Changes to gene expression associated with hybrid speciation in plants: further insights from transcriptomic studies in Senecio

Abstract

Interspecific hybridization is an important mechanism of speciation in higher plants. In flowering plants, hybrid speciation is usually associated with polyploidy (allopolyploidy), but hybrid speciation without genome duplication (homoploid hybrid speciation) is also possible, although it is more difficult to detect. The combination of divergent genomes within a hybrid can result in profound changes to both genome and transcriptome. Recent transcriptomic studies of wild and resynthesized homoploid and allopolyploid hybrids have revealed widespread changes to gene expression in hybrids relative to expression levels in their parents. Many of these changes to gene expression are 'non-additive', i.e. not simply the sum of the combined expression levels of parental genes. Some gene expression changes are far outside the range of gene expression in either parent, and can therefore be viewed as 'transgressive'. Such profound changes to gene expression may enable new hybrids to survive in novel habitats not accessible to their parent species. Here, we give a brief overview of hybrid speciation in plants, with an emphasis on genomic change, before focusing discussion on findings from recent transcriptomic studies. We then discuss our current work on gene expression change associated with hybrid speciation in the genus Senecio (ragworts and groundsels) focusing on the findings from a reanalysis of gene expression data obtained from recent microarray studies of wild and resynthesized allopolyploid Senecio cambrensis. These data, showing extensive non-additive and transgressive gene expression changes in Senecio hybrids, are discussed in the light of findings from other model systems, and in the context of the potential importance of gene expression change to hybrid speciation in plants.

Figure 1

Recombinational speciation as a consequence of hybridization. A simple model for recombinational speciation sensu Grant (1981) is presented, in which two parental species with the same diploid chromosome number differ by two reciprocal translocations. The F1 hybrid is heterozygous for these rearrangements, and thus 75% of the possible gametic combinations will be inviable due to deletion/insertion events (not shown). Half of the remaining gametes (not shown) will recover parental chromosome combinations, while the remaining half (shown) will possess recombinant karyotypes. If selfed, a small number of F₂ individuals will possess novel karyotypes. These will be fertile, but only partly interfertile with either or both of the progenitor species (adapted with permission from Hegarty & Hiscock 2004).

Figure 2

Hybrid speciation in Senecio and experimental design of microarray analysis. (a) Hybridization events involved in the origins of the diploid hybrid, S. squalidus, and the allohexaploid hybrid, S. cambrensis. (b) Experimental design employed in microarray comparisons of gene expression between the allopolyploid S. cambrensis and its progenitor taxa, S. vulgaris and S. squalidus, and their sterile triploid F₁ hybrid, S. x baxteri. Experimental details can be found in Hegarty et al. (2005), but, briefly, mature flower bud tissue was harvested from a mixed population of approximately 30 plants and pooled prior to RNA extraction to create an ‘average’ for each taxon. Labelled cDNA for each taxon was hybridized to a custom floral cDNA microarray. Two taxa were differentially labelled and compared per array hybridization (with 10 replicate hybridizations performed per comparison) using dye swaps to account for any bias in labelling efficiency. Each taxon was compared with the other three, for a total of 30 array hybridizations per taxon. Raw expression data for each taxon were extracted from these 30 replicates and imported separately into the GeneSpring microarray analysis software (Silicon Genetics) to enable comparison between all four taxa.

Figure 3

‘Transcriptome shock’ in Senecio x baxteri is ameliorated in the allohexaploid derivative S. cambrensis. Normalized microarray expression data for 475 cDNA clones previously identified as displaying significant differences in expression between either S. x baxteri (Sb) or S. cambrensis (Sc) compared with one or both of the parental taxa S. squalidus (Ss) and S. vulgaris (Sv). The arrows highlight the reduction in the severity (variance) of altered gene expression in S. cambrensis relative to the initial triploid hybrid S. x baxteri.

Figure 4

Functional classes of genes affected by allopolyploidization and hybridization. Basic gene ontologies for cDNA clones displaying (a) conserved expression changes in both wild and synthetic Senecio cambrensis relative to S. x baxteri (genes affected by allopolyploidy, 540 clones), (b) expression changes relative to the parental taxa S. squalidus and S. vulgaris in both hybrid taxa (genes affected by hybridization, 99 clones) and (c) genes showing no expression difference between the parental and hybrid taxa (unaffected by hybridization or polyploidy, 289 clones). With the exception of a higher proportion of floral/pollen-related genes in (a,b) compared with (c), there are no substantial differences between the classes of affected genes (adapted with permission from Hegarty et al. 2006).

Figure 5

Frequency distributions of d/a ratios for (a) S. x baxteri and (b) S. cambrensis, between the values of −1.5 and +1.5 (data outside this range not shown). The dotted line in both cases highlights the expected ratio if gene expression is additive. The graphs demonstrate that expression in S. x baxteri is largely skewed towards a level similar to that in the lower expressing parent, while the opposite trend is observed in S. cambrensis.

Figure 6

Functional classes of genes showing non-additive expression in triploid hybrid S. x baxteri and allohexaploid S. cambrensis. Non-additive gene expression change in (a) S. x baxteri and (b) S. cambrensis: numbers are taken from the 378 and 81 clones differing by more than 1.5-fold from the parental midpoint value for S. x baxteri and S. cambrensis, respectively. Genes of unknown function (which represent the majority of genes identified, see text) are not included.

Figure 7

Comparison of non-additive expression changes resulting from hybridization in maize and hybridization/polyploidy in Senecio and Arabidopsis. The formation of the hybrids is shown in each case, together with the level of non-additive gene expression in the hybrids expressed as a percentage of the features on the microarray platform used. Finally, the top five functional gene classes affected (ignoring unknowns) for each hybrid are displayed for comparison. Red indicates a functional gene class affected in all four hybrid systems, blue indicates a functional class affected in at least one of the Senecio hybrids and one of the other two hybrid taxa, and green indicates a functional class affected in both Senecio hybrids but not in either Arabidopsis or maize. For Arabidopsis suecica, gene function data were taken from Wang et al. (2006b), and for maize from an extrapolation of the supplementary data given in Stupar et al. (2007). Sb, S. x baxteri; Sc, S. cambrensis.