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


CONCLUSIONS
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(R) is a highly promising strategy to study complex biological responses and illustrates the potential of such strategies for gene discovery in non-model species.
Davey
Mark W
MW
Laboratory for Fruit Breeding and Biotechnology, Department of Biosystems, Katholieke Universiteit Leuven, Box 2747, Willem De Croylaan 42, B-3001, Heverlee, Leuven, Belgium. mark.davey@biw.kuleuven.be
Graham
Neil S
NS
Vanholme
Bartel
B
Swennen
Rony
R
May
Sean T
ST
Keulemans
Johan
J
D003080:Cold Temperature; D055028:Comparative Genomic Hybridization; D018744:DNA, Plant / Q000235:genetics; D055864:Droughts; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D028521:Musa / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics; D040641:Quantitative Trait Loci
D018744:DNA, Plant