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A Model System

The report Kay and his colleagues published appeared at the same time as the report of the Arabidopsis genome was published in the journal Nature, another milestone in the history of genomics, since Arabidopsis is the first plant to have its full genome sequenced.

There are many reasons why this work is important. Genetic variations between particular strains of Arabidopsis may shed light. It may enable us to understand why some strains of a particular plant are different than others and find ways to use those differences to, for instance, make the plants flower more often.

Sequencing several plant genomes will allow us to access diversity in plants. The genetic codes of several different species can be compared to one another in the not too distant future, and the rice genome is right around the corner, due to be finished some time in the next couple of years. Another genome, the legume Lotus japonicus, is being sequenced along with its nitrogen fixing bacteria in the interest of uncovering the genetic basis for this cooperative nitrogen fixing.

Such comparisons promise to be directly relevant to our lives in many ways, not the least of which is the possibility that we will use what we learn to boost food production. “The danger of running out of arable land is very real,” says Kay, “and we have to solve the problem of feeding an rapidly increasing population in the next 10 years.”

Certain crop species may eventually be modified by incorporating diverse plant genes into crop plant genomes so that the conditions under which they can be grown are broader. Perhaps plants can be made to bear fruit faster and in larger and more nutritious yields. “Understanding plant diversity from genome sequences is going to have a huge effect on the whole of biology,” says Kay. “People should not put their heads in the sand.”

Arabidopsis is a good model organism for several reasons. It is tiny and has a fast generation time, both of which fit well in the modern tight-on-space-and-time laboratory. It also produces an overabundance of seeds at the end of its reproductive cycle. Finally, as a weed, Arabidopsis is easily grown.

Plant genomics stands to benefit more than just the vegetables of the world. As more and more genomes are solved, comparisons across genomes will become commonplace, with discoveries in one informing on mysteries in others.

Studies involving the circadian control of Arabidopsis have direct relevance to studies in humans because, in theory, genes similar to those that exhibit daily fluctuations in another species could undergo the same sort of rhythms. The first human circadian disorder, a mutation in the gene hPer2, was identified this year in people with familial advanced sleep phase syndrome, a type of insomnia. There is a similar gene to hPer2 in Drosophila melanogaster, which makes the fruit fly an excellent system for subsequent studies that will not just seek to understand sleep and wake cycles but find ways to address disorders associated with those cycles.

Likewise other human genes will no doubt find their long lost cousins in Arabidopsis. Genetically, the tiny Arabidopsis plants are more similar to humans than the genomes of yeast and the nematode. There are 11,000 different types of gene families in the Arabidopsis genome, and many of these genes have their counterparts in humans.

With its 25,498 genes spread over some 115 million base pairs of DNA and organized into 5 chromosomes, Arabidopsis has a very dense genome, which Kay speculates is insurance against the deleterious effect of mutations or genetic diversity to combat pathogens and fungi. “Quite a large part of this genome seems to be dedicated to combating things that nibble on it,” he says.

Moreover, says Kay, there are remarkable similarities between the innate immunity of plants and that of humans. A lot of the molecules that plants use to recognize pathogens are similar to molecules in the human body that perform tasks of innate immunity recognition performed by phagocytes.

At the same time, there are some 8,000 other genes that have been annotated but have no known function and no corresponding gene in some other organisms. Only time will tell what these genes will tell us. But Kay sees a bright future.

“The Arabidopsis genome will ultimately have equal effect on improving the health and welfare of the population as the human genome sequence,” he says. “I truly believe that.”


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Arabidopsis began appearing in scientific literature in the late 1800’s, and has been used as a model plant system for over half a century. The plant emigrated to American laboratories with George Rédei in 1957 when he carried their seeds with him in a plastic pouch as he swam out of Hungary. (Drawings from the Bilder ur Nordens Flora of Arabidopsis thaliana by Carl Axel Magnus Lindman, courtesy of Project Runeberg.)







For more Information:

The Kay Lab

The Arabidopsis Information Resource

The Nature issue in which the Arabidopsis genome appears

The Science issue in which the Arabidopsis circadian study appears