July 11, 2011 A high quality draft sequence of the potato genome has been published in the journal Nature.
The Potato Genome Sequencing Consortium (PGSC), an international team of scientists -- including Teagasc representing Ireland -- whose goal was to develop a high quality draft sequence of the potato genome, has just published its findings. The PGSC was initiated in January 2006 by the Plant Breeding Department of Wageningen UR (University & Research Centre) in the Netherlands and, during the course of the project, developed into a global consortium of 29 research groups from 14 countries. The Teagasc group, led by geneticist Dr. Dan Milbourne of the Crops, Environment and Land Use Research programme, based at Oak Park in Carlow, was amongst the earliest members of the consortium.
In addition to its continued importance to the Irish diet, potato is the world's third most important food crop. It is a key member of the Solanaceae family of plants which includes tomato, pepper, and aubergine. The potato genome sequence, the "genetic blueprint" of how a potato plant grows and reproduces, will assist potato scientists and breeders improve yield, quality, nutritional value and disease resistance of potato varieties, a process that has been slow in this genetically complex crop. The potato genome sequence will permit potato breeders to reduce the 10-12 years currently needed to breed new varieties. The study has also yielded valuable insights into the biology and evolution of potato; significantly how expansion of particular gene families has contributed to the evolution of the potato tuber -- the edible storage organ that is the most striking feature of this important crop plant.
The Teagasc group contributed directly to the whole genome sequencing effort, and also performed an in-depth analysis of a region on chromosome 4, which harbours genes that confer natural resistance to late blight and the potato cyst nematode, the two most significant limitations to potato production.
"The biological insights afforded by the genome sequence are fascinating, but Teagasc's main interest in participating in the project was to utilise the data to breed better potato varieties," said Dr. Milbourne. "We've already started to exploit the knowledge of the chromosomal location of naturally occurring disease-resistance genes in the Teagasc potato breeding programme, using an approach called marker assisted selection (MAS). "This will increase our ability to breed highly disease-resistant potato varieties -- later we should be able to expand this to more genetically complex characteristics such as cooking quality and nutrient uptake by the plant to reduce fertiliser use, which can be very difficult to breed for."
"Teagasc has been breeding potatoes for over 40 years and, together with our commercial partners, Irish Potato Marketing, we've had some notable successes with cultivars such as Rooster and Cara," said Teagasc potato breeder Dr Denis Griffin.
"The capacity to combine cutting edge genomics-based technologies like MAS with our expertise and experience in traditional breeding methods will contribute significantly to our continued success in developing high quality potato varieties for both Irish and international markets."
In late 2009, the PGSC released a preliminary draft sequence of the potato genome online. Since that time the PGSC has been refining the genome assembly, as well as performing exhaustive analysis and interpretation of the data. The genome assembly covers approximately 95% of the genes in potato, and was facilitated by radical advances in DNA sequencing technology that have occurred over the past few years, and new software developed by the Beijing Genomics Institute, one of the Chinese partners in the PGSC. Analysis of the genome sequence data has revealed that the potato contains approximately 39,000 protein coding genes. For over 90% of the genes the location on one of potato's 12 chromosomes is now known. The potato genome assembly and other resources are now available in the public domain at www.potatogenome.net, where a complete listing and contact details for all PGSC members can be found.
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- The Potato Genome Sequencing Consortium. Genome sequence and analysis of the tuber crop potato. Nature, 2011; DOI: 10.1038/nature10158
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