Please use this identifier to cite or link to this item:
Scopus Web of Science® Altmetric
Type: Journal article
Title: Comparative transcriptomics in the Triticeae
Author: Schreiber, A.
Sutton, T.
Caldo, R.
Kalashyan, E.
Lovell, B.
Mayo, G.
Muehlbauer, G.
Druka, A.
Waugh, R.
Wise, R.
Langridge, P.
Baumann, U.
Citation: BMC Genomics, 2009; 10(1):1-17
Publisher: BioMed Central Ltd.
Issue Date: 2009
ISSN: 1471-2164
Statement of
Andreas W. Schreiber, Tim Sutton, Rico A. Caldo, Elena Kalashyan, Ben Lovell, Gwenda Mayo, Gary J. Muehlbauer, Arnis Druka, Robbie Waugh, Roger P. Wise, Peter Langridge and Ute Baumann
Abstract: <h4>Background</h4>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.<h4>Results</h4>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.<h4>Conclusion</h4>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 homoeologs. 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.
Keywords: Hordeum
RNA, Messenger
RNA, Plant
Oligonucleotide Array Sequence Analysis
Gene Expression Profiling
Genome, Plant
Comparative Genomic Hybridization
Description: © 2009 Schreiber et al; licensee BioMed Central Ltd.
DOI: 10.1186/1471-2164-10-285
Published version:
Appears in Collections:Agriculture, Food and Wine publications
Aurora harvest

Files in This Item:
There are no files associated with this item.

Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.