Genomic technologies are set to revolutionise plant biology and we have already seen significant advances in the rate of gene discovery and new ideas engendered by the sequencing of genomes from two model plants, Arabidopsis and rice. This is pushing the frontiers with new developments in biotechnology as plant scientists start to now try to understand what all the genes in these plants do and how we might manipulate them to improve our crops. Monsanto, for example, is reported to be developing new drought stress tolerance transgenes for crops that has come out of studies of master stress regulator genes first identified in Arabidopsis. Some of the research from these model plants will flow through to cotton but to achieve the maximum benefit, particularly in the area of fibre, as these biological structures are not found in rice and Arabidopsis, we must develop a capacity for genomic studies in cotton. CSIRO has taken the first steps in this direction by developing cDNA microarray technologies for cotton that will help us understand better what genes are important in fibre development as well as in other aspects of cotton biology.

Microarrays are formed by robotically depositing specific fragments of DNA (genes) at indexed locations onto glass microscope slides. The microarrays can then be probed with the genes expressed in particular tissues or under particular conditions that have been chemically tagged with a coloured dye. Scanning the slide can then tell you, by the colour of the spots where the DNA has been printed, how much each genes is expressed in those conditions – thousands of genes at a time, giving a whole picture of the differences in gene expression. Knowing what sequence and hence inferred function of the different genes on the slide can then tell you what genes expression is contribution to the problem under investigation.

This project has focussed on developing a microarray slide that contains unique representatives of large numbers of the genes expressed in cotton (concentrating on those expressed in fibres, but also some other tissues). While it will still be a long way from having all the genes present in cotton (Arabidopsis has at least 30,000 genes) it should have a large enough representation that it will be useful for dissecting many important problems in cotton biology and biotechnology. CSIRO had already printed and used a slide containing over 10,000 cotton genes, but only a small fraction had been sequenced. During this project we added new clones to the set and sequenced about a third of the genes and were able to get the rest sequenced by a collaborator in the US. To add to the genes we already had, we were able to purchase another 13,000 unique genes from the US Cotton Genomics Centre (Thea Wilkins, Director) and have been using bioinformatics programs to search through the gene sequences and weed out those that occur more than once, so that we can produce a so-called uni-gene set (where each different gene is only represented once). This allows us to put more informative genes on the slide as they currently have a limit of about 25,000 spots. The laborious process of amplifying up each gene to produce enough DNA to print hundreds of slides and checking that each gene has been amplified properly has been completed and all that remains now is to assemble the sequences into the unigene set ready for printing. The project has generated an important new tool for cotton researches and the array should contain about 25,000 unique genes - the biggest of its type for cotton available anywhere in the world. We will shortly start to use the slide in a project designed to discover what genes are important in determining fibre quality traits like length, strength and fineness and will hopefully help our breeder’s improve the quality of Australian cotton.