Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 1/10/2004
Publication Date: 1/10/2004
Citation: Wise, R.P., Caldo, R.A., Nettleton, D.S., Dickerson, J.A. 2004. Probe-level analysis of gene-for-gene-specified responses in barley-powdery mildew interactions. Plant and Animal Genome Conference Proceedings. XII Conference. p. W264.
Technical Abstract: Global expression analysis was conducted to elucidate the complex regulatory pathways associated with gene-for-gene specified resistance to powdery mildew using 22K Barley1 GeneChip probe arrays. Our goal was to identify genes that are differentially expressed in incompatible (resistant) vs. compatible (susceptible) interactions of plants and fungal biotrophs. A split-split-plot design with 108 experimental units (2 isolates x 3 genotypes x 6 time points x 3 replications) was used to profile near-isogenic lines harboring the Mla1, Mla6, and Mla13 CC-NBS-LRR resistance genes in response to infection with Blumeria graminis f. sp. hordei isolates 5874 (AvrMla1, AvrMla6) and K1 (AvrMla1, AvrMla13). A mixed linear model analysis was conducted for each of the 22,840 probe sets on the Barley1 GeneChip using the SAS mixed procedure. Although the logarithm of the Affymetrix MAS 5.0 expression measure was used as the response variable in the initial analyses, more detailed analysis of the probe-level data was conducted for selected probe sets that appeared to be of greatest scientific interest based on the initial analyses. Tests of primary scientific interest for each gene involve time-course-expression-profile comparisons among various isolate/genotype combinations. Data will be housed in BarleyBase, a MIAME-compliant, MySQL relational database for GeneChip probe arrays. BarleyBase serves as a public resource for the cereal research community as well as statisticians desiring access to probe-level data. Research supported by USDA-IFAFS grant no. 2001-52100-11346, USDA-NRI grant no. 2002-35300-12619, and the North American Barley Genome Project.