Research article

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

Mark W Davey^1* , Neil S Graham^2* , Bartel Vanholme³ , Rony Swennen⁴ , Sean T May² and Johan Keulemans¹

¹  Laboratory for Fruit Breeding and Biotechnology, Department of Biosystems, Katholieke Universiteit Leuven, Box 2747, Willem De Croylaan 42, B-3001, Heverlee, Leuven, Belgium

²  Nottingham Arabidopsis Stock Centre, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK

³  Department of Plant Systems Biology, VIB, and Department of Molecular Genetics, Universiteit Gent, Technologiepark 927, B-9052 Gent, Belgium

⁴  Department of Biosystems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 13 Box 2455, B - 3001 Leuven, Belgium

author email corresponding author email* Contributed equally

BMC Genomics 2009, 10:436doi:10.1186/1471-2164-10-436

Published:	16 September 2009

Abstract

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.