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A QUICK and cheap way of comparing genomes could transform animal and plant
breeding programmes and conservation efforts, especially in developing
countries.

“It could have an enormous impact,” says Peter Langridge of the Waite
Agricultural Research Institute in Adelaide, South Australia. “In a single
assay, you can survey the entire genome of an individual.”

The technique, called diversity array technology, or DArT, was developed by a
team lead by Andrzej Kilian of the Center for the Application of Molecular
Biology to International Agriculture in Canberra.

DArT works by using certain enzymes to chop up the genome of an animal or
plant, and then fixing those fragments to a glass slide. The genome to be
compared is chopped up in the same way and the fragments are washed over the
glass. Where the second genome differs from the first, the enzymes will break up
the DNA differently. Complementary DNA sequences stick together, so examining
the slide will reveal where fragments have paired up and where the two genomes
differ. “It’s insanely simple. It’s shocking no one thought of it before,” says
Kilian. “In a few days, you can analyse a fair-sized population.”

John Gibson of the International Livestock Research Institute in Nairobi
hopes to use DArT to survey local breeds of cattle as part of an international
drive to conserve livestock with useful traits such as resistance to disease.
“You need genetic diversity information to make strategic decisions, to maximise
the diversity that is conserved,” he says. “We’re hopeful [DArt] can reduce
costs by five to tenfold.”

Common techniques for surveying the genetic differences between individuals
are costly and can take months. And while gene chips can detect variations
within hours, creating such chips depends on multimillion-dollar sequencing
efforts. This means they will only be available for species that are
commercially important.

“Cowpea is a crop of the very poor, and it’s Africa-specific, so there’s been
zero sequencing,” says Kilian. DArT could be used to identify genetic “markers”,
even though the sequence will remain unknown. That will make it much easier to
breed strains with, say, improved drought resistance.

DArT could also be used to work out the diversity within a population of wild
animals or plants. Studying genetic diversity can reveal whether a population is
under threat. “There’s been no [simple] scientific way to do this until now,”
says Langridge.

Kilian estimates that it will only cost a few dollars to test each animal or
plant with DArT once the necessary equipment has been bought. The team has
applied for an international patent. “We hope to get a good price from wealthy
corporations, but for many African labs it would be free of charge,” says
Kilian.