Cross-species hybridizations to spotted microarrays as a tool for functional genomics of horticultural plants

Genomic-scale gene profiling using DNA microarrays has become a powerful approach for the study of gene expression in diversity of species. Nevertheless, for many species of interest, including many horticulturally important plants, ready made microarrays are still not available. Therefore, for functional genomics studies of such plants, a possible tool for gene expression profiling is the use of a microarray of a phylogenetically related organism for cross-species hybridizations (CSHs). We examined the ability of cross-species hybridization to reflect a biological process. As a benchmark experiment we generated two datasets: one of potato RNA hybridized to tomato microarray (CSH), the other of potato RNA hybridized to potato microarray (species-specific hybridization; SSH). Results were compared on a transcriptomic scale. The results demonstrated difficulties for the transcriptomic data obtained from CSH to reproduce the results obtained from SSH. Nevertheless, once the data were filtered for the matched probe sets, the CSH data showed higher consistency with that of the SSH and facilitated identification of significantly regulated genes, some of which were mutual to both CSH and SSH data. The considerations outlined as a result are serving for CSH of Brunfelsia flowers (a Solanaceae) with the potato microarray, resulting in further refinement of the approach of CSH for profiling horticulturally relevant, biological processes.