Limits...
Comparative transcriptomics of Central Asian Vitis vinifera accessions reveals distinct defense strategies against powdery mildew.

Amrine KC, Blanco-Ulate B, Riaz S, Pap D, Jones L, Figueroa-Balderas R, Walker MA, Cantu D - Hortic Res (2015)

Bottom Line: To identify potential Ren1-dependent transcriptional responses and functions associated with the different levels of resistance, we sequenced and analyzed the transcriptomes of these Central Asian accessions at two time points of PM infection.Transcriptomes were compared to identify constitutive differences and PM-inducible responses that may underlie their disease resistant phenotype.This study provides a first exploration of the functions associated with varying levels of partial resistance to PM in V. vinifera accessions that can be exploited as sources of genetic resistance in grape breeding programs.

View Article: PubMed Central - PubMed

Affiliation: Department of Viticulture and Enology, University of California , Davis, Davis, CA 95616, USA.

ABSTRACT
Grape powdery mildew (PM), caused by the biotrophic ascomycete Erysiphe necator, is a devastating fungal disease that affects most Vitis vinifera cultivars. We have previously identified a panel of V. vinifera accessions from Central Asia with partial resistance to PM that possess a Ren1-like local haplotype. In this study, we show that in addition to the typical Ren1-associated late post-penetration resistance, these accessions display a range of different levels of disease development suggesting that alternative alleles or additional genes contribute to determining the outcome of the interaction with the pathogen. To identify potential Ren1-dependent transcriptional responses and functions associated with the different levels of resistance, we sequenced and analyzed the transcriptomes of these Central Asian accessions at two time points of PM infection. Transcriptomes were compared to identify constitutive differences and PM-inducible responses that may underlie their disease resistant phenotype. Responses to E. necator in all resistant accessions were characterized by an early up-regulation of 13 genes, most encoding putative defense functions, and a late down-regulation of 32 genes, enriched in transcriptional regulators and protein kinases. Potential Ren1-dependent responses included a hotspot of co-regulated genes on chromosome 18. We also identified 81 genes whose expression levels and dynamics correlated with the phenotypic differences between the most resistant accessions 'Karadzhandahal', DVIT3351.27, and O34-16 and the other genotypes. This study provides a first exploration of the functions associated with varying levels of partial resistance to PM in V. vinifera accessions that can be exploited as sources of genetic resistance in grape breeding programs.

No MeSH data available.


Related in: MedlinePlus

Specific responses to PM among the most resistant Central Asian accessions (a) Multiple factor analysis (MFA) of the seven PM-partially resistant genotypes using three variables: log2 fold-changes of differentially expressed genes, PM visual scores, and E. necator biomass measured by qPCR (as previously reported in Figure 1). Each point represents a biological replicate for a given genotype. Ellipses define confidence areas (95%) for each genotype, while black squares represent their correspondent center of gravity. DIM, dimension. (b) Enriched GO terms (P < 0.05) in the set of genes that drive the separation of ‘Karadzhandal’, DVIT3351.27, and O34-16 in the MFA (R > 0.7, P < 0.01). To highlight closely related enriched GO terms, terms were organized into undirected sub-graphs using the REViGO web server.37 (c) Genes correlated with the most resistant accessions (positive dimension 1) in Panel (a), which also present a contrasting expression pattern in the susceptible ‘Carignan’ accession.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4591678&req=5

fig6: Specific responses to PM among the most resistant Central Asian accessions (a) Multiple factor analysis (MFA) of the seven PM-partially resistant genotypes using three variables: log2 fold-changes of differentially expressed genes, PM visual scores, and E. necator biomass measured by qPCR (as previously reported in Figure 1). Each point represents a biological replicate for a given genotype. Ellipses define confidence areas (95%) for each genotype, while black squares represent their correspondent center of gravity. DIM, dimension. (b) Enriched GO terms (P < 0.05) in the set of genes that drive the separation of ‘Karadzhandal’, DVIT3351.27, and O34-16 in the MFA (R > 0.7, P < 0.01). To highlight closely related enriched GO terms, terms were organized into undirected sub-graphs using the REViGO web server.37 (c) Genes correlated with the most resistant accessions (positive dimension 1) in Panel (a), which also present a contrasting expression pattern in the susceptible ‘Carignan’ accession.

Mentions: Multivariate analysis was performed to identify genes whose expression correlates with the most resistant disease phenotypes. Fold changes, along with PM visual scores and qPCR measurements of E. necator biomass, were used as quantitative variables in a multiple factor analysis (MFA, Figure 6a). The most resistant accessions ‘Karadzhandal’, O34-16, and DVIT3351.27 separated from the other Central Asian accessions along dimension 1, with ‘Late Vavilov’, the most susceptible genotype isolated from the rest. Similar clustering of accessions was obtained when normalized gene expression counts were used (Supplementary Figure S5). Variables with strong correlation with the main dimension 1 were extracted (R ≥ 0.7, P < 0.01) and filtered to identify genes specifically associated with the transcriptional profiles of the three most resistant accessions. Thirty-five PM-responsive genes were discovered with similar patterns of differential regulation in ‘Karadzhandal’, O34-16, and DVIT3351.27 and opposite trends in ‘Carignan’. We also identified 46 genes consistently more expressed in ‘Karadzhandal’, O34-16, and DVIT3351.27 compared to ‘Carignan’ (Supplementary Figure S5b). Functions related to hormone regulation, cellular transport, pectin metabolism, and xenobiotic catabolic processes were significantly over-represented in this set of 81 genes (Figure 6c). Interesting candidates included NB-LRRs (VIT_13s0139g00130, VIT_13s0158g00210, VIT_12s0034g01260, VIT_09s0002g04950), a cinnamyl alcohol dehydrogenase (VIT_00s0615g00010), and a MATE transporter (VIT_03s0038g00410) similar to EDS5, an essential component of salicylic acid signaling in Arabidopsis.62


Comparative transcriptomics of Central Asian Vitis vinifera accessions reveals distinct defense strategies against powdery mildew.

Amrine KC, Blanco-Ulate B, Riaz S, Pap D, Jones L, Figueroa-Balderas R, Walker MA, Cantu D - Hortic Res (2015)

Specific responses to PM among the most resistant Central Asian accessions (a) Multiple factor analysis (MFA) of the seven PM-partially resistant genotypes using three variables: log2 fold-changes of differentially expressed genes, PM visual scores, and E. necator biomass measured by qPCR (as previously reported in Figure 1). Each point represents a biological replicate for a given genotype. Ellipses define confidence areas (95%) for each genotype, while black squares represent their correspondent center of gravity. DIM, dimension. (b) Enriched GO terms (P < 0.05) in the set of genes that drive the separation of ‘Karadzhandal’, DVIT3351.27, and O34-16 in the MFA (R > 0.7, P < 0.01). To highlight closely related enriched GO terms, terms were organized into undirected sub-graphs using the REViGO web server.37 (c) Genes correlated with the most resistant accessions (positive dimension 1) in Panel (a), which also present a contrasting expression pattern in the susceptible ‘Carignan’ accession.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4591678&req=5

fig6: Specific responses to PM among the most resistant Central Asian accessions (a) Multiple factor analysis (MFA) of the seven PM-partially resistant genotypes using three variables: log2 fold-changes of differentially expressed genes, PM visual scores, and E. necator biomass measured by qPCR (as previously reported in Figure 1). Each point represents a biological replicate for a given genotype. Ellipses define confidence areas (95%) for each genotype, while black squares represent their correspondent center of gravity. DIM, dimension. (b) Enriched GO terms (P < 0.05) in the set of genes that drive the separation of ‘Karadzhandal’, DVIT3351.27, and O34-16 in the MFA (R > 0.7, P < 0.01). To highlight closely related enriched GO terms, terms were organized into undirected sub-graphs using the REViGO web server.37 (c) Genes correlated with the most resistant accessions (positive dimension 1) in Panel (a), which also present a contrasting expression pattern in the susceptible ‘Carignan’ accession.
Mentions: Multivariate analysis was performed to identify genes whose expression correlates with the most resistant disease phenotypes. Fold changes, along with PM visual scores and qPCR measurements of E. necator biomass, were used as quantitative variables in a multiple factor analysis (MFA, Figure 6a). The most resistant accessions ‘Karadzhandal’, O34-16, and DVIT3351.27 separated from the other Central Asian accessions along dimension 1, with ‘Late Vavilov’, the most susceptible genotype isolated from the rest. Similar clustering of accessions was obtained when normalized gene expression counts were used (Supplementary Figure S5). Variables with strong correlation with the main dimension 1 were extracted (R ≥ 0.7, P < 0.01) and filtered to identify genes specifically associated with the transcriptional profiles of the three most resistant accessions. Thirty-five PM-responsive genes were discovered with similar patterns of differential regulation in ‘Karadzhandal’, O34-16, and DVIT3351.27 and opposite trends in ‘Carignan’. We also identified 46 genes consistently more expressed in ‘Karadzhandal’, O34-16, and DVIT3351.27 compared to ‘Carignan’ (Supplementary Figure S5b). Functions related to hormone regulation, cellular transport, pectin metabolism, and xenobiotic catabolic processes were significantly over-represented in this set of 81 genes (Figure 6c). Interesting candidates included NB-LRRs (VIT_13s0139g00130, VIT_13s0158g00210, VIT_12s0034g01260, VIT_09s0002g04950), a cinnamyl alcohol dehydrogenase (VIT_00s0615g00010), and a MATE transporter (VIT_03s0038g00410) similar to EDS5, an essential component of salicylic acid signaling in Arabidopsis.62

Bottom Line: To identify potential Ren1-dependent transcriptional responses and functions associated with the different levels of resistance, we sequenced and analyzed the transcriptomes of these Central Asian accessions at two time points of PM infection.Transcriptomes were compared to identify constitutive differences and PM-inducible responses that may underlie their disease resistant phenotype.This study provides a first exploration of the functions associated with varying levels of partial resistance to PM in V. vinifera accessions that can be exploited as sources of genetic resistance in grape breeding programs.

View Article: PubMed Central - PubMed

Affiliation: Department of Viticulture and Enology, University of California , Davis, Davis, CA 95616, USA.

ABSTRACT
Grape powdery mildew (PM), caused by the biotrophic ascomycete Erysiphe necator, is a devastating fungal disease that affects most Vitis vinifera cultivars. We have previously identified a panel of V. vinifera accessions from Central Asia with partial resistance to PM that possess a Ren1-like local haplotype. In this study, we show that in addition to the typical Ren1-associated late post-penetration resistance, these accessions display a range of different levels of disease development suggesting that alternative alleles or additional genes contribute to determining the outcome of the interaction with the pathogen. To identify potential Ren1-dependent transcriptional responses and functions associated with the different levels of resistance, we sequenced and analyzed the transcriptomes of these Central Asian accessions at two time points of PM infection. Transcriptomes were compared to identify constitutive differences and PM-inducible responses that may underlie their disease resistant phenotype. Responses to E. necator in all resistant accessions were characterized by an early up-regulation of 13 genes, most encoding putative defense functions, and a late down-regulation of 32 genes, enriched in transcriptional regulators and protein kinases. Potential Ren1-dependent responses included a hotspot of co-regulated genes on chromosome 18. We also identified 81 genes whose expression levels and dynamics correlated with the phenotypic differences between the most resistant accessions 'Karadzhandahal', DVIT3351.27, and O34-16 and the other genotypes. This study provides a first exploration of the functions associated with varying levels of partial resistance to PM in V. vinifera accessions that can be exploited as sources of genetic resistance in grape breeding programs.

No MeSH data available.


Related in: MedlinePlus