The Food Standards Agency is supporting the project, ‘Development of a standard, validated procedure for the isolation of transgene flanking regions in genetically modified (GM) crops and detailed analysis of transgene insertion’, for a period of two years as part of its G03 programme. The project is in collaboration with the group of Dr Wendy Harwood at the John Innes Centre Norwich and SCRI. The SCRI team consists of Danny Cullen, Howard Davies and Mark Taylor.

Methodologies for the production of GM plants are continually being improved such that there is greater control over the transformation process. However, one aspect of the process that cannot at present be controlled is the exact location of the transgene insertion within the host genome.

For this reason, analysis of the transgene insertion site is an important part of any safety assessment. By determining the genomic regions flanking the transgene insertion it is possible; by sequence alignment with published mapping, expressed sequence tags (EST) and sequence data; to determine the position of the transgene in the genome.

It can also determine whether any functional or regulatory genes have been disrupted and whether any new open reading frames (ORFs) have been created, resulting in the possible synthesis of novel proteins. Knowledge of the flanking sequences also provides information on unique identification sequences that can be used to detect the transgenic event in question (traceability).

There are currently a number of polymerase chain reaction (PCR) based protocols that have been used to isolate the genomic regions flanking transgenes. However, there is no standard, validated method that has been shown to be appropriate for a range of different GM plants and a range of different types of insertion.

The primary aim of this project is therefore to develop standard, validated procedures for the isolation of transgene flanking regions in a range of GM crops, with a range of different transgene insertion patterns. It is anticipated that the recommendations made in this proposal will be relevant to emerging regulations for the safe development of transgenic crops.

Work at SCRI will focus on lines of transgenic potato. For transgenic lines that contain single or low numbers of transgenes, several methods for determining the junction sequence have proved effective. These methods are now being applied to more complex situations where several transgenes have been introduced into potato.