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

Davey, M W and Graham, N S and Vanholme, B and Swennen, R and May, S T and Keulemans, J (2009) Heterologous oligonucleotide microarrays for transcriptomics in a non-model species; a proof-of-concept study of drought stress in Musa. BMC Genomics, 10 (436). pp. 1-19.

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'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.

Item Type: Article
Additional Information: The authors gratefully acknowledge stimulating discussion with Otto Van Poeselaere and Eva A. Davey during the preparation of this manuscript. Access to the Syngenta Musa 3'EST database, donated by Syngenta to Bioversity International within the framework of the Global Musa Genomics Consortium is gratefully acknowledged. Financial resources: 42 This work was partly supported by the GARNet transcriptomics and Bioinformatics service III. Grant reference BBE01772X1
Author Affiliation: Katholieke Universiteit Leuven, Box 2747, Willem De Croylaan 42, B-3001, Heverlee, Leuven, Belgium
Subjects: Plant Production
Agricultural Engineering
Crop Improvement
Divisions: Other Crops
Depositing User: Mr. SanatKumar Behera
Date Deposited: 04 Jan 2012 09:37
Last Modified: 04 Jan 2012 09:38
Official URL: http://dx.doi.org/10.1186/1471-2164-10-436
URI: http://eprints.icrisat.ac.in/id/eprint/2888

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