An eQTL analysis of partial resistance to Puccinia hordei in barley

Xinwei Chen, Christine A. Hackett, Rients E. Niks, Peter E. Hedley, Clare Booth, Arnis Druka, Thierry C. Marcel, Anton Vels, Micha Bayer, Iain Milne, Jenny Morris, Luke Ramsay, David Marshall, Linda Cardle, Robbie Waugh

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Abstract

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.

Original languageEnglish
Article numbere8598
JournalPLoS ONE
Volume5
Issue number1
DOIs
Publication statusPublished - 6 Jan 2010

Fingerprint

Puccinia hordei
Quantitative Trait Loci
Hordeum
quantitative trait loci
Genes
barley
leaf rust
genes
vpr Genes
phospholipid-hydroperoxide glutathione peroxidase
Pathogens
Haploidy
doubled haploids
Population
Synteny
Host-Pathogen Interactions
Microarrays
host-pathogen relationships
genetic resistance
Genetic Association Studies

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Chen, X., Hackett, C. A., Niks, R. E., Hedley, P. E., Booth, C., Druka, A., ... Waugh, R. (2010). An eQTL analysis of partial resistance to Puccinia hordei in barley. PLoS ONE, 5(1), [e8598]. https://doi.org/10.1371/journal.pone.0008598
Chen, Xinwei ; Hackett, Christine A. ; Niks, Rients E. ; Hedley, Peter E. ; Booth, Clare ; Druka, Arnis ; Marcel, Thierry C. ; Vels, Anton ; Bayer, Micha ; Milne, Iain ; Morris, Jenny ; Ramsay, Luke ; Marshall, David ; Cardle, Linda ; Waugh, Robbie. / An eQTL analysis of partial resistance to Puccinia hordei in barley. In: PLoS ONE. 2010 ; Vol. 5, No. 1.
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Chen, X, Hackett, CA, Niks, RE, Hedley, PE, Booth, C, Druka, A, Marcel, TC, Vels, A, Bayer, M, Milne, I, Morris, J, Ramsay, L, Marshall, D, Cardle, L & Waugh, R 2010, 'An eQTL analysis of partial resistance to Puccinia hordei in barley', PLoS ONE, vol. 5, no. 1, e8598. https://doi.org/10.1371/journal.pone.0008598

An eQTL analysis of partial resistance to Puccinia hordei in barley. / Chen, Xinwei; Hackett, Christine A.; Niks, Rients E.; Hedley, Peter E.; Booth, Clare; Druka, Arnis; Marcel, Thierry C.; Vels, Anton; Bayer, Micha; Milne, Iain; Morris, Jenny; Ramsay, Luke; Marshall, David; Cardle, Linda; Waugh, Robbie.

In: PLoS ONE, Vol. 5, No. 1, e8598, 06.01.2010.

Research output: Contribution to journalArticle

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T1 - An eQTL analysis of partial resistance to Puccinia hordei in barley

AU - Chen, Xinwei

AU - Hackett, Christine A.

AU - Niks, Rients E.

AU - Hedley, Peter E.

AU - Booth, Clare

AU - Druka, Arnis

AU - Marcel, Thierry C.

AU - Vels, Anton

AU - Bayer, Micha

AU - Milne, Iain

AU - Morris, Jenny

AU - Ramsay, Luke

AU - Marshall, David

AU - Cardle, Linda

AU - Waugh, Robbie

PY - 2010/1/6

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N2 - 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.

AB - 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.

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Chen X, Hackett CA, Niks RE, Hedley PE, Booth C, Druka A et al. An eQTL analysis of partial resistance to Puccinia hordei in barley. PLoS ONE. 2010 Jan 6;5(1). e8598. https://doi.org/10.1371/journal.pone.0008598