DNA technique and plant evolution

03 March 2008

Scientists have used a DNA technique, originally developed for use in agriculture, to detect genetic diversity in wild plants.

Reported in the journal PLoS ONE, it is the first trial of the technique in undomesticated plants and the results give new insights into plant evolution and prove useful in detecting hybrid plants.

Diversity Arrays Technology

Natural History Museum botanists, working together with an Australian company, employed the technique called Diversity Arrays Technology (DArT) to investigate evolution in wild plants.

DArT builds on an existing technique called a DNA micro-array that is used to detect small genetic differences among people and other organisms for which the full genome sequence is known. DArT uses micro-arrays in a new way to detect differences even without prior knowledge of the genome.

DArT was originally used to locate, or 'map', desirable traits in economically important crop plants such as rice and barley.  However, Museum geneticist, Dr Karen James, realised its potential to help us understand and conserve the diversity of wild organisms as well.

'In 2003, I came across a conference abstract about DArT being used to detect natural genetic variation in rice,' said Dr James.  'Unlike other micro-array techniques that I knew about, DArT didn't require any prior knowledge about an organism's genome.  That got me really excited because it meant DArT could be used to detect genetic variation in any organism, not just in the handful of lab organisms that have had their genomes sequenced.'

Testing the technique

Dr James formed a partnership with Dr Andrzej Kilian, the inventor of DArT and director of Diversity Arrays Technology Pty Ltd, to test the technique on two trial groups of undomesticated plants. 

The green spleenwort Asplenium viride and the moss Garovaglia elegans were chosen for the trial to reflect existing Botany Department areas of expertise.  Prof Harald Schneider, Dr Johannes Vogel and Dr Stephen Ansell are actively researching the evolution of Asplenium and Dr Angela Newton and Dr Niklas Pedersen the evolution of Garovaglia.  They assembled an appropriate selection of specimens and posed specific evolutionary questions to be addressed by the DArT technique.

Results

Using DArT, the team found over 1000 new variable sites in the genomes (that is, fragments of DNA both within and between genes) of the two test groups. Follow-up studies on nearly 150 of these sites showed that about 20% have known cellular functions based on comparison with GenBank, a database of DNA sequences from all kinds of organisms.

Identifying new variable sites such as these helps scientists investigate the evolutionary relationships within and among species. For example, geography and habitat type were confirmed to be important factors in the evolution of Asplenium viride.

Detecting hybrids

The team also found that the technique can detect hybrids, a notoriously difficult task in plants. This would have practical applications in biodiversity conservation, for example, to detect hybrids between native and non-native plants.

'Our research shows that DArT is a valuable addition to the molecular toolkit used by evolutionary biologists to understand the relationships between organisms and the evolutionary processes that result in those relationships,' said Dr James. 

'We hope that our study will give other scientists the confidence to jump onto this new technique and start using it to study not just ferns and mosses but all kinds of organisms, ultimately leading to better understanding and conservation of biodiversity.'