Major investments have been made in the last few years at SCRI and by research groups around the world to establish extensive catalogues of genes, as expressed sequence tags (ESTs) in crop plants and through whole genome sequencing of plant microbial pathogens.

Gene sequencing is only the first stage of linking genotype to important phenotypes and traits of interest. In order for these resources to be fully exploited in crop improvement and research programmes, high-throughput parallel monitoring of gene expression is essential.

Determination of co-ordinated changes in gene expression over time, throughout development, or in response to manipulation, stress or pathogens, will allow novel insights into how they respond to environmental challenges. The Microarray Facility at SCRI has led to the exploitation of gene expression profiling by many collaborative groups on-site.

Microarrays have been successfully applied to both plant pathogen (Pectobacterium) and crop (potato, barley, raspberry and blackcurrant) species. Studies include determination of pathogenicity factors, analysis of host-pathogen interactions, dissection of food quality traits, expression QTL (eQTL) isolation, characterisation of bud dormancy, microRNA expression and single-nucleotide polymorphism (SNP) discovery.

Next generation (non-Sanger) sequencing, including 454 (Roche) and Solexa (Illumina) are being utilised by SCRI research groups for deep transcriptional analysis in crop plant species. Such technologies are exploited through collaboration with Mark Blaxter at The Gene Pool, Edinburgh University. These ‘open’ transcriptomics platforms are not limited by pre-defined organism-specific gene sequences and can lead to discovery of novel low-abundance transcripts, small RNAs, alternative splicing events and SNPs for functional mapping studies.