Salk Institute for Biological Studies: InsideSalk

Arabidopsis Takes Root: Hunting for Missing Genes

All of these findings would not have been possible without studying plant genetics, Chory says. But they were conducted by studying one gene at a time to determine its function. That all changed beginning in late 2000 when a team of scientists around the world completed the Arabidopsis genome-sequencing project.

Joe Ecker, a leading plant geneticist and professor in Salk's Plant Biology Laboratory, was part of a team of multi-national scientists that helped sequence the plant's approximate 25,500 genes. Knowing the gene sequence now enables plant biologists worldwide to study the genome as a whole, he says.
Having the genome sequenced doesn't necessarily tell scientists each gene's function, however. But a major project in Ecker's lab recently funded with a $4 million grant is chipping away at this mystery. The long-term goal is to develop a database that describes the role and cross-function of all 25,500 genes through a network of researchers who will test mutant forms of Arabidopsis genes, a standard trick to determine their function.

"What we'll be able to start to see is an interconnection of the biology that you might not ever test if your particular lab only works on [response to] light," Ecker explains. "But if you can see that someone else found that the mutation affects another process, then you can say, 'I found a new connection.' The idea is to integrate the biology through the gene networks."

A valuable and highly used resource for gene testing is readily available through the Salk Institute's Genomic Analysis Laboratory, which preserves a massive collection of Arabidopsis gene mutations, copies of which are used for research worldwide.

Just steps away from Ecker's office is the temperature-controlled room that houses what is perhaps the world's largest bank of Arabidopsis seeds that represent 400,000 insertions, or points on the genome where bacterial "transfer-DNA," or T-DNA, entered and caused a unique gene mutation.

Ecker developed the sophisticated technique that enables his lab to identify the exact location of each insertion point. In 2003, Science published the revolutionary study, which has since been cited more than 1,100 times and is ranked No. 14 among ISI's highly cited, "Super Hot" papers.

"The plant biology world knows Salk because the Institute is linked to these seeds," Ecker says. "But again, by using Arabidopsis as the reference plant, the functions of its genes can be determined by studying their mutations. By having a complete genetic guide to Arabidopsis, we can then apply that knowledge to other plants like soybean or wheat."

Of course, being able to develop a genetic reference book for Arabidopsis assumes that the structures and functions of all the genes in the genome are known. But this isn't the case, Ecker says. Although plant biologists now have the genome, Ecker estimates that the exact structures for many of the genes are still waiting to be discovered.

How is this possible? Some genes are expressed at very low levels and their signals can't always be detected. To hunt them down, Ecker's lab developed powerful high-throughput DNA sequencing technology. The new-generation sequencing machine maps the precise location of the missing genes by isolating their byproduct: RNA.

"By performing a deep sequencing of the transcriptome, we're asking the genome to tell us, 'Where are your genes?' " Ecker says.

This is an ongoing project in his lab, but others in the scientific community have taken notice of this new tool.

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InsideSalk 10|08 Issue | © Salk Institute for Biological Studies