Sequencing the 'gene space' of potato chromosome IV

The Potato Genome Sequencing Consortium (PGSC) was an international collaboration that formed to sequence the 'gene-rich' regions of the potato genome by the end of 2010. The UK effort was focussed on chromosome IV. 

The genome of the potato, in common with other organisms, is comprised of a series of ‘bases’ often referred to by the letters A, C, T and G that are linked together in ‘strings’ called chromosomes. One copy of the potato genome is 850 million bases spread over 12 chromosomes and which encode approximately 39,000 genes. Each potato variety has four, often highly distinct copies of each of these genes. An important aspect of the PGSC’s work was the use of a ‘doubled monoploid’ (DM) clone of the Phureja group of potatoes which has two identical copies of each gene. This clone was made some time ago in the USA by making a ‘monoploid’ with only one set of chromosomes then doubling it using tissue culture techniques. Phureja types are virtually identical to conventional potatoes in their genome sequence and the use of DM made the task of sequencing the genome much simpler.

Potato DNA is isolated by a simple procedure used for all plants, and then it is physically ‘sheared’ into small pieces using a sonication process. The small DNA fragments are then sequenced using NGS technology which can sequence about 1 million small fragments of DNA at one time. The major task is in ‘assembling’ the genome which involves matching millions of short sequences to find the overlaps between them to build larger and larger sequence ‘contigs’, a highly computationally intensive task only possible with sophisticated software and massive computing power. Another major step in the genome analysis is known as ‘annotation’, the process by which the genes are identified and if possible ascribed a putative function based on the sequence similarity to genes from other species and certain other sequence features.

Prior to sequencing the genome, the PGSC had developed a very dense ‘genetic and physical’ map of potato whereby the genetic position of a large number of markers was known in relation to ‘physical’ locations of genome features. However this effort did not tell us about the specific genes contained in a potato variety, and it is the genes that are responsible for all potato traits. Nor did it tell us where the genes reside in relation to the locations of previously analysed traits such as tuber quality and disease resistance. A full genome sequence provides the exact location of the genes in relation to genetic maps and the markers they contain. Once we know the location of a trait gene, say tuber shape, we can use the locations of markers near the trait ‘locus’ to see directly into the genome and identify the genes that may be responsible for the trait.

In July 2011 the international team of scientists from 14 countries published the full potato genome sequence in the journal Nature. A technical summary report is provided below.

A project funded by Defra, AHDB Potatoes, Scottish Government and BBSRC to support the British component of the Potato Genome Sequencing Consortium.