A  WONDERFUL  WEED  AND  SOME  LESS  WONDERFUL  HYPE

If you thought nothing could top the hype generated by the sequencing of the human genome, then watch out!

The first complete DNA sequence for a plant is already being described as something that “could have more impact than its human equivalent”.  Pretty amazing when you consider the human equivalent was meant to cure all diseases known to man etc. etc.

But as the ‘wonder weed’ hype begins, note in the New Scientist piece below a little humility:

“But finding out the roles for the multitude of unknown genes won’t be easy, explains Zabeau.  In knockout experiments, duplicate genes can make life tough. When one copy is knocked out, its unaffected doppelganger elsewhere in the genome steps in to do its job, making it impossible to figure out what the knocked-out gene does. “What we see is that only 10 per cent of knockouts show any clearly observable [features],” says Zabeau.

And, just as interestingly, in the article’s final paragraph:

“...by identifying genes linked with important traits, it may be possible to find wild plants already carrying the trait simply by examining their genes. The traits could then be cross-bred into related crops without genetic engineering.”

This is exactly what happened with so-called “super-broccoli”. The required results were achieved without any use of GM - despite all the previous (and continuing!!) hype about only GM making such plant breeding possible with broccoli.

[https://members.tripod.com/~ngin/broccoli.htm]

So less hype, more subtlety, please!
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New Scientist - More at: Nature (vol 408, p 796, p 816, p 820 and p 823)
http://www.newscientist.com/news/news.jsp?id=ns226920

It’s a wonderful weed

IT MAY be just a few centimetres high, but a frail weed this week became a colossus of plant science. Arabidopsis thaliana, otherwise known as thale cress, is now the first plant to have its genome fully sequenced.

A worldwide consortium of botanists crowned a 10-year effort by publishing the full genome of Arabidopsis in the journal Nature. They expect it to yield vital information on the genetic secrets of all plants, helping scientists to transform crop plants so the world can be fed with less harm to the environment.

“It’s a huge milestone,” says Jeff Dangl, a member of the consortium based at the University of North Carolina in Chapel Hill, who has been studying how Arabidopsis defends itself against plant pests. “It’s a launch pad for understanding all plant biology, and we hope in the next 10 years or so to work out what every plant gene does.”

Arabidopsis joins the elite but rapidly growing club of sequenced organisms. Other members include the fruit fly, the nematode worm, 30 or so bacteria, brewer’s yeast and, of course, a “working draft” of Homo sapiens. Biologists can now compare these genomes to learn what they have in common, what makes them different, and where their paths crossed during evolution.
So why thale cress? For a start, it’s easy to grow in the lab and doesn’t need much space. Each plant takes just 6 weeks to grow and produce as many as 5000 seeds. Botanists can knock out genes at will, and see the consequences within weeks. This reveals the function of the missing gene.
More importantly for genetics, the weed’s genome is unusually compact.  Its 115 million pairs of nucleotide-base building blocks span five chromosomes and include some 26,000 genes. This makes it 30 times smaller than the human genome, and many times smaller than most plant genomes too, including those of crop plants.

Amazingly for such a tiny genome, as much as 58 per cent of it consists of duplicated genes. This is because when Arabidopsis evolved around 100 million years ago it merged two sets of chromosomes into one, giving duplicates of almost every gene.

“Plants are very promiscuous internally and among relatives,” says Marc Zabeau, a member of the consortium at the University of Ghent in Belgium. This gene duplication is thought to help plants develop new gene functions. “It’s like having a spare you can play around with,” Zabeau says.

Although the consortium now has the complete genome, their work is far from done New Scientist, 2 December, p 36). “Of the 26,000 genes, only 3000 have been experimentally studied so far,” says Mike Bevan, a key member of the consortium at the John Innes Centre in Norwich.
But those that have been studied have already thrown up some surprises.  Some 200 Arabidopsis genes have been found that resemble human genes linked with disease. These include genes for repairing DNA—which trigger cancer if damaged—and others linked to ageing. There’s even a counterpart of Separation anxiety, a gene linked with behavioural disorders.

Arabidopsis also seems to have inherited a large chunk of DNA—some 800 genes—wholesale from cyanobacteria, photosynthetic microbes which pre-dated plants. Most of these genes are vital for photosynthesis, the process by which plants harness energy from sunlight to make their food.
But many of the genes in Arabidopsis—around 30 per cent—are different to anything so far seen in other sequenced organisms. Different too, are the regulatory regions—the plethora of switches and promoters that turn genes on and off.

Already, discoveries in Arabidopsis have helped botanists to improve crop plants. These include genes to protect wheat against disease, ripen tomatoes and double yields of rapeseed oil.
But finding out the roles for the multitude of unknown genes won’t be easy, explains Zabeau. In knockout experiments, duplicate genes can make life tough. When one copy is knocked out, its unaffected doppelganger elsewhere in the genome steps in to do its job, making it impossible to figure out what the knocked-out gene does. “What we see is that only 10 per cent of knockouts show any clearly observable [features],” says Zabeau.

Knowing the entire genome might solve this problem. Researchers could identify any copies of a gene and neutralise them all with “antisense” copies that bind to the genes and inactivate them.
The researchers acknowledge that some environmental groups may continue to oppose attempts to improve plants by swapping genes around. But they believe that by identifying genes linked with important traits, it may be possible to find wild plants already carrying the trait simply by examining their genes. The traits could then be cross-bred into related crops without genetic engineering.

“As far as GM is concerned, the genome adds knowledge to the debate,” says Bevan.
“Genetic transformation is just one particular wrench in the biotechnology tool box. We have lots of other tools to accelerate the development of new wheat varieties.... It’s a numbers game and ultimately non-transformation [ie non-GM] biotech offers the greatest potential.”

- Tom Crosbie, Monsanto’s global head of plant breeding

“We have come a long way, but we can go much further with conventional breeding to obtain higher yields and better disease resistance and grain quality.”
-  Professor John Snape of the John Innes Centre (Farmers Weekly, 10 March 2000)

“Oilseed crops can replace oil from non-renewable fossil sources and genetically modified crops need not play any role in the revolution.  This is a novel strategy that is not widely appreciated as yet. But it could provide a real alternative to the use of GMOs. This approach could enhance agricultural diversity and supply us with valuable, renewable products for as long as the sun shines on the earth.”
- Professor Dennis Murphy, Head of Brassicas and Oilseeds Department, John Innes Centre (Annual conference of the British Association for the Advancement of Science, 1998)