Development of anonymous cDNA microarrays to study changes to theSeneciofloral transcriptome during hybrid speciation

Abstract

Interspecific hybridization is an important process through which abrupt speciation can occur. In recent years, genetic changes associated with hybrid speciation have been identified through a variety of techniques, including AFLP/SSR mapping, GISH/FISH and cDNA-AFLP differential display. However, progress in using microarray technology to analyse whole genome/transcriptome changes associated with hybrid speciation has been limited due to the lack of extensive sequence data for many hybrid species and the difficulties in extrapolating results from commercially available microarrays for model species onto nonmodel hybrid taxa. Increasingly therefore researchers studying nonmodel systems are turning to the development of 'anonymous' cDNA microarrays, where the time and cost of producing microarrays is reduced by printing unsequenced cDNA clones, and sequencing only those clones that display interesting expression patterns. Here we describe the creation, testing and preliminary use of anonymous cDNA microarrays to study changes in floral transcriptome associated with allopolyploid speciation in the genus Senecio. We report a comparison of gene expression between the allohexaploid hybrid, Senecio cambrensis, its parental taxa Senecio squalidus (diploid) and Senecio vulgaris (tetraploid), and the intermediate triploid (sterile) hybrid Senecioxbaxteri. Anonymous microarray analysis revealed dramatic differences in floral gene expression between these four taxa and demonstrates the power of this technique for studies of the genetic impact of hybridization in nonmodel flowering plants.

Mechanisms of genomic rearrangements and gene expression changes in plant polyploids

“…(88) The data suggest that during autopolyploid formation the dosage-dependent regulatory mechanisms prevail. (89) In another study, Hegarty et al (2005) found dramatic differences in floral gene expression between the allohexaploid hybrid, Senecio cambrensis, its parental taxa Senecio squalidus (diploid) and Senecio vulgaris (tetraploid), and the intermediate triploid (sterile) hybrid Senecio  baxteri. (90) Therefore, reprogramming gene regulatory networks in interspecific hybrids and allotetraploids is a consequence of mediating transcriptome divergence originating in two species rather than simple genome doubling.…”

“…(89) In another study, Hegarty et al (2005) found dramatic differences in floral gene expression between the allohexaploid hybrid, Senecio cambrensis, its parental taxa Senecio squalidus (diploid) and Senecio vulgaris (tetraploid), and the intermediate triploid (sterile) hybrid Senecio  baxteri. (90) Therefore, reprogramming gene regulatory networks in interspecific hybrids and allotetraploids is a consequence of mediating transcriptome divergence originating in two species rather than simple genome doubling. To separate the effects of hybridization and genome ''doubling,'' one may compare gene expression variation between F 1 hybrids (hybridization) and allotetraploids (genome-doubling).…”

Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids

“…In natural cotton polyploids, a micro-array study of 1383 genes found biased expression in 70% of homoeologue pairs, 24% of which seem to have biased expression immediately on diploid hybridisation of the parental species (Flagel et al, 2008). In synthetic Senecio cambrensis allopolyploids, anonymous microarrays with B6000 cDNA clones showed that gene expression changes are extensive in diploid hybrids of the parental species, but are ameliorated by polyploidisation (Hegarty et al, 2005(Hegarty et al, , 2006. In synthetic allopolyploids between A. thaliana and A. suecica, a microarray study with 26 090 annotated genes found that B5% showed expression changes (Madlung et al, 2005;Wang et al, 2006).…”

Numerous and Rapid Nonstochastic Modifications of Gene Products in Newly SynthesizedBrassica napusAllotetraploids

“…Genomewide analyses can now be undertaken using the promising cDNA microarray technology. This approach is planned for Brassica polyploids Lee et al 2004;Wang et al 2005) and has been recently applied to the synthetic allopolyploids Senecio cambrensis (Hegarty et al 2005) and A. suecica (Wang et al 2006), revealing several modifications of gene expression.…”