Sequencing the potato genome: outline and first results to come from the elucidation of the sequence of the world's third most important food crop

• Published in: American journal of potato research 2009, Vol.86 (6), p.417-429
• Main Authors: Visser, R.G.F, Bachem, C.W.B, Boer, J.M. de, Bryan, G.J, Chakrabati, S.K, Feingold, S, Gromadka, R, Ham, R.C.H.J. van, Huang, S, Jacobs, J.M.E, Kuznetsov, Boris, Melo, P. de, Milbourne, D, Orjeda, G, Sagredo, Boris, Tang, X
• Format: Article
• Language: English
• Subjects: Agriculture; amplified fragment length polymorphism; bacterial artificial chromosomes; bacterial wilt; Biomedical and Life Sciences; broad-spectrum resistance; chromosome mapping; chromosomes; cytogenetics; disease resistance; DNA fingerprinting; fluorescence in situ hybridization; gene-cluster; genetic markers; genome; haploidy; international cooperation; late blight resistance; Life Sciences; molecular sequence data; nucleotide sequences; phytophthora-infestans; Plant Breeding/Biotechnology; plant genetic resources; plant genetics; Plant Genetics and Genomics; Plant Pathology; Plant Sciences; Potato Genome Sequencing Consortium; potatoes; quantitative trait loci; Review; Solanum tuberosum; solanum-bulbocastanum; system; tomato
• ISSN: 1099-209X; 1874-9380
• DOI: 10.1007/s12230-009-9097-8

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, the third most important food crop in the world. The PGSC is a collaboration between 13 research groups from China, India, Poland, Russia, the Netherlands, Ireland, Argentina, Brazil, Chile, Peru, USA, New Zealand and the UK. 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. The sequencing project builds on a diploid potato genomic bacterial artificial chromosome (BAC) clone library of 78000 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 30000 BACs are anchored to the Ultra High Density genetic map of potato, composed of 10000 unique AFLP TM 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.