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.ResultsFollowing 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.ConclusionOur 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.
Highlights
Bananas and plantains are large herbaceous monocots from the genus Musa of the family Musaceae
It has been recently demonstrated that commercially available high-density oligonucleotide microarrays from closely related, heterologous species can be used to probe the transcriptomes of nonmodel plants
Similar high density oligonucleotide Affymetrix microarrays exist for important monocotolydenous crops, including maize, wheat, barley and sugar cane, but the Affymetrix Rice Genome Array contains many more probe-sets (~57,000), and covers a larger portion of the transcriptome than these other arrays
Summary
Bananas and plantains are large herbaceous monocots from the genus Musa of the family Musaceae. The vast majority of cultivated bananas are hybrids derived from natural inter- and intraspecific crosses between two diploid wild species, Musa acuminata (designated by genome A) and M. balbisiana (designated by genome B) [1]. These diploid, triploid or tetraploid hybrids are of great economic importance in sub-Saharan Africa, South and Central America and Asia, where they are a staple food for an estimated 400 million people. It has been recently demonstrated that commercially available high-density oligonucleotide microarrays from closely related, heterologous species can be used to probe the transcriptomes of nonmodel plants. In addition a tomato array has been used to study fruit ripening and development in tomato, aubergine and pepper [20], as well as in potato [21]
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