Panning for golden genes
supermarket shelves despite the cynical consumer if policy-makers,
soon to take a decision on the sale of Syngenta's Bt11 GM maize ,
take a yes vote. A recent breakthrough in analysis used on maize
genomes could bring the seeds to market earlier.
Researchers in the US recently used two complementary methods that remove from analysis vast stretches of DNA that do not contain genes, thereby dramatically speeding up the process of decoding.
The approaches, applied jointly in efforts to determine the gene sequences in maize and carried out by two groups of researchers at The Institute for Genomic Research (TIGR) in Rockville, and Cold Spring Harbor Laboratory in New York, are described in the 19 December issue of the journal Science.
Only about a quarter of the maize genome codes for genes , and these are found in small clusters scattered through a mixture of non-coding DNA and transposons (mobile DNA segments).
Two different methods tested by the TIGR group successfully captured parts of the maize genome containing genes. The gene-sequences are of most interest because they provide the specific blueprint for an organism's development, structure and physiology.
With so much non-gene sequence to deal with, it has not been feasible to sequence and assemble the whole maize genome with current technologies. "Collecting the maize genes for sequencing is like panning for gold," said Jane Silverthorne, programme director for NSF's plant genome program. "Just as gold can be separated from the surrounding rock because it is denser, maize genes can be separated from the surrounding DNA by their chemical and sequence properties."
The first method tested called methylation filtration, developed by a team led by Robert Martienssen and Richard McCombie at Cold Spring Harbor laboratory, removes sequences that contain a chemical modification (methylation) found on most of the repeated sequences and transposons, leaving behind the proverbial gold of genes.
The second method, developed by researchers at the university of Georgia, removes the repeated sequences by separating the DNA into "high-copy," gene-poor segments and "low-copy," gene-rich segments.
Led by Cathy Whitelaw, the research team at TIGR compared sequences obtained by the two methods. About one fourth of the genes in each collection matched known gene sequences. About 35 per cent of the genes were represented in both collections.
As both methods yielded short stretches of sequence, a major challenge was to reassemble these into complete genes, report the researchers.
To do this, the Cold Spring Harbor group lined up the sequence pieces from maize along the rice genome sequence, a deep draft of which was completed in 2002 by an international consortium. The researchers then reassembled selected sets of sequence fragments into complete genes.
"Together, these findings suggest that scientists could be able to sift out the approximately 450 million base pairs of DNA containing the genes from the maize genome and then reassemble the sequence,' said Silverthorne.
Such a comprehensive genomic resource would provide growers and breeders a wealth of tools to improve maize, as well as other cereal crops, he added.
Earlier this month, a divided Europe saw member states failing to suppport the Commission proposal to authorise the first GM foodstuff - BT11 sweetmaize, a strain of genetically modified sweetcorn developed by Swiss firm Syngenta - since the de facto moratorium begun five years ago. The vote now passes to Europe's agriculture ministers and is expected to take place in early 2004.
Widespread opposition to GM foodstuffs in Europe has seen a food industry reluctant to take on board GM ingredients into their final food products.
