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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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Size of some defense related gene families in model species: Arabidopsis thaliana, Populus trichocarpa, Oryza sativa, Carica papaya, Medicago truncatula, Castanea molissima, and Castanea dentate.
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Figure 4: Size of some defense related gene families in model species: Arabidopsis thaliana, Populus trichocarpa, Oryza sativa, Carica papaya, Medicago truncatula, Castanea molissima, and Castanea dentate.

Mentions: From the 34,800 and 48,335 contigs, a total of 11,431 and 10,016 large transcript contigs (more than 800 nucleotides) were identified from American chestnut and Chinese chestnut, respectively. The size of the transcript contigs assembled including large ones ranged from 258 bp to 1038 bp with approx. 4-12% of the American and Chinese chestnut contigs covering at least 70% of the length of the coding sequences relative to the respective genes in Arabidopsis thaliana. Analyses of the length of contigs showed that 344 (6.0%) and 874 (6.7%) contigs were full length in American chestnut and Chinese chestnut, respectively. Analysis of gene family size, both in American and Chinese chestnut as well as in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa, showed that the numbers of genes per family identified in chestnuts is similar to their counterpart in the model plant species suggesting a good coverage of the transcriptome in these two Fagaceae species (Figure 4). For instance, the number of members per gene family correlates well between American chestnut, Chinese chestnut, and the other model plant species (Additional file 1: Figure S1), with correlations coefficients of R = 0.8 for Chinese chestnut versus Arabidopsis and R = 0.74 for Chinese chestnut versus Populus.


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)

Size of some defense related gene families in model species: Arabidopsis thaliana, Populus trichocarpa, Oryza sativa, Carica papaya, Medicago truncatula, Castanea molissima, and Castanea dentate.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Size of some defense related gene families in model species: Arabidopsis thaliana, Populus trichocarpa, Oryza sativa, Carica papaya, Medicago truncatula, Castanea molissima, and Castanea dentate.
Mentions: From the 34,800 and 48,335 contigs, a total of 11,431 and 10,016 large transcript contigs (more than 800 nucleotides) were identified from American chestnut and Chinese chestnut, respectively. The size of the transcript contigs assembled including large ones ranged from 258 bp to 1038 bp with approx. 4-12% of the American and Chinese chestnut contigs covering at least 70% of the length of the coding sequences relative to the respective genes in Arabidopsis thaliana. Analyses of the length of contigs showed that 344 (6.0%) and 874 (6.7%) contigs were full length in American chestnut and Chinese chestnut, respectively. Analysis of gene family size, both in American and Chinese chestnut as well as in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa, showed that the numbers of genes per family identified in chestnuts is similar to their counterpart in the model plant species suggesting a good coverage of the transcriptome in these two Fagaceae species (Figure 4). For instance, the number of members per gene family correlates well between American chestnut, Chinese chestnut, and the other model plant species (Additional file 1: Figure S1), with correlations coefficients of R = 0.8 for Chinese chestnut versus Arabidopsis and R = 0.74 for Chinese chestnut versus Populus.

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