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

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.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.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 Centr