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United States Department of Agriculture

Agricultural Research Service

Research Project: FUNCTIONAL GENOMICS OF CEREAL DISEASE DEFENSE Title: Exploiting Regulatory Variation to Identify Genes Underlying Quantitative Resistance to the Wheat Stem Rust Pathogen Puccinia graminis f. sp. tritici in Barley

item Druka, Arnis - SCOTTISH CROP RES. INST.
item Potokina, Elena - UNIV. BIRMINGHAM, U.K.
item Luo, Zewei - UNIV. BIRMINGHAM, U.K.
item Bonar, Nicola - SCOTTISH CROP RES. INST.
item Druka, Ilze - UNIV. ABERTAY, U.K.
item Marshall, David - SCOTTISH CROP RES. INST.
item Steffenson, Brian - UNIV. OF MINNESOTA
item Close, Timothy - UNIV. OF CALIFORNIA
item Wise, Roger
item Kleinhofs, Andris - WASHINGTON STATE UNIV.
item Williams, Robert - UNIV. OF TENNESSEE
item Kearsey, Michael - UNIV. BIRMINGHAM, U.K.
item Waugh, Robbie - SCOTTISH CROP RES. INST.

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 8, 2008
Publication Date: April 30, 2008
Repository URL:
Citation: Druka, A., Potokina, E., Luo, Z., Bonar, N., Druka, I., Zhang, L., Marshall, D.F., Steffenson, B.J., Close, T.J., Wise, R.P., Kleinhofs, A., Williams, R.W., Kearsey, M.J., Waugh, R. 2008. Exploiting Regulatory Variation to Identify Genes Underlying Quantitative Resistance to the Wheat Stem Rust Pathogen Puccinia graminis f. sp. tritici in Barley. Theoretical and Applied Genetics. 117(2):261-272. Available:

Interpretive Summary: We are interested in understanding the molecular genetics of stem rust resistance in cereals to develop cultivars with wide-spectrum and durable resistance. Such investigations could lead to the development of novel control strategies using host resistance. Phenotypic variation is frequently determined by regulatory regions of DNA sequence that affect mRNA abundance. By subjecting variation in mRNA abundance observed in individuals from meiotic mapping populations to genetic analysis, each mRNA can be treated as a heritable, quantitative trait. Subsequently, the chromosomal loci that regulate the abundance of specific mRNAs in a given biological sample can be identified as expression Quantitative Trait Loci (eQTLs). This article reports a fusion of previous quantitative response to pathogen infection in the Steptoe x Morex population, combined with eQTL analysis using the Affymetrix Barley1 GeneChip, to identify candidate genes associated with stem rust resistance in barley. Three goals were achieved by this investigation: i) Extraction of polymorphic markers from RNA profiling data, ii) Determination of the expression level for each gene on the Barley1 GeneChip in a mapping population to identify gene expression QTL (eQTLs), and iii) Correlation of these eQTLs with traits of commercial importance. Thus, these eQTLs can be utilized by researchers for selective improvement for food, energy, and other materials.

Technical Abstract: We previously mapped mRNA transcript abundance traits 1 eQTL (expression- quantitative trait loci) using the Barley1 Affymetrix array and "whole plant" tissue from 139 progeny of the Steptoe x Morex (St/Mx) reference barley mapping population. Of the 22,840 probesets (genes) on the array, 15,987 reported transcript abundance signals that were suitable for eQTL analysis, and this revealed a genome-wide distribution of 23,738 significant eQTLs. Here we have explored the potential of using these mRNA abundance eQTL traits as surrogates for the identification of candidate genes underlying the interaction between barley and the wheat stem rust fungus Puccinia graminis f. sp. tritici. We re-analyzed quantitative "resistance phenotype" data collected on this population in 1990/1991 and identified six loci associated with barley’s reaction to stem rust. One of these coincided with the major stem rust resistance locus Rpg1, that we had previously positionally cloned using this population. Correlation analysis between phenotype values for rust infection and mRNA abundance values reported by the 22,840 GeneChip probe sets placed Rpg1, which is on the Barley1 GeneChip, in the top five candidate genes for the major QTL on chromosome 7H corresponding to the location of Rpg1. A second co-located with the rpg4/Rpg5 stem rust resistance locus that has been mapped in a different population, and the remaining four were novel. Similar correlation analyses identified candidate genes for the rpg4/Rpg5 locus on chromosome 5H. By combining our data with additional published mRNA profiling data sets, we identify a putative sensory transduction histidine kinase as a strong candidate for a novel resistance locus on chromosome 2H and compile candidate gene lists for the other three loci.

Last Modified: 10/30/2014
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