Considerable divergence has occurred between bread wheat (Triticum aestivum
) and barley (Hordeum vulgare
) since evolution from a common ancestor 10–14 million years ago. Since then, these two members of the Triticeae
have been subjected to largely parallel processes of cultivation and domestication, starting in the fertile crescent over 10,000 years ago [1
]. Barley has remained diploid with a base chromosome number of 7 (HH genome, 2n = 2x = 14) while bread wheat is the product of a series of hybridization events between related species that has resulted in an allo-hexaploid genome with three homoeologous sets of 7 chromosome pairs (AABBDD genome, 2n = 6x = 42 [2
]). Despite these major genomic perturbations during its evolution, genetic mapping [3
] and detailed structural genomic studies [4
] have shown that the wheat and barley genomes are highly conserved. Indeed, barley chromosomes can even be substituted for wheat chromosomes [5
]. As a consequence of its simplified genetics, many have suggested that barley is a good genetic model for its genetically more complex cousin. This assertion is supported by the broad range of common morphological and developmental characteristics shared by both species, though fundamental biological differences do exist (such as spike and spikelet morphology).
Polyploidization is common across the plant kingdom and the process has been associated with a range of changes in newly synthesized hybrids of several species. These include the genome-wide removal of some (but not all) duplicated, and hence redundant, genetic information, sub- and/or neo-functionalization of duplicated genes, pseudogenization, differential cytosine methylation and epigenetic reprogramming of gene expression (silencing and activation), and transposable element activation (reviewed in [6
]). Levy and Feldman [7
] summarized some of the major consequences resulting from the recent polyploidization of the wheat genome. In common with other plant species, the outcome for wheat was more than simply the additive combination of genomes and included many of the features described across the species range [8
Wheat is an important species for studying the impact of polyploidization because it is a relatively recent polyploid. Moreover, the outcomes can be studied in very early generations because it is possible to artificially re-synthesize polyploids from their diploid and tetraploid relatives. In such cases, epigenetic silencing of duplicated genes appears to be a common response, with indications of reciprocal silencing in different organs an early sign of sub-functionalization [11
]. Gene activation or silencing may also occur as a result of transcriptional interference associated with stochastic rearrangements of non-coding RNA [8
]. Over longer time frames, the evolutionary consequences of such events are better observed in ancient polyploids. In Arabidopsis (an ancient tetraploid), for example, Blanc and Wolfe [16
] reported that more than half of the observed gene pairs retained in the genome exhibited differential transcript abundance in different tissues. An immediate impact of polyploidy is therefore to provide the raw genetic material for adaptation and the evolution of phenotype.
The close evolutionary relationship between wheat and barley, reflected in largely parallel morphological and developmental patterns, makes a comparison of their transcriptomes particularly intriguing. It may provide insight, for example, into consequences of speciation and polyploidization. Ideally a genomic-scale comparison of this sort would be carried out once the genomes have been sequenced. This would permit the reliable disentanglement of the evolutionary relationships between individual genes and also provide the foundation on which to build dependable expression analysis platforms. Regrettably, the size and complexity of the wheat and barley genomes has been a major impediment to full-scale sequencing, so that even the diploid barley genome is not expected to be available before 2012 http://barleygenome.org/
. In short, among plants comparative transcriptomics is rare: comprehensive pair-wise comparisons have so far only been carried out in rice and Arabidopsis [17
], various cotton species [18
] and in poplar and Arabidopsis [19
]. Recently, a three-way study between Arabidopsis, poplar and rice has also appeared [20
Compared to genome-wide studies, comparisons of expression patterns of individual orthologous gene pairs, individual gene families and/or in connection with a particular phenotypic characteristic are more frequent. For example, Mangelsen et al. [21
] compared, within a number of tissues, expression patterns of members of the WRKY transcription factor family among barley, rice and Arabidopsis and found that, at least within this gene family, coordinated conservation of expression patterns and sequence. Horvath et al. [22
] found that groups of genes associated with cell division were consistently expressed preferentially in shoot apices in Arabidopsis, wild oats, poplar and leafy spurge. Differential gene expression, on the other hand, has been observed in some members of the ZIP and NAS metal homeostatis gene families in two closely related Arabidopsis species when exposed to both low and high Zn levels, presumably associated with different Zn accumulation patterns in these two species [23
]. Analogously, differential time-dependent expression of a small number genes in response to salt stress in both barley (relatively salt tolerant) and rice (relatively salt sensitive) were studied by Ueda et al. [24
], while Taji et al. [25
] performed a similar comparative study in salt cress (tolerant) and Arabidopsis (intolerant).
Comprehensive Affymetrix GeneChip platforms have now been developed for both wheat and barley, based on extensive EST collections for both species (Ref. [26
). The Barley1 GeneChip has already been used to develop an atlas of gene expression covering the entire developmental cycle of the barley cultivar Morex [27
] and intra-species varietal comparisons have been carried out both for Morex and Golden Promise [27
] as well as Morex and Steptoe [29
]. Taking advantage of these resources, we have sampled a similar set of biological material collected through the developmental cycle of wheat (Chinese Spring), grown under near-identical conditions to those in Druka et al. [27
]. This permits the first comprehensive comparison of developmental expression patterns in these two important crop species. We report on this transcriptome-wide comparison here. At the same time, in order to facilitate more detailed studies of individual homologous genes motivated, say, by particular phenotypic differences as in [21
], we make available a convenient web-based comparative tool enabling access to the developmental expression profiles of any
individual wheat and barley homologs probed by the two GeneChips.
It is well known that meaningful comparative expression analyses using microarray platforms based solely on EST collections can be difficult because of the frequent and confounding presence of multiple splice forms, paralogs and orthologs, as well as, in the case of polyploids, homoeologs with near-identical sequence [31
]. Because of this, we have also investigated, in some detail, the specificity of the Wheat GeneChip to individual homoeologs and expended considerable effort to avoid misidentification of orthologs in the two species.