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Background  'Systems-wide' approaches such as microarray RNA-profiling are ideally suited to the study of the complex overlapping responses of plants to biotic and abiotic stresses. However, commercial microarrays are only available for a limited number of plant species and development costs are so substantial as to be prohibitive for most research groups. Here we evaluate the use of cross-hybridisation to Affymetrix oligonucleotide GeneChip ®  microarrays to profile the response of the banana ( Musa  spp.) leaf transcriptome to drought stress using a genomic DNA (gDNA)-based probe-selection strategy to improve the efficiency of detection of differentially expressed  Musa  transcripts.    Results  Following cross-hybridisation of  Musa  gDNA to the Rice GeneChip ®  Genome Array, ~33,700 gene-specific probe-sets had a sufficiently high degree of homology to be retained for transcriptomic analyses. In a proof-of-concept approach, pooled RNA representing a single biological replicate of control and drought stressed leaves of the  Musa  cultivar 'Cachaco' were hybridised to the Affymetrix Rice Genome Array. A total of 2,910  Musa  gene homologues with a >2-fold difference in expression levels were subsequently identified. These drought-responsive transcripts included many functional classes associated with plant biotic and abiotic stress responses, as well as a range of regulatory genes known to be involved in coordinating abiotic stress responses. This latter group included members of the ERF, DREB, MYB, bZIP and bHLH transcription factor families. Fifty-two of these drought-sensitive  Musa  transcripts were homologous to genes underlying QTLs for drought and cold tolerance in rice, including in 2 instances QTLs associated with a single underlying gene. The list of drought-responsive transcripts also included genes identified in publicly-available comparative transcriptomics experiments.    Conclusion  Our results demonstrate that despite the general paucity of nucleotide sequence data in  Musa  and only distant phylogenetic relations to rice, gDNA probe-based cross-hybridisation to the Rice GeneChip ®  is a highly promising strategy to study complex biological responses and illustrates the potential of such strategies for gene discovery in non-model species.

Heterologous oligonucleotide microarrays for transcriptomics in a non-model species; a proof-of-concept study of drought stress in Musa