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Major technological advances foreshadow 21st century genomics revolution

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Lunch with Brazilians­

Tree people: Leandro Neves (EMBRAPA, Brazil), Dorothy Steane (UTAS), Danielle Faria (EMBRAPA, Brazil) and Derek Drost (University of Florida).

­Dinner with SCU­

Australians enjoy Italian ambience in San Diego.  From left: Kimberley Ritter (formerly Southern Cross University (SCU), now living in USA), Rosanne Casu (SCU), Dorothy Steane (UTAS), Karen Aitken (SCU), Peter Bundock (formerly UTAS, now SCU) and Robert Henry (SCU).

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­ Dorothy Steane
University of Tasmania


Conference Report
Plant and Animal Genomes XVII
San Diego, California, USA
10-14 January 2009


Completed in 2003, the Human Genome Project (HGP) took 13 years and cost in the vicinity of three billion US dollars.  Originally estimated to take 15 years, rapid technological advances accelerated progress and cut two years from the project’s time line.  Just six years since the completion of the HGP the advances in DNA sequencing information technology are so huge that we are now contemplating sequencing individual human genomes in less than an hour for a cost of $US100.  This, and many other mind-blowing gems, was revealed to me in January at the seventeenth Plant and Animal Genome Conference (PAG), in San Diego, California, USA.

Each year PAG is held in sunny San Diego. For many people the Mediterranean climate of this city provides a welcome break from the rigors of the northern hemisphere winter.  For me, it was like going to Queensland’s sunshine coast in July – palm trees and all! – but with the added bonus of excellent Mexican food and Margaritas … not to mention an overwhelming amount of cutting edge science!

As its title suggests, this conference tends to be frequented by gene jockeys and genetics research managers of all persuasions. There were over 2300 delegates with interests ranging from sequencing technology through agricultural and industrial applications to population and conservation genomics.  Some are regulars who attend every year or two to keep up with the rapid and giant advances in technology and research, to attend satellite meetings of international collaborative groups and to catch up with old friends and colleagues.  There are many industry sales representatives peddling their wares and there are numerous fresh young graduate students who get blown away by the “awesomeness” of the whole experience.  
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Obviously, the conference was HUGE!  Each morning and afternoon started with a couple of plenary sessions by experts in various fields.  The best I saw was delivered by Professor Lee Hood from the Institute for Systems Biology (Seattle, Washington), who spoke about “Systems Biology and Systems Medicine”.  Prof. Hood and his team think BIG.  They are trying to revolutionise health care using a “P4” approach to medicine: Predictive, Preventive, Personalised and Participatory. Rather than taking a reactive approach to illness as we do at present, Hood’s vision involves examining the genetics and protein-profile of each individual, at regular intervals from birth onwards, to assess their probability of developing various diseases and initiating appropriate (preventative) treatments even before the onset of a disease. For more information on the P4 approach to medicine, click here.  A prototype of a health care system based on the P4 approach is being trialled in Luxembourg.  Prof. Hood has briefed President Obama’s transition team on the P4 vision (see related news item); it will be interesting to see whether anything radical happens to the USA's health system over the next five years!

After the plenary sessions the conference split into as many as ten concurrent workshops.  Some were just a few hours long, while others went for many hours.  For example, the Forest Trees Workshop, in which I presented my paper, went from 8 am until 6 pm with a half hour break for lunch (there were no plenaries that day).  The Forest Trees session included everything from a progress report on the Eucalyptus genome project to marker development and QTL discovery for economically important traits, to technology for viewing root structure without having to take the roots out of soil.  My presentation, “DArT markers herald a new era of Eucalyptus phylogenomics” aimed to inform the Eucalyptus genetics community of an international collaborative project, spearheaded and coordinated by the University of Tasmania and the CRC for Forestry, that has developed a large set of molecular markers called Diversity Arrays Technology (DArT) markers for Eucalyptus. DArT markers are very diverse in their applications and will be useful in assembling the Eucalyptus grandis genome sequence (that will be publicly available in 2010) and linking it to other Eucalyptus genomes.  Dario Grattapaglia, one of our collaborators from Brazil, presented some hot-off-the-press (completed at 4 am that morning!) genetic linkage maps from E. grandis showing the positions of over 3000 of our DArT markers (click here for abstract).  Other new developments included studies of “epigenetics” that have found microRNAs that influence gene expression by binding to messenger RNAs rather than directly affecting the transcription of DNA.  Genetic, proteomic and metabolomic studies are being used to understand mechanisms and timing of wood formation, dormancy and insect resistance.  Trendy network theory is being applied to genetic systems in trees to show interactions between mRNAs and transcription factors that influence insect resistance and growth traits.  For people working on Eucalyptus, CUGI (Clemson University Genomics Institute) are in the process of making BAC libraries from E. globulus that will be publicly available and can be ordered on line (see CUGI website).

Other workshops focused on swine, horses, fruit and nuts, pests and pathogens, weeds and invasive plants, wheat, barley, abiotic stresses, gene discovery, transcriptome analysis, proteomics, metabolomics, biofuel production … and the list goes on (and on and on!)  Some of the 105 industrial exhibitors also put on workshops (sweetened by free gifts such as chocolates, icecreams and memory sticks) to showcase the truly impressive advances in genomics technology, including next generation and solid platform sequencing. One technology that is currently being developed is called Single Molecule Real Time (SMRT) sequencing. It involves using a metal slide perforated with thousands of tiny holes, supported by a glass base through which we can ‘spy’ on a DNA synthesis reaction taking place in each of the holes (or wells).  Each well contains a single molecule of DNA-synthesising enzyme that makes DNA using fluorescent bases.  Each time a base is incorporated into the new strand of DNA there is a flash of light of a base-specific colour.  A computer can translate the coloured flashes into names of bases and thereby record the DNA sequence.  Easy!  This technology provides long, rapid, accurate reads that much easier for a computer to handle than the multitude of short reads produced by ‘next generation’ sequencing.  The company responsible for SMRT sequencing boasts that it will soon be possible to sequence a human genome in less than an hour for the cost of $US100.  A short (4 minute) video about SMRT sequencing can be viewed at the Pacific Biosciences Website.  A short article about the technology can be found here.

The abstracts from the conference can be found at http://www.intl-pag.org/.  The easiest way to find items of interest is to look at the conference program, pick out the authors of interest or the subjects of interest and then search the site (a search facility is provided on the front page of the conference website).

I would like to thank the CRC for Forestry and the University of Tasmania for conference support funding as well as the PAG Organising Committee and Sponsors for awarding me the Jerome P. Mikshe Tr­avel Grant.

Biobuzz issue eight, March 2009