Journal Article

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

Keulemans, Johan, Davey, Mark W, May, Sean T, Swennen, Rony, Graham, Neil S, Vanholme, Bartel

2009

Overview

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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Animal Genetics and Genomics / Banana / Bioinformatics / Biomedical and Life Sciences / Cloning / Cold Temperature / Cold tolerance / Comparative Genomic Hybridization / Cultivars / Design / DNA microarrays / DNA, Plant - genetics / Drought / Droughts / Flowers & plants / Fruits / Gene Expression Profiling - methods / Gene Expression Regulation, Plant / Genes / Genes, Plant / Genetic aspects / Genome, Plant / Genomes / Genomics / Leaves / Life Sciences / Microarrays / Microbial Genetics and Genomics / Musa / Musa - genetics / Oligonucleotide Array Sequence Analysis / Oryza - genetics / Plant Genetics and Genomics / Plant species / Proteomics / Quantitative Trait Loci / Research Article