Research article

Comparative transcriptomics in the Triticeae

Andreas W Schreiber¹ , Tim Sutton¹ , Rico A Caldo² , Elena Kalashyan¹ , Ben Lovell¹ , Gwenda Mayo¹ , Gary J Muehlbauer³ , Arnis Druka⁴ , Robbie Waugh⁴ , Roger P Wise^2,5 , Peter Langridge¹ and Ute Baumann¹

¹Australian Centre for Plant Functional Genomics, Univ of Adelaide, PMB 1 Glen Osmond, SA 5064, Australia

²Dept. of Plant Pathology and Center for Plant Responses to Environmental Stresses, Iowa State Univ., Ames, IA 50011-1020, USA

³Dept. of Agronomy and Plant Genetics, Univ of Minnesota, St. Paul, MN 55108, USA

⁴Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK

⁵Corn Insects and Crop Genetics Research, USDA-ARS, Iowa State Univ, Ames, IA 50011-1020, USA

author email corresponding author email

BMC Genomics 2009, 10:285doi:10.1186/1471-2164-10-285

Published:	29 June 2009

Abstract

Background

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.

Results

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.

Conclusion

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.