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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

Genetic diversity of the sequenced transcriptomes (a) Barplots showing the total number of homozygous SNPs resulting in synonymous or non-synonymous substitutions, or premature stop codons (b) Unrooted phylogenetic tree obtained from multiple alignment of synthetic transcripts reconstructed by incorporating the detected homozygous SNPs. Based on relatedness, genotypes were assigned to four groups.
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fig2: Genetic diversity of the sequenced transcriptomes (a) Barplots showing the total number of homozygous SNPs resulting in synonymous or non-synonymous substitutions, or premature stop codons (b) Unrooted phylogenetic tree obtained from multiple alignment of synthetic transcripts reconstructed by incorporating the detected homozygous SNPs. Based on relatedness, genotypes were assigned to four groups.

Mentions: Transcript sequence analyses confirmed the high degree of heterozygosity in the grape genome.45–47 Similarly to what was previously reported by Velasco et al.,48 a heterozygous SNP rate of 2.30 ± 0.10 SNPs/Kb in the protein-coding regions was observed. This confirmed that rates of exonic heterozygous SNPs within an individual grape genotype are higher than the rates of fixed exonic SNPs between accessions (1.57 ± 0.08 SNPs/Kb). Homozygous SNP data were incorporated into reconstructed synthetic genes of each accession to enable further analysis of genetic diversity (Figure 2). Phylogenetic analysis based on multiple alignment of all reconstructed transcripts confirmed the closer genetic relatedness between first-degree relatives ‘Late Vavilov’ and ‘Karadzhandal’17 (group I) and between the two accessions originating from Afghanistan (‘Khalchili’ and ‘Husseine’, group II). Closer relationships between the two V. vinifera spp. sylvestris genotypes (O34-16 and DVIT3351.27, group III) and the susceptible varieties ‘Carignan’ and ‘PN40024’ (group IV) were also observed, while ‘Sochal’ did not cluster with any other accession.


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)

Genetic diversity of the sequenced transcriptomes (a) Barplots showing the total number of homozygous SNPs resulting in synonymous or non-synonymous substitutions, or premature stop codons (b) Unrooted phylogenetic tree obtained from multiple alignment of synthetic transcripts reconstructed by incorporating the detected homozygous SNPs. Based on relatedness, genotypes were assigned to four groups.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig2: Genetic diversity of the sequenced transcriptomes (a) Barplots showing the total number of homozygous SNPs resulting in synonymous or non-synonymous substitutions, or premature stop codons (b) Unrooted phylogenetic tree obtained from multiple alignment of synthetic transcripts reconstructed by incorporating the detected homozygous SNPs. Based on relatedness, genotypes were assigned to four groups.
Mentions: Transcript sequence analyses confirmed the high degree of heterozygosity in the grape genome.45–47 Similarly to what was previously reported by Velasco et al.,48 a heterozygous SNP rate of 2.30 ± 0.10 SNPs/Kb in the protein-coding regions was observed. This confirmed that rates of exonic heterozygous SNPs within an individual grape genotype are higher than the rates of fixed exonic SNPs between accessions (1.57 ± 0.08 SNPs/Kb). Homozygous SNP data were incorporated into reconstructed synthetic genes of each accession to enable further analysis of genetic diversity (Figure 2). Phylogenetic analysis based on multiple alignment of all reconstructed transcripts confirmed the closer genetic relatedness between first-degree relatives ‘Late Vavilov’ and ‘Karadzhandal’17 (group I) and between the two accessions originating from Afghanistan (‘Khalchili’ and ‘Husseine’, group II). Closer relationships between the two V. vinifera spp. sylvestris genotypes (O34-16 and DVIT3351.27, group III) and the susceptible varieties ‘Carignan’ and ‘PN40024’ (group IV) were also observed, while ‘Sochal’ did not cluster with any other accession.

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