Differential gene expression in nearly isogenic lines with QTL for partial resistance to Puccinia hordei in barley

Abstract

BackgroundThe barley-Puccinia hordei (barley leaf rust) pathosystem is a model for investigating partial disease resistance in crop plants and genetic mapping of phenotypic resistance has identified several quantitative trait loci (QTL) for partial resistance. Reciprocal QTL-specific near-isogenic lines (QTL-NILs) have been developed that combine two QTL, Rphq2 and Rphq3, the largest effects detected in a recombinant-inbred-line (RIL) population derived from a cross between the super-susceptible line L94 and partially-resistant line Vada. The molecular mechanism underpinning partial resistance in these QTL-NILs is unknown.ResultsAn Agilent custom microarray consisting of 15,000 probes derived from barley consensus EST sequences was used to investigate genome-wide and QTL-specific differential expression of genes 18 hours post-inoculation (hpi) with Puccinia hordei. A total of 1,410 genes were identified as being significantly differentially expressed across the genome, of which 55 were accounted for by the genetic differences defined by QTL-NILs at Rphq2 and Rphq3. These genes were predominantly located at the QTL regions and are, therefore, positional candidates. One gene, encoding the transcriptional repressor Ethylene-Responsive Element Binding Factor 4 (HvERF4) was located outside the QTL at 71 cM on chromosome 1H, within a previously detected eQTL hotspot for defence response. The results indicate that Rphq2 or Rphq3 contains a trans-eQTL that modulates expression of HvERF4. We speculate that HvERF4 functions as an intermediate that conveys the response signal from a gene(s) contained within Rphq2 or Rphq3 to a host of down-stream defense responsive genes. Our results also reveal that barley lines with extreme or intermediate partial resistance phenotypes exhibit a profound similarity in their spectrum of Ph-responsive genes and that hormone-related signalling pathways are actively involved in response to Puccinia hordei.ConclusionsDifferential gene expression between QTL-NILs identifies genes predominantly located within the target region(s) providing both transcriptional and positional candidate genes for the QTL. Genetically mapping the differentially expressed genes relative to the QTL has the potential to discover trans-eQTL mediated regulatory relays initiated from genes within the QTL regions.

Genome-Wide Analysis and Differential Expression of Chitinases in Banana Against Root Lesion Nematode (Pratylenchus coffeae) and Eumusa Leaf Spot (Mycosphaerella eumusae) Pathogens

“…Among different defense-related enzymes, the role of chitinases in hypersensitive reactions during induced host resistance in tissues followed by pathogen infection was demonstrated by several research workers [5]. Chitin-mediated resistance has been proved against fungal diseases in various crops such as rice, grapevine, and peanut [6][7][8] and nematode infection in rice and tomato [9]. Similarly in the case of banana, more accumulation of endochitinases and putative chitinase transcripts, which are involved in fungal cell wall degradation, was reported in Mycosphaerella musicola-challenged leaves [10].…”

Host and Nonhost Response to Attack by Fungal Pathogens

“…The transcriptome of rust-attacked barley has been analysed recently aiming at a general description of host changes as well as the identification of expression QTL (eQTL) loci for partial resistance (Chen et al 2010b;Moscou et al 2011b). Barley recognizes the presence of rust spores from approximately 12 h.a.i.…”

“…Barley recognizes the presence of rust spores from approximately 12 h.a.i. onwards, while fungal development is still confined to the leaf or stem surface, before penetration of stomata by appressoria, and responds with the differential regulation of a large number of transcripts (Chen et al 2010b;Zellerhoff et al 2010). Over all analysed time points (12-48 h.a.i.…”

Gene Expression: A Review on Methods for the Study of Defense-Related Gene Differential Expression in Plants

“…Microarrays have been used in a study to assess differential expression in two barley cultivars (L94, susceptible, Vada, partially resistant) infected or uninfected with Puccinia hordei, with the identification of 802 fragments related to plant genes responsive to this fungus being present in inoculated plants but absent from uninoculated controls [37]. Of the genes detected, 584 were common to both cultivars, 34 were specific to L94, 24 were specific to Vada and 160 showed no homology to genes described in the literature and thus represented potential genes to be studied.…”

“…Microarrays enable the study of many genes simultaneously, in a semi-quantitative way, and have been widely used to address several biological, genetic and biochemical issues [37,58]. Normally this analysis is performed with previously known gene sequences inserted into an array.…”