Submitted to: International Triticeae Mapping Initiative Workshop
Publication Type: Abstract Only
Publication Acceptance Date: 5/22/2004
Publication Date: 5/22/2004
Citation: Cho, S., Garvin, D.F., Muehlbauer, G.J. 2004. Barley gene expression in wheat-barley chromosome addition lines and transcriptome-based physical mapping of barley genes [abstract]. International Triticeae Mapping Initiative Workshop. Abstract No. 18. Interpretive Summary:
Technical Abstract: Microarray analysis of wheat-barley addition lines enabled an exploration of barley gene expression on an individual chromosome basis. Using the Barley1 Affymetrix GeneChip, which represents 22,860 barley genes, gene expression was examined in the barley cultivar Betzes, the wheat cultivar Chinese Spring, a Chinese Spring-Betzes disomic addition line harboring chromosome 6H, and ditelosomic addition lines with chromosome arms 6HL and 6HS. Three replicates of RNA samples isolated from 3-day-old seedlings were used for synthesis of biotin-labeled cRNA and hybridization to the Barley1 GeneChips. Using the data-extracting algorithm Robust Multiple-array Average (RMA) at a quality level of 0.001, we detected 7,811 and 1,407 expressed genes in Betzes and Chinese Spring, respectively. The number of genes specific to Betzes and not to Chinese Spring was 6,472. Four-hundred twenty one genes exhibited 6H-specific expression and 238 and 183 of these showed 6HL- and 6HS-specific expression, respectively. Additionally, 64 of 1,051 genes identified across all lines showed a quantitative increase in expression relative to Chinese Spring in the 6H addition line at the false discovery rate of 1%. BLASTn searches of the barley genes that are hypothetically located on chromosome 6H based on expression data were conducted against the mapped wheat ESTs and the rice genome sequence. Our results showed that approximately 70% of the genes were homologous either to wheat ESTs mapped to group 6 chromosomes or to rice sequences on the syntenous chromosome 2. These results indicate that microarray-based analysis of barley gene expression using wheat-barley chromosome addition lines is an efficient method to physically map large numbers of genes to specific barley chromosomes and also provides unique insights into the nature of alien gene expression in wheat. Further experiments to assign more barley genes to their respective chromosomes are underway.