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Chestnut resistance to the blight disease: insights from transcriptome analysis.

Barakat A, Staton M, Cheng CH, Park J, Yassin NB, Ficklin S, Yeh CC, Hebard F, Baier K, Powell W, Schuster SC, Wheeler N, Abbott A, Carlson JE, Sederoff R - BMC Plant Biol. (2012)

Bottom Line: A significant number of additional DTA genes involved in the defense-response not reported in a previous study were identified here.The similar set of GDTAs in American chestnut and Chinese chestnut suggests that the variation in sensitivity to this pathogen between these species may be the result of different timing and amplitude of the response of the two to the pathogen infection.Resources developed in this study are useful for functional genomics, comparative genomics, resistance breeding and phylogenetics in the Fagaceae.

View Article: PubMed Central - HTML - PubMed

Affiliation: The School of Forest Resources, and The Huck Institutes of the Life Sciences, Pennsylvania State University, 326 Forest Resources Building, University Park, PA 16802, USA. abaraka@clemson.edu

ABSTRACT

Background: A century ago, Chestnut Blight Disease (CBD) devastated the American chestnut. Backcross breeding has been underway to introgress resistance from Chinese chestnut into surviving American chestnut genotypes. Development of genomic resources for the family Fagaceae, has focused in this project on Castanea mollissima Blume (Chinese chestnut) and Castanea dentata (Marsh.) Borkh (American chestnut) to aid in the backcross breeding effort and in the eventual identification of blight resistance genes through genomic sequencing and map based cloning. A previous study reported partial characterization of the transcriptomes from these two species. Here, further analyses of a larger dataset and assemblies including both 454 and capillary sequences were performed and defense related genes with differential transcript abundance (GDTA) in canker versus healthy stem tissues were identified.

Results: Over one and a half million cDNA reads were assembled into 34,800 transcript contigs from American chestnut and 48,335 transcript contigs from Chinese chestnut. Chestnut cDNA showed higher coding sequence similarity to genes in other woody plants than in herbaceous species. The number of genes tagged, the length of coding sequences, and the numbers of tagged members within gene families showed that the cDNA dataset provides a good resource for studying the American and Chinese chestnut transcriptomes. In silico analysis of transcript abundance identified hundreds of GDTA in canker versus healthy stem tissues. A significant number of additional DTA genes involved in the defense-response not reported in a previous study were identified here. These DTA genes belong to various pathways involving cell wall biosynthesis, reactive oxygen species (ROS), salicylic acid (SA), ethylene, jasmonic acid (JA), abscissic acid (ABA), and hormone signalling. DTA genes were also identified in the hypersensitive response and programmed cell death (PCD) pathways. These DTA genes are candidates for host resistance to the chestnut blight fungus, Cryphonectria parasitica.

Conclusions: Our data allowed the identification of many genes and gene network candidates for host resistance to the chestnut blight fungus, Cryphonectria parasitica. The similar set of GDTAs in American chestnut and Chinese chestnut suggests that the variation in sensitivity to this pathogen between these species may be the result of different timing and amplitude of the response of the two to the pathogen infection. Resources developed in this study are useful for functional genomics, comparative genomics, resistance breeding and phylogenetics in the Fagaceae.

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Comparison of the percentage of American and Chinese chestnut contigs that have best hits on the proteome of each of the model plants.
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Figure 3: Comparison of the percentage of American and Chinese chestnut contigs that have best hits on the proteome of each of the model plants.

Mentions: BLASTX searches were then conducted against the proteomes of all of the plant species for which the whole genome sequence were available at the time of this study, including Vitis vinifera, Carica papaya, Medicago truncatula, Oryza sativa, Populus trichocarpa, Physcomitrella patens, and Selaginella moellendorffii. A large fraction of chestnut contigs had better BLAST alignment scores to woody species than to the herbaceous species (Figure 3). For instance, over 35% of contigs from American and Chinese chestnut had best alignments to Vitis vinifera and Populus trichocarpa. Only ~5% of the contigs had best alignments to Arabidopsis thaliana. This bias cannot be attributed to a GC content difference between contigs from woody versus herbaceous species as their GC content have similar distributions (data not shown).


Chestnut resistance to the blight disease: insights from transcriptome analysis.

Barakat A, Staton M, Cheng CH, Park J, Yassin NB, Ficklin S, Yeh CC, Hebard F, Baier K, Powell W, Schuster SC, Wheeler N, Abbott A, Carlson JE, Sederoff R - BMC Plant Biol. (2012)

Comparison of the percentage of American and Chinese chestnut contigs that have best hits on the proteome of each of the model plants.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3376029&req=5

Figure 3: Comparison of the percentage of American and Chinese chestnut contigs that have best hits on the proteome of each of the model plants.
Mentions: BLASTX searches were then conducted against the proteomes of all of the plant species for which the whole genome sequence were available at the time of this study, including Vitis vinifera, Carica papaya, Medicago truncatula, Oryza sativa, Populus trichocarpa, Physcomitrella patens, and Selaginella moellendorffii. A large fraction of chestnut contigs had better BLAST alignment scores to woody species than to the herbaceous species (Figure 3). For instance, over 35% of contigs from American and Chinese chestnut had best alignments to Vitis vinifera and Populus trichocarpa. Only ~5% of the contigs had best alignments to Arabidopsis thaliana. This bias cannot be attributed to a GC content difference between contigs from woody versus herbaceous species as their GC content have similar distributions (data not shown).

Bottom Line: A significant number of additional DTA genes involved in the defense-response not reported in a previous study were identified here.The similar set of GDTAs in American chestnut and Chinese chestnut suggests that the variation in sensitivity to this pathogen between these species may be the result of different timing and amplitude of the response of the two to the pathogen infection.Resources developed in this study are useful for functional genomics, comparative genomics, resistance breeding and phylogenetics in the Fagaceae.

View Article: PubMed Central - HTML - PubMed

Affiliation: The School of Forest Resources, and The Huck Institutes of the Life Sciences, Pennsylvania State University, 326 Forest Resources Building, University Park, PA 16802, USA. abaraka@clemson.edu

ABSTRACT

Background: A century ago, Chestnut Blight Disease (CBD) devastated the American chestnut. Backcross breeding has been underway to introgress resistance from Chinese chestnut into surviving American chestnut genotypes. Development of genomic resources for the family Fagaceae, has focused in this project on Castanea mollissima Blume (Chinese chestnut) and Castanea dentata (Marsh.) Borkh (American chestnut) to aid in the backcross breeding effort and in the eventual identification of blight resistance genes through genomic sequencing and map based cloning. A previous study reported partial characterization of the transcriptomes from these two species. Here, further analyses of a larger dataset and assemblies including both 454 and capillary sequences were performed and defense related genes with differential transcript abundance (GDTA) in canker versus healthy stem tissues were identified.

Results: Over one and a half million cDNA reads were assembled into 34,800 transcript contigs from American chestnut and 48,335 transcript contigs from Chinese chestnut. Chestnut cDNA showed higher coding sequence similarity to genes in other woody plants than in herbaceous species. The number of genes tagged, the length of coding sequences, and the numbers of tagged members within gene families showed that the cDNA dataset provides a good resource for studying the American and Chinese chestnut transcriptomes. In silico analysis of transcript abundance identified hundreds of GDTA in canker versus healthy stem tissues. A significant number of additional DTA genes involved in the defense-response not reported in a previous study were identified here. These DTA genes belong to various pathways involving cell wall biosynthesis, reactive oxygen species (ROS), salicylic acid (SA), ethylene, jasmonic acid (JA), abscissic acid (ABA), and hormone signalling. DTA genes were also identified in the hypersensitive response and programmed cell death (PCD) pathways. These DTA genes are candidates for host resistance to the chestnut blight fungus, Cryphonectria parasitica.

Conclusions: Our data allowed the identification of many genes and gene network candidates for host resistance to the chestnut blight fungus, Cryphonectria parasitica. The similar set of GDTAs in American chestnut and Chinese chestnut suggests that the variation in sensitivity to this pathogen between these species may be the result of different timing and amplitude of the response of the two to the pathogen infection. Resources developed in this study are useful for functional genomics, comparative genomics, resistance breeding and phylogenetics in the Fagaceae.

Show MeSH
Related in: MedlinePlus