression analysis of thousands of genes, has made it possible to study the numerous pathways and regulatory networks-systems--that operate to produce a desirable fruit. This systems approach in the new fields of metabolic and functional genomics is producing the tools, information, and biological materials needed for screening and breeding efforts in tomato and other members of the Solanaceae.

Dr. Fernando Carrari and his colleagues, Laura Kamenetzky, Ramon Asis, Luisa Bermudez, Ariel Bazzini, Sebastian Asurmendi, Marie-Anne Van Sluys, Jim Giovannoni, Alisdair Fernie, and Magdalena Rossi use a systems approach that integrates genomic, genetic, and biochemical tools to model the metabolic networks that interact in the process of tomato fruit development. Dr. Carrari, of the Instituto de Biotecnologia, (INTA), Argentina, will be presenting this work at a symposium on the Biology of Solanaceous Species at the annual meeting of the American Society of Plant Biologists in Mérida, Mexico (June 29, 9:10 AM).

Tomato (Solanum lycopersicum) is a member of the Solanaceae or nightshade family, which also includes potato, eggplant, tobacco, and chili peppers. The center of origin and diversity of tomato species is in the northern Andes, where endemic populations of wild tomato species still grow. These wild populations represent considerable genetic diversity, whereas cultivated tomatoes are genetically very narrow. The Tomato Genome Consortium is an international collaboration that is sequencing, mapping and analyzing the genomes of both wild and cultivated varieties. Carrari and his co-workers, as well as other scientists, have begun to make use of this wealth of sequence data in functional and metabolic analyses of tomato and other crops.

Plants produce an immense variety of chemical compounds for growth, metabolism, signaling, defense, and reproduction. These metabolites function in complex networks and pathways in which they regulate and are regulated by parallel networks of genes. It is not possible to realistically model these metabolic systems one compound or gene at a time. Moreover, many, if not most traits in tomato, are not the result of one gene, but of many genes located together in chromosomal regions called quantitative trait loci (QTLs), because they produce a range of values in fruit or plant size or color, rather than just two extremes. Thus metabolites, enzymes, and genes must be analyzed simultaneously and in parallel in order to capture their dynamic relationships. To accomplish this, Carrari and his colleagues made use of the high genetic diversity of an ancestral tomato species, Solanum pennellii.

Through crosses, chromosomal segments of S. pennellii were introgressed into the genome of the cultivar Solanum lycopersicum var. Roma. Different lines of the cultivar were then created that differed only in the chromosomal segment received from the wild species. In this way, over 1200 metabolic QTLs or quantitative metabolic loci (QMLs) were identified and analyzed. Almost 900 of these QMLs were found to be associated with fruit metabolism.

The scientists then sampled a number of metabolites such as carbohydrates, pigments, and hormones, among others, throughout flower and fruit development. They also used microarrays to determine which genes were expressed at those same times. Pairwise comparisons and network analyses were then made to determine which of those genes and metabolites are associated in possible functional networks. These associations do not establish causality or regulatory direction, because they are only correlational. Expression of certain genes may regulate metabolite activity, but metabolites may also have a regulatory effect on gene expression. To begin to define causal direction, Carrari and his colleagues perturbed these systems by treatment with external metabolites and followed the transmission of information from metabolite to gene. In continuing research, Carrari and co-workers are using these methods, as well as RNA interference and transgenesis to map QMLs and to identify and utilize candidate genes that function at network nodes.

These systems approaches make it possible to model the whole organism throughout its development. Moreover, an understanding of metabolic networks will make it possible to alter metabolic pathways to produce fruits with different secondary compounds that influence texture, taste, aroma, and nutrition, as well as to improve yield. Metabolite analysis also has possible applications in drug discovery, nutrient enhancement and biofuel production. One important goal is the use of ancestral genetic resources in place of simplistic genetic modification to avoid possible deleterious environmental effects as well as resistance by consumers to genetically modified food.

American Society of Plant Biologists



Related Tomato News Articles Tomato News and Current Tomato Events RSS Tomato News and Current Tomato Events RSS
Sesame seed extract and konjac gum may help ward off Salmonella and E. coli
A new study in SCI's Journal of the Science of Food and Agriculture shows that konjac gum and sesame seed extract may offer protection against different strains of E. coli and Salmonella bacteria.

Can tomatoes carry the cure for Alzheimer's?
The humble tomato could be a suitable carrier for an oral vaccine against Alzheimer's disease, according to HyunSoon Kim from the Korea Research Institute of Bioscience and Biotechnology (KRIBB) in Korea and colleagues from Digital Biotech Inc. and the Department of Biological Science at Wonkwang University. Although their research1, just published online in Springer's journal Biotechnology Letters, is still in the early stages, it is a promising first step towards finding an edible vaccine against the neurodegenerative disease.

Watermelon May Have Viagra-Effect
A cold slice of watermelon has long been a Fourth of July holiday staple. But according to recent studies, the juicy fruit may be better suited for Valentine's Day.

Genome communication
In the late 19th century Gregor Mendel used peas to show that one copy of a gene (allele) is inherited from the mother and one from the father.

Drought tolerance in potatoes
Climate change is expected to exacerbate drought events throughout the world, resulting in large-scale ecosystem alteration and failure of drought-sensitive crops.

Evolution of fruit size in tomato
Domesticated tomatoes can be up to 1000 times larger than their wild relatives. How did they get so big? In general, domesticated food plants have larger fruits, heads of grain, tubers, etc, because this is one of the characteristics that early hunter-gatherers chose when foraging for food.

SEX4, starch and phosphorylation
Energy from the sun and carbon dioxide fuel photosynthesis in plants and algae, making life on earth possible. Carbon that is fixed by plants is converted to starch and sucrose, which are utilized by plants for energy and to build biomass.

Salmonella: Trickier than we imagined
Salmonella is serving up a surprise not only for tomato lovers around the country but also for scientists who study the rod-shaped bacterium that causes misery for millions of people.

Certain form of tomatoes could be key to prostate cancer prevention
New cancer research from the University of Missouri suggests that eating a certain form of tomato product could be the key to unlocking the prostate cancer-fighting potential of the tomato.

Dehydrated tomatoes show promise for preventing prostate cancer
New research suggests that the form of tomato product one eats could be the key to unlocking its prostate cancer-fighting potential, according to a report in the June 1 issue of Cancer Research, a journal of the American Association for Cancer Research.
More Tomato News Articles


Heirloom: Notes from an Accidental Tomato Farmer
by Tim Stark

Situated beautifully at the intersection of Michael Pollan, Ruth Reichl, and Barbara Kingsolver, Heirloom is an inspiring, elegiac, and gorgeously written memoir about rediscovering an older and still vital way of life.Fourteen years ago, Tim Stark was living in Brooklyn, working days as a management consultant, and writing unpublished short stories by night. One evening, chancing upon a Dumpster...



The Heirloom Tomato: From Garden to Table: Recipes, Portraits, and History of the World's Most Beautiful Fruit
by Amy Goldman

From the world-class garden of acclaimed food writer Amy Goldman, a gorgeously illustrated guide to the world’s most beautiful and delicious tomatoes.Every year, renowned grower Amy Goldman produces an amazing 500 varieties of tomatoes on her farm in New York’s Hudson Valley. Here, in 250 gorgeous photos and Goldman’s erudite, charming prose, is the cream of the crop, from...



Survey of Accounting
by Carl S. Warren

SURVEY OF ACCOUNTING 3e, is designed for a one-term introductory accounting course. It provides an overview of the basic topics in financial and managerial accounting, without the extraneous accounting principles topics that must be skipped or otherwise modified to fit into a one-term course. Written for students who have no prior knowledge of accounting, the text emphasizes how accounting...



I Will Never Not Ever Eat a Tomato (Charlie and Lola)

Lola is a very fussy eater. Carrots are for rabbits and peas are "too small and too green." One day, after rattling off her long list of despised foods, she ends with the vehement pronouncement, "And I absolutely will never not ever eat a tomato." Not convinced, Lola's older sister Charlie has an idea. She tells Lola that the orange things on the table are not carrots, but "orange twiglets...



The Jamlady Cookbook
by Beverly Ellen Schoonmaker Alfeld

THE JAMLADY COOKBOOK "Jamlady is at your side every step of the way, with history, cautions . . . and a sense of good taste. --from the foreword For years, visitors to Chicagoland farmers markets have counted on Jamladys impressive selection of jams and jellies to add excitement to meals. This cookbook puts a dazzling array of foods often thought of as mere condiments front and center, within...



Patty Reed's Doll: The Story of the Donner Party
by Rachel K. Laurgaard

In the winter of 1846, the Donner Party was stranded by heavy snows in the Sierra Nevada mountains. The pioneers endured bitter hardships, and many of them died. But some survived, including 8-year-old Patty Reed, a girl filled with dignity and determination in the face of mortal danger. This is her story, as told by Dolly, the wooden doll she kept hidden in her...



The $64 Tomato: How One Man Nearly Lost His Sanity, Spent a Fortune, and Endured an Existential Crisis in the Quest for the Perfect Garden
by William Alexander

Bill Alexander had no idea that his simple dream of having a vegetable garden and small orchard in his backyard would lead him into life-and-death battles with groundhogs, webworms, weeds, and weather; midnight expeditions in the dead of winter to dig up fresh thyme; and skirmishes with neighbors who feed the vermin (i.e., deer). Not to mention the vacations that had to be planned around the...



The Tomato Festival Cookbook: 150 Recipes that Make the Most of Your Crop of Lush, Vine-Ripened, Sun-Warmed, Fat, Juicy, Ready-to-Burst Heirloom Tomatoes
by Lawrence Davis-Hollander

With 150 tempting recipes for those lush, vine-ripened, sun-warmed, fat, juicy, and ready-to-burst heirloom tomatoes, The Tomato Festival Cookbook is the landmark cookbook for America's favorite garden vegetable. Author Lawrence Davis-Hollander presents an exhaustive collection of everything about the tomato--from tomato lore, gardening how-to, expert advice on seed saving and preservation to...



The Heirloom Tomato Cookbook
by Mimi Luebbermann

Whether you say "to-may-to" or you say "to-mah-to," chances are you'll agree there's nothing like the taste of a sun-ripened heirloom tomato and this beautifully photographed book is a cornucopia for the tomato lover. First there are the recipes: 50 in all, provided by such notable food names as One Market, Caprial's Bistro, Jimtown Store, and DaVero Olive Oil. Perfect for brunch, cocktails, or...



It's a Long Road to a Tomato: Tales of an Organic Farmer Who Quit the Big City for the (Not So) Simple Life
by Keith Stewart

Twenty years ago, just beyond his 40th birthday, Keith Stewart exchanged life in New York's corporate grind for a farm in Orange County, NY, where he and a small crew of seasonal workers grow about 100 organic vegetables and herbs. What started as a yearning—"to live on a piece of land, closer to nature; to work outside with my body as well as my brain; to leave behind the world of...

© 2008 BrightSurf.com