Comparing genomes of wild and domestic tomato

Jun 26, 2013
Researchers can now compare not only the genomes, but all the genes expressed, by domestic and wild tomatoes. L to R: Solanum lycopersicum, and wild relatives S. pimpinellifolium, S. habrochaites and S. pennellii. Credit: Brad Townsley, UC Davis.

You say tomato, I say comparative transcriptomics. Researchers in the U.S., Europe and Japan have produced the first comparison of both the DNA sequences and which genes are active, or being transcribed, between the domestic tomato and its wild cousins.

The results give insight into the genetic changes involved in domestication and may help with future efforts to breed new traits into tomato or other crops, said Julin Maloof, professor of plant biology in the College of Biological Sciences at the University of California, Davis. Maloof is senior author on the study, published June 24 in the journal Proceedings of the National Academy of Sciences.

For example, breeding new traits into tomatoes often involves crossing them with wild relatives. The new study shows that a large block of genes from one species of wild tomato is present in domestic tomato, and has widespread, unexpected effects across the whole genome.

Maloof and colleagues studied the domestic tomato, Solanum lycopersicum, and wild relatives S. pennellii, S. habrochaites and S. pimpinellifolium. Comparison of the plants' genomes shows the effects of evolutionary bottlenecks, Maloof noted—for example at the original domestication in South America, and later when tomatoes were brought to Europe for cultivation.

Among other findings, genes associated with fruit color showed among domesticated, red-fruited tomatoes and green-fruited wild relatives. And S. pennellii, which lives in desert habitats, had accelerated evolution in genes related to , heat and salinity.

New technology is giving biologists the unprecedented ability to look at all the genes in an organism, not just a select handful. The researchers studied not just the plants' DNA but also the messenger RNA being transcribed from different genes. RNA transcription is the process that transforms information in genes into action. If the DNA sequence is the list of parts for making a , the messenger RNA transcripts are the step-by-step instructions.

Gene-expression profiling, combined with an understanding of the plants' biology, allows researchers to understand how genes interact to create complex phenotypes, said Neelima Sinha, professor of plant biology at UC Davis and co-author on the paper.

"Genomics has fast-tracked previous gene-by-gene analyses that took us years to complete," she said.

"We could not have done a study like this ten years ago—certainly not on any kind of reasonable budget," Maloof said. "It opens up a lot of new things we can do as plant scientists."

Explore further: Iberian pig genome remains unchanged after five centuries

Related Stories

Red tomatoes thanks to meteorite

Jun 08, 2012

(Phys.org) -- The meteorite which crashed into the Earth 60 to 70 million years ago, wiping out dinosaurs, had probably given us nice red tomatoes as well. This can be deduced from a tomato genome analysis, published on 30 May in Nature. ...

Tomato genome fully sequenced

May 30, 2012

For the first time, the genome of the tomato, Solanum lycopersicum, has been decoded, and it becomes an important step toward improving yield, nutrition, disease resistance, taste and color of the tomato and ...

Process that controls tomato ripening discovered

Jan 30, 2013

(Phys.org)—Everyone loves a juicy, perfectly ripened tomato, and scientists have long sought ways to control the ripening process to improve fruit quality and prevent spoilage.

Recommended for you

Iberian pig genome remains unchanged after five centuries

18 hours ago

A team of Spanish researchers have obtained the first partial genome sequence of an ancient pig. Extracted from a sixteenth century pig found at the site of the Montsoriu Castle in Girona, the data obtained indicates that ...

New concepts based on advances in animal systematics

21 hours ago

The way in which most multicellular organisms have been classified has been the same for more than a century. Only recently have scientists developed the tools and knowledge to question the way we classify ...

New dawn for pasta wheat in Australia

Sep 17, 2014

The University of Adelaide's durum breeding program today at the Hart Field Day will release a new durum wheat variety called DBA-Aurora which promises a step-change in potential durum production in southern Australia.

User comments : 0