Gene discovery and function

Science programme: Gene discovery and function

The Gene Function Discovery Team focuses on New Zealand fruit genes that have valuable traits for plant breeding and compound production. Gene functions are discovered using bioinformatics data from the HortResearch Expressed Sequence Tag (EST) database; over-expression and/or knockout technologies of selected genes in the model plant, Arabidopsis thaliana; and transient expression in the tobacco plant, Nicotiana benthamiana .

To link science to commercial prospects at the earliest stage, the team includes business development and intellectual property management personnel working alongside information navigators and science researchers. The science personnel encompass a wide skill range including bioinformatics and gene mining, biochemistry, protein chemistry, molecular biology, and pure chemistry. Our capability is also integrated with other existing teams at HortResearch including metabolomics, microarray, plant phenotyping, and proteomics.

The team has chosen to target genes involved in transcription regulation and secondary metabolite biosynthesis. The transcription factors serve to either turn other genes “on” or “off”, while the secondary metabolite biosynthesis genes are those that are directly involved in making a particular compound, in a particular cell, at a particular time. Both the biosynthetic genes and those that regulate them are therefore of importance for plant breeding and compound production.

The transcription factors that have been targeted to date include genes from the myb, b-zip, tubby, and basic helix-loop-helix families. These are being over-expressed in Arabidopsis to observe effects on plant development, and also undergo both microarray and metabolomics profiling to identify changes in RNA expression and compound production.

In addition, the transcription factor genes are screened against a panel of promoters, to identify those transcription factors that may regulate our specific genes of interest. In this discovery step, each promoter has been isolated from our gene of interest, and acts as a recognition base for the transcription factor to dock with it (or not) to turn the gene “on”.

Genes involved in secondary metabolite synthesis produce scaffold compounds that are then decorated with specific chemical groups to generate complex and very specific compounds e.g. the compound blend of ripe kiwifruit or apples. Secondary metabolite production involves a series of genes such as synthases, cytochrome p450s, and moiety-transferases. Each of these gene families is being targeted so that entire compound pathways may be modulated or reconstructed.

Plants have evolved to produce a large array of secondary metabolite compounds and these have a wide range of activities. Some key compounds of interest to HortResearch are the terpenes that provide fragrance, flavour, and compounds that affect human health and performance. However, our plants of interest produce many other compounds whose activities are yet to be discovered.

Within the Gene discovery and function team, we have identified three key horticultural targets;

• Colour and Health
• Dormancy, pereniality, bud break
• Plant response to cold and high temperature stresses

To do this we have developed transformation capabilities in two model plants.  These provide for rapid assignment of gene function and give us the opportunity to relate our work to the extensive knowledge and resources available in the public domain.

• Stable transformation in Arabidopsis thaliana
• Transient expression in Nicotiana benthamiana

To date we have developed an extensive collection of over 800 full-length transcription factors (TFs) from our fruit crops.  We have also developed techniques that allow us to identify the specific regulators of co-ordinately expressed genes. Key skill in the group include:

• mining of gene families and genomic DNA/unprocessed RNA;
• expression analysis (post-microarray analysis, qPCR and small RNA);
• phenotypic analysis, cell and whole plant physiology;
• Promoter Isolation and DNA cloning;
• Duel™ Luciferase Assays

Contacts Roger P. Hellens