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

• Published in: BMC genomics Vol. 10; no. 1; p. 436
• Main Authors: Davey, Mark W, Graham, Neil S, Vanholme, Bartel, Swennen, Rony, May, Sean T, Keulemans, Johan
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 16-09-2009; BioMed Central; BMC
• Subjects: Banana; Bioinformatics; Cloning; Cold Temperature; Cold tolerance; Comparative Genomic Hybridization; Design; DNA microarrays; DNA, Plant - genetics; Droughts; Flowers & plants; Fruits; Gene Expression Profiling - methods; Gene Expression Regulation, Plant; Genes; Genes, Plant; Genetic aspects; Genome, Plant; Genomes; Genomics; Musa; Musa - genetics; Oligonucleotide Array Sequence Analysis; Oryza - genetics; Quantitative Trait Loci; Belgium; United Kingdom
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/1471-2164-10-436

'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.
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.
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.