Submitted to: BioMed Central (BMC) Genetics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 6/11/2009
Publication Date: 6/29/2009
Publication URL: www.biomedcentral.com/1471-2164/10/285
Citation: Schreiber, A.W., Sutton, T., Caldo, R.A., Kalashyan, E., Lovell, B., Mayo, G., Muehlbauer, G.J., Druka, A., Waugh, R., Wise, R.P., Langridge, P., Baumann, U. 2009. Comparative Transcriptomics in the Triticeae. BioMed Central (BMC) Genetics. 10:285. Interpretive Summary: 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. 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. Comprehensive Affymetrix GeneChip platforms have now been developed for both hexaploid wheat and diploid barley, based on extensive Expressed Sequence Tag (EST) collections for both species. The Barley1 GeneChip has already been used to develop an atlas of gene expression covering its entire developmental cycle. Taking advantage of these resources, we have sampled a similar set of biological material collected through the developmental cycle of hexaploid wheat, grown under near-identical conditions to the archetype study for barley. This study is the first comprehensive comparison of developmental expression patterns in these two large-genome crop species. Triticeae cereal grains are one of our most important food sources, thus, these findings provide new knowledge of broad significance to plant scientists, and to growers who utilize important agronomic and pest resistance genes to enhance crop production.
Technical Abstract: Barley and particularly wheat are two grass species of immense agricultural importance. In spite of polyploidization events within the latter, studies have shown that genotypically and phenotypically these species are very closely related and, indeed, fertile hybrids can be created by interbreeding. The advent of two genome-scale Affymetrix GeneChips now allows studies of the comparison of their transcriptomes. We have used the Wheat GeneChip to create a "gene expression atlas" for the wheat transcriptome (cv. Chinese Spring). For this, we chose mRNA from a range of tissues and developmental stages closely mirroring a comparable study carried out for barley (cv. Morex) using the Barley1 GeneChip. This, together with large-scale clustering of the probesets from the two GeneChips into "homologous groups," has allowed us to perform a genomic-scale comparative study of expression patterns in these two species. We explore the influence of the polyploidy of wheat on the results obtained with the Wheat GeneChip and quantify the correlation between conservation in gene sequence and gene expression in wheat and barley. In addition, we show how the conservation of expression patterns can be used to elucidate, probeset by probeset, the reliability of the Wheat GeneChip. While there are many differences in expression on the level of individual genes and tissues, we demonstrate that the wheat and barley transcriptomes appear highly correlated. This finding is significant not only because, given small evolutionary distance between the two species, it is widely expected but also because it demonstrates that it is possible to use the two GeneChips for comparative studies. This is the case even though their probeset composition reflects rather different design principles as well as, of course, the present incomplete knowledge of the gene content of the two species. We also show that, in general, the Wheat GeneChip is not able to distinguish contributions from individual homeologs. Furthermore, the comparison between the two species leads us to conclude that the conservation of both gene sequence as well as gene expression is positively correlated with absolute expression levels, presumably reflecting increased selection pressure on genes coding for proteins present at high levels. In addition, the results indicate the presence of a correlation between sequence and expression conservation within the Triticeae.