Potato is a member of the Solanaceae, a plant family that includes several other economically important species, such as tomato, eggplant, petunia, tobacco and pepper. The Potato Genome Sequencing Consortium (PGSC) aims to elucidate the complete genome sequence of potato. Potato is an important global food source. After wheat and rice, potato is the third most important food crop, with a world-wide production of 309 million tons in 2007 . By 2020 it is estimated that more than two billion people worldwide will depend on potato for food, feed, or income. Optimization of production levels and resistance to biotic and abiotic stresses are key objectives of global potato breeding programs.
The potato has one of the richest genetic resources of any cultivated plant . The tuber-bearing Solanum species are very widely distributed in the Americas, from the South Western USA to Southern Chile and Argentina and from sea level to the highlands of the Andes Mountains. Many wild species can be crossed directly with the common potato and moreover, possess a wide range of resistances to pests and diseases, tolerances to frost and drought and many other valuable traits, making them a useful resource for breeding new cultivars.
However, potato genetics is complicated by its polyploid genome and many important qualitative and quantitative agronomic traits are poorly understood. Yet, an understanding of its genetic composition is a basic requirement for developing more efficient breeding methods. The potato genome sequence will provide a major boost to gaining a better understanding of potato trait biology, underpinning future breeding efforts.
Worldwide, an economic loss on the potato crop of about €3 billion per year is estimated from diseases such as late blight. These diseases are still largely controlled by frequent application of fungicides. It is expected that one of the first benefits of a potato sequence will be a major breakthrough in our ability to characterize and select genes involved in disease resistance.
Potato Genome Sequencing Consortium
The potato genome consists of 12 chromosomes and has a (haploid) length of approximately 840 million base pairs, making it a medium-sized plant genome.
A high quality, well-annotated genome sequence of potato, combined with established mapping techniques and the continuing advances in high throughput analyses of the transcriptome, proteome and metabolome promises to radically enhance our ability to identify the desirable allelic variants of genes underlying important quantitative traits in potato. The Potato Genome Sequencing Consortium (PGSC) seeks to provide such a resource to the potato research and breeding community in the near future, allowing the full potential of biotechnology-based improvement of this important crop plant to be realized.
The international Potato Genome Sequencing Consortium (PGSC) is a collaboration between 16 research groups; Argentina, Brazil, China, Chile, India, Ireland, The Netherlands, New Zealand, Peru, Poland, Russia, the United Kingdom and the United States. The PGSC has its basis in long-standing research on the molecular genetics of potato within the partner organizations, ranging from the construction of genetic linkage maps in diploid and tetraploid potato.
The PGSC is sequencing two varieties:
The PGSC originally started out with sequencing RH. This part of the project builds on a diploid potato genomic bacterial artificial chromosome (BAC) clone library of 78,000 clones, which has been fingerprinted and aligned into ~7000 physical map contigs. In addition, the BAC-ends have been sequenced and are publicly available. Approximately 30,000 BACs are anchored to the Ultra High Density genetic map of potato, composed of 10,000 unique AFLPTM markers.
From this integrated genetic-physical map, between 50 to 150 seed BACs have currently been identified for every chromosome. Fluorescent in situ hybridization experiments on selected BAC clones confirm these anchor points. The seed clones provide the starting point for a BAC-by-BAC sequencing strategy. This strategy is being complemented by whole genome shotgun sequencing approaches using both 454 GS FLX and Illumina GA2 instruments. Assembly and annotation of the sequence data will be performed using publicly available and tailor-made tools. The availability of the annotated data will help to characterize germplasm collections based on allelic variance and to assist potato breeders to more fully exploit the genetic potential of potato.
Sequencing of DM was started because the overall progress in RH was slow. The heterozygosity of RH has limited the progress of physical mapping and will complicate the assembly of the genome sequence. Whole genome shotgun sequencing of DM1-3 516R44 (CIP801092), a doubled monoploid potato clone, is expected to eliminate the complexity in assembly.