UNDER THE MICROSCOPE:THE GENOME OF an organism is all the genetic information in the chromosomes of the organism. This genetic information is coded in DNA in sequences of chemicals called nucleotides, popularly called the letters of the genetic code, and these letters are grouped into words called genes. Sequencing the information in a genome is a massive first step towards understanding the entire genetic information that determines the organism. Several species have now had their genomes sequenced and, soon, another genome of particular relevance to Ireland will be sequenced.
The international Potato Genome Sequencing Consortium (PGSC) held its annual meeting at Teagasc Crops Research Centre, Oak Park, from June 10th to 12th. The PGSC is a group of nearly 20 research groups worldwide who have come together to sequence the entire potato genome by 2011. Results from this project have already allowed improved selection for resistance to the pest, potato cyst nematode, in the Oak Park potato-breeding programme run by Denis Griffin.
One of the most significant scientific endeavours in human history – the sequencing of the human genome – was completed in 2003. This multinational project determined the approximately three billion letters of the DNA-based genetic code of humans. Sequencing the genome was the first step in identifying the 20,000–25,000 genes that are responsible for all biological processes in humans. Completion of the human genome project has already enabled scientists to make inroads into finding some of the genes responsible for conditions such as leukaemia, Alzheimer’s disease, diabetes and heart disease. Genomics, the new science of identifying genes, is developing at a rapid rate.
The human genome project developed technologies and computer software that have vastly increased our speed and capacity to sequence DNA and it is now feasible to consider sequencing the entire genome of any organism, including our most useful crop plant species. This is no trivial task, since the genomes of some plants are bigger than the human genome. Already, the genome sequences of both Arabidopsis thaliana (a weedy plant used for genetic analysis in laboratories worldwide) and rice (the world’s most important food crop) have been determined. Genome sequencing projects are also under way for the world’s second, third and fourth most important food crops – wheat, maize and potato.
The potato, a plant with deep historical and cultural significance in Ireland, remains a staple food and the main source of carbohydrate in the Irish diet. The Teagasc Oak Park Research Centre is home to Ireland’s national potato breeding programme, which develops cultivars for both the home and foreign markets, and has had notable successes with varieties such as Cara and Rooster. In recent years a new plant biotechnology programme began at Oak Park, kick-started by a €4 million investment and the hiring of experienced researchers. One main goal is to exploit tools developed in human genome research and to apply them to develop innovative solutions to problems faced in Irish agriculture. Oak Park scientists Dr Dan Milbourne and Prof Jimmy Burke are participating in the international consortium of research groups whose goal is to sequence the entire potato genome. At 850 million nucleotides distributed over 12 chromosomes, the potato genome is just under a quarter the size of the human genome, and the consortium plans to have a first draft of the complete sequence very soon.
Teagasc hopes to exploit the genome sequence information to breed better potato varieties faster. It takes upwards of 12 years of crossing and selection to develop a successful potato variety combining all the characteristics desired by consumers, retailers and growers. Consumers are interested in texture, flavour and cooking quality, retailers are interested in uniformity of size and shape, and good skin quality, while growers seek potatoes with high levels of natural resistance to pests and diseases. Some of these traits, such as shape and colour of potato tubers, are controlled by relatively few genes, whereas others, such as disease resistance, flavour and cooking quality are controlled by complex interaction of many genes with the environment.
The goal of potato genomics research at Oak Park is to identify many of the genes responsible for these simple and complex characteristics. It will then be possible to identify potato plants which carry desirable genes, and cross these plants with each other to produce varieties which have all the desired characteristics listed above. Ultimately, sequencing the potato genome will result in a far greater choice of potatoes, and will change the way we look at (and use) the humble spud!
William Reville is associate professor of biochemistry and public awareness of science officer at University College Cork – http://understandingscience.ucc.ie
