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An eQTL analysis of partial resistance to Puccinia hordei in barley

An eQTL analysis of partial resistance to Puccinia hordei in barley,10.1371/journal.pone.0008598.t002,PLOS One,Xinwei Chen,Christine A. Hackett,Rients

An eQTL analysis of partial resistance to Puccinia hordei in barley   (Citations: 7)
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Xinwei Chen, Christine A. Hackett, Rients E. Niks, Peter E. Hedley, Clare Booth, Arnis Druka, Thierry C. Marcel, S. A. Vels, Micha Bayer, Iain Milne, Jenny Morris, Luke Ramsayhttp://academic.research.microsoft.com/io.ashx?type=5&id=33778662&selfId1=0&selfId2=0&maxNumber=12&query=
Background - Genetic resistance to barley leaf rust caused by Puccinia hordei involves both R genes and quantitative trait loci. The R genes provide higher but less durable resistance than the quantitative trait loci. Consequently, exploring quantitative or partial resistance has become a favorable alternative for controlling disease. Four quantitative trait loci for partial resistance to leaf rust have been identified in the doubled haploid Steptoe (St)/Morex (Mx) mapping population. Further investigations are required to study the molecular mechanisms underpinning partial resistance and ultimately identify the causal genes.Methodology/Principal Findings - We explored partial resistance to barley leaf rust using a genetical genomics approach. We recorded RNA transcript abundance corresponding to each probe on a 15K Agilent custom barley microarray in seedlings from St and Mx and 144 doubled haploid lines of the St/Mx population. A total of 1154 and 1037 genes were, respectively, identified as being P. hordei-responsive among the St and Mx and differentially expressed between P. hordei-infected St and Mx. Normalized ratios from 72 distant-pair hybridisations were used to map the genetic determinants of variation in transcript abundance by expression quantitative trait locus (eQTL) mapping generating 15685 eQTL from 9557 genes. Correlation analysis identified 128 genes that were correlated with resistance, of which 89 had eQTL co-locating with the phenotypic quantitative trait loci (pQTL). Transcript abundance in the parents and conservation of synteny with rice allowed us to prioritise six genes as candidates for Rphq11, the pQTL of largest effect, and highlight one, a phospholipid hydroperoxide glutathione peroxidase (HvPHGPx) for detailed analysis.Conclusions/Significance - The eQTL approach yielded information that led to the identification of strong candidate genes underlying pQTL for resistance to leaf rust in barley and on the general pathogen response pathway. The dataset will facilitate a systems appraisal of this host-pathogen interaction and, potentially, for other traits measured in this population
Journal: PLOS One , vol. 5, no. 1, 2010
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    • ...eQTL analyses in barley have addressed the global genetic architecture of transcript abundance in [22], the phenomenon of limited pleiotropy [23] and as an approach to identify the causal or candidate genes underlying partial resistance to fungal diseases [24,25]...
    • ...Here, using a previously reported Agilent 15 k custom array [25], we performed differential expression analysis of QTL-NILs and their recurrent parental lines at 18 hours post-inoculation (hpi) with Puccinia hordei .O ur major objective was to identify candidate genes for Rphq 2a ndRphq3...
    • ...Genome-wide Ph-responsive genes have previously been investigated [25] using Steptoe (St) and Morex (Mx), two barley cultivars with similar, intermediate levels of resistance to P. hordei (leaf materials were prepared from the same experiment as the current study with L94 and Vada)...
    • ...FC >2, FDR <0.05) a total of 1154 genes were identified as Ph-responsive in St/Mx [25]...
    • ...Identification of positional candidates for Rphq2 and Rphq3 To determine the map position of the 55 QTL-specific and differentially expressed genes, we took advantage of available datasets previously generated in three different eQTL studies (germinating embryos [22]; P. tritici infected leaves http://genenetwork.org, R. Wise, unpublished data) and Ph-infected seedling leaves [25]...
    • ...Of the 55 genes highlighted in our comparisons between NILs and recurrent parents, 40 detected eQTL in at least one of the three previous eQTL studies and co-located at the QTL regions, most (83%) having high LOD/LRS scores [22,25] (Table S5)...
    • ...previously to be almost always cis-eQTL [22,25,26] placing these genes within the Rphq 2o rRphq 3Q TL regions...
    • ...The observation that so many significantly differentially expressed genes appeared to be regulated in cis- is in agreement with previous studies [25,29]...
    • ...In our previous experiment with Steptoe and Morex, cultivars with similar but intermediate levels of partial resistance to leaf rust, we also observed that HvERF4 was significantly up-regulated by Ph-infection but no differential expression (p > 0.2) was observed between the parents [25]...
    • ...However, of direct relevance is a previously highlighted eQTL hotspot for genes that was associated with OPA-SNP 11_20157 [25] at 70 cM (98 cM on the consensus map [28]) on chromosome 1H spanning the region containing HvERF4...
    • ...This hotspot comprised 127 eQTL in less than a 10 cM interval and contained genes primarily involved in defence response [25]...
    • ...Blue diamond, red dots and green triangles represent eQTL identified by Potokina et al. [22], Chen et al. [25] and Wise et al. (unpublished results) respectively...
    • ...We generated a robust expression data set in reciprocal Rphq2/Rphq 3Q TL-NILs at 18 hpi, which is the timepoint previously described as being the most critical during P. hordei invasion in barley [25]...
    • ...A limitation of our experiment is, therefore, that defence response scenarios constructed on the transcriptional profiles of the 802 Ph-responsive genes identified here is simply a snapshot of a dynamic process, at the point when infection hyphae have just attempted penetration of the host cells forming haustoria [25]...
    • ...Plant growth and leaf inoculations were performed as previously described [25]...
    • ...The plant growth conditions were as described by Chen et al. [25]...
    • ...The inoculation was described in Chen et al. [25]...
    • ...Detailed protocols are described in Chen et al. [25]...
    • ...Data extraction, normalisation and significance criteria for differential expression Data extraction and normalisation were done independently for the three different experiments with GeneSpring (v.7.3) software as described previously [25]...

    Xinwei Chenet al. Differential gene expression in nearly isogenic lines with QTL for par...

    • ...This observation is important because even at the time of this writing there are still eQTL papers being published that use legacy mapping methods for their analysis [39-42], ostensibly because the more modern methods are not as accessible...

    Jacob J Michaelsonet al. Data-driven assessment of eQTL mapping methods

    • ...In contrast, several gene maps have been constructed for barley [21-25] (Hordeum vulgare L.) that diverged from wheat ~10-12 MYA [26,27] and belongs to the same tribe (Triticeae)...
    • ...Barley expression microarray and hybridisations The barley Agilent 15K expression microarray contains 15208 barley 60-mer probes derived from unigenes of HarvEST assembly #25 used to originally design probe sets for the 22K Barley1 Affymetrix GeneChip [21]...
    • ...Synteny and collinearity analyses In total, five barley genetic maps [21-25] were used to establish a barley neighbour map using the same criteria as the IBM neighbour map of maize [41]...

    Camille Rustenholzet al. Specific patterns of gene space organisation revealed in wheat by usin...

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