Exploiting regulatory variation to identify genes underlying quantitative resistance to the wheat stem rust pathogen Puccinia graminis f. sp. tritici in barley

Arnis Druka, Elena Potokina, Zewei Luo, Nicola Bonar, Ilze Druka, Ling Zhang, David F. Marshall, Brian J. Steffenson, Timothy J. Close, Roger P. Wise, Andris Kleinhofs, Robert Williams, Michael J. Kearsey, Robbie Waugh

Research output: Contribution to journalArticle

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Abstract

We previously mapped mRNA transcript abundance traits (expression-QTL or eQTL) using the Barley1 Affymetrix array and 'whole plant' tissue from 139 progeny of the Steptoe × 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-analysed 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. 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.

Original languageEnglish (US)
Pages (from-to)261-272
Number of pages12
JournalTheoretical And Applied Genetics
Volume117
Issue number2
DOIs
StatePublished - Jul 1 2008

Fingerprint

Puccinia graminis
stem rust
Hordeum
Triticum
barley
Messenger RNA
loci
wheat
pathogens
Chromosomes
Genetic Association Studies
Population
Genes
genes
chromosomes
Phenotype
quantitative trait loci
histidine kinase
phenotype
rust diseases

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Agronomy and Crop Science
  • Genetics

Cite this

Exploiting regulatory variation to identify genes underlying quantitative resistance to the wheat stem rust pathogen Puccinia graminis f. sp. tritici in barley. / Druka, Arnis; Potokina, Elena; Luo, Zewei; Bonar, Nicola; Druka, Ilze; Zhang, Ling; Marshall, David F.; Steffenson, Brian J.; Close, Timothy J.; Wise, Roger P.; Kleinhofs, Andris; Williams, Robert; Kearsey, Michael J.; Waugh, Robbie.

In: Theoretical And Applied Genetics, Vol. 117, No. 2, 01.07.2008, p. 261-272.

Research output: Contribution to journalArticle

Druka, A, Potokina, E, Luo, Z, Bonar, N, Druka, I, Zhang, L, Marshall, DF, Steffenson, BJ, Close, TJ, Wise, RP, Kleinhofs, A, Williams, R, Kearsey, MJ & 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, vol. 117, no. 2, pp. 261-272. https://doi.org/10.1007/s00122-008-0771-x
Druka, Arnis ; Potokina, Elena ; Luo, Zewei ; Bonar, Nicola ; Druka, Ilze ; Zhang, Ling ; Marshall, David F. ; Steffenson, Brian J. ; Close, Timothy J. ; Wise, Roger P. ; Kleinhofs, Andris ; Williams, Robert ; Kearsey, Michael J. ; Waugh, Robbie. / Exploiting regulatory variation to identify genes underlying quantitative resistance to the wheat stem rust pathogen Puccinia graminis f. sp. tritici in barley. In: Theoretical And Applied Genetics. 2008 ; Vol. 117, No. 2. pp. 261-272.
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AU - Wise, Roger P.

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